Common Minimum Technical Standards and Protocols for Biobanks Dedicated to Cancer Research

COMMON MINIMUM TECHNICAL STANDARDS AND PROTOCOLS FOR BIOBANKS DEDICATED TO CANCER RESEARCH

MAIMUNA MENDY, ELODIE CABOUX, RITA T. LAWLOR, JESSICA WRIGHT, AND CHRISTOPHER P. WILD

IARC TECHNICAL PUBLICATION NO. 44 COMMON MINIMUM TECHNICAL STANDARDS AND PROTOCOLS FOR BIOBANKS DEDICATED TO CANCER RESEARCH

MAIMUNA MENDY, ELODIE CABOUX, RITA T. LAWLOR, JESSICA WRIGHT, AND CHRISTOPHER P. WILD

IARC TECHNICAL PUBLICATION NO. 44 Published by the International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France

©International Agency for Research on Cancer, 2017

Distributed by WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 3264; fax: +41 22 791 4857; email: [email protected]).

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Cover image: Paraffin-embedded tissues processed and stored within the context of various IARC research projects (Credit: R. Dray/IARC).

This book is also available in electronic format from http://publications.iarc.fr.

IARC Library Cataloguing in Publication Data

Common minimum technical standards and protocols for biobanks dedicated to cancer research / Maimuna Mendy, Elodie Caboux, Rita T. Lawlor… [et al.]

(IARC Technical Publications; 44)

1. Biological Specimen Banks – Standards 2. Biological Specimen Banks – Organization & Administration 3. Biological Specimen Banks – Methods 4. Neoplasms I. Mendy, M. II. Title III. Series

ISBN 978-92-832-2463-1 (NLM Classification: W1) ISSN 1012-7348 Table of contents

Contributors ...... iv Acknowledgements ...... v Foreword ...... vi Preamble ...... vii Abbreviations ...... ix

Section 1 ...... 1 Glossary and definitions

Section 2 ...... 5 Role of biobanks in cancer research

Section 3 ...... 11 Recommendations for biobanks

Section 4 ...... 55 Selected protocols

References ...... 63

Annex 1 ...... 69 IARC policy on access to human biological materials

Annex 2 ...... 75 Guidelines for informed consent

Annex 3 ...... 80 Template consent form for biobanking

Annex 4 ...... 91 Template Material/Data Transfer Agreement (MTA/DTA)

Annex 5 ...... 97 Biobank, collection, study, and sample minimum data set and associated standards

Disclosures of interests ...... 101 Contributors

Authors Dr Joakim Dillner Dr Ghislaine Scélo Karolinska Institutet Genetic Epidemiology Group, Dr Maimuna Mendy Stockholm, Sweden Section of Genetics Head, Laboratory Services and International Agency for Research Ms Marianne Henderson Biobank Group on Cancer (IARC) Senior Advisor for Division International Agency for Research Lyon, France Resources, Office of the Director, on Cancer (IARC) Division of Cancer Epidemiology Ms Anne-Marie Tassé Lyon, France and Genetics Executive Director, Dr Elodie Caboux Senior Advisor on Biobanking, Public Population Project in Laboratory Services and Center for Global Health, National Genomics and Society (P3G) Biobank Group Cancer Institute, National Institutes Montreal, Canada International Agency for Research of Health, Division of Health and Dr Jim Vaught on Cancer (IARC) Human Services President, International Society Lyon, France Rockville, MD, USA for Biological and Environmental Dr Rita T. Lawlor Dr Jan-Eric Litton Repositories (ISBER) ARC-NET Centre for Applied Director General, Biobanking and Editor in Chief, Biopreservation Research on Cancer BioMolecular resources Research and Biobanking University of Verona Infrastructure–European Research Senior Research Fellow, Verona, Italy Infrastructure Consortium (BBMRI- International Prevention Research ERIC) Institute, Lyon, France Dr Jessica Wright Graz, Austria Study Manager, Sheffield Clinical Dr Kurt Zatloukal Trials Research Unit Dr Manuel Morente Deputy Head, Institute of Pathology The University of Sheffield Biobank Scientific Director, Spanish Medical University of Graz Sheffield, United Kingdom National Cancer Research Centre Graz, Austria (CNIO) Mr Ma’n H. Zawati Dr Christopher P. Wild Coordinator, Spanish National Executive Director, Centre of Director, International Agency for Biobank Network Genomics and Policy Research on Cancer (IARC) Past-President, European, Middle McGill University Lyon, France Eastern and African Society for Montreal, Canada Biopreservation and Biobanking (ESBB) Reviewers Madrid, Spain Production Team The authors are grateful to the Dr Sabina Rinaldi following expert colleagues who Biomarkers Group, Section of Karen Müller English Editor contributed comments, advice, Nutrition and Metabolism corrections, and protocols in the International Agency for Research Sylvia Lesage preparation of this book. on Cancer (IARC) Publishing Assistant Lyon, France

iv Contributors Acknowledgements

We would like to acknowledge the authors of Common Minimum Technical Standards and Protocols for Biological Resource Centres Dedicated to Cancer Research (published by IARC in 2007): an IARC Secretariat composed of Dr Elodie Caboux, Dr Amelie Plymoth, and Dr Pierre Hainaut, joined by the Working Group participants.

The authors would like to thank Ms Sally Moldan, for her excellent contribution towards the compilation of this book, and the members and partners of the Low- and Middle-Income Countries (LMICs) Biobank and Cohort Building Network (BCNet), for sharing their real-life experiences working in resource-constrained settings.

Acknowledgements v Foreword

Biological specimens collected, from the International Agency for what goes into a biobank but also on processed, and stored under opti- Research on Cancer (IARC). The what comes out. There is a risk that mal conditions increasingly provide purpose of the text is to provide biobanks remain untouched or un- a necessary foundation for cancer clear and practical advice on the derexploited, a deposit that is rarely research. Information obtained from common practices needed to create put to work for the common good. such samples opens opportunities and maintain biobanks, recognizing While this book aims to ensure that to learn more about the causes, that the circumstances faced by the what goes into a biobank is of high prevention, and treatment of the curators of biobanks vary across quality and well managed, it has as disease. International comparisons the world. The international coop- its ultimate objective to drive the use made possible by the study of sam- eration that went into formulating of those same biospecimens in re- ple collections from different parts of these Common Minimal Technical search. This will involve the analysis the world are also invaluable in the Standards provides confidence that of biospecimens, but to maximize the pursuit of the evidence base for can- the content is realistic, while at the benefits it will also require linkage to cer control. same time maintaining the minimal other well-documented epidemio- However, the above-mentioned standards needed in order for the logical and clinical data sets. In this opportunities are accompanied by biospecimens to be valid and to period of spiralling numbers of can- many challenges and potential pit- yield the reliable research data be- cer cases and costs of cancer care, falls. At times, pragmatic decisions ing sought. In providing this Fore- the failure to use stored samples to have to be made in response to the word, I would like to place on record answer critical research questions is constraints faced when conducting my thanks to all authors and review- indefensible. clinical or population-based studies. ers who have contributed to this final In conclusion, I trust that readers These constraints may be techni- product, as well as to all the contrib- will find this publication to be a sup- cal, may relate to infrastructure or utors to Common Minimum Techni- port to successful biobanking and finance, or may be ethical, legal, cal Standards and Protocols for Bio- will find herein one important foun- or social in nature. Being unaware logical Resource Centres Dedicated dation for cancer research in the of these types of risk to successful to Cancer Research, known as the 21st century. biobanking can place important sci- “Green Book”, published by IARC in entific advances in jeopardy. 2007. Dr Christopher P. Wild In this context, it is a great plea- In publishing this book, my hope Director, International Agency sure to introduce this publication is for a balanced focus, not only on for Research on Cancer

vi Foreword Preamble

The International Agency for In response to these develop- (LMICs). The recommendations are Research on Cancer (IARC) pub- mental changes and to promote col- based on validated and/or evidence- lished Common Minimum Technical laborative projects, a wide range of based guidelines, taking into account Standards and Protocols for Biologi- biobanking stakeholders are estab- the current knowledge of biobanking cal Resources Centres Dedicated lishing approaches and mechanisms practices and standards resulting to Cancer Research, known as the for the harmonization of resources, from projects such as Standardisa- “Green Book”, in 2007. The recom- including data. These stakehold- tion and Improvement of Generic Pre- mendations and protocols in that ers include international organiza- analytical Tools and Procedures for In publication were largely based on tions, societies, and institutions, Vitro Diagnostics (SPIDIA), BBMRI– guidelines, procedures, and docu- such as the United States National Large Prospective Cohorts (BBMRI- mentation on biorepositories devel- Cancer Institute (NCI), the Interna- LPC), and the International Geno- oped by several working groups, tional Society for Biological and En- mics Consortium (IGC), as well as the institutions, regulatory bodies, and vironmental Repositories (ISBER), European Committee for Standard- organizations, including the World the European, Middle Eastern and ization (CEN) Technical Specifica- Health Organization. African Society for Biopreserva- tions for molecular in vitro diagnostic However, biobanking has devel- tion and Biobanking (ESBB), and examinations and International Or- oped at a rapid pace over the years, the Biobanking and BioMolecular ganization for Standardization (ISO) driven mainly by the push for person- resources Research Infrastructure– norm 15189 (ISO, 2012). ISO 15189 is alized medicine, the need for high- European Research Infrastructure currently under revision (https://www. quality biological resources and as- Consortium (BBMRI-ERIC). Their iso.org/obp/ui/#iso:std:iso:15189:ed- sociated data for scientific research, activities include the improvement of 3:v2:en), and the working groups and technological advancement of biobanking protocols and standards of the Technical Committee of ISO analytical platforms for molecular to provide high-quality samples and 276 (http://www.iso.org/iso/home/ and genetic research. These devel- to adequately address ethical, legal, standards_development/list_of_iso_ opments have enabled the collec- and social issues (ELSI). technical_committees/iso_technical_ tion and analysis of large numbers This IARC Technical Publica- committee.htm?commid=4514241) of biospecimens in combination with tion includes guidelines and recom- are dealing with biobanking qual- epidemiological and clinical data mendations for biobanks not only in ity issues, including terminology, collected across populations and in- high-income countries but also in bioresearch, bioprocessing, pre- volving multiple biobanks. low- and middle-income countries analytical methods, isolation of

Preamble vii analytes, and data processing and fective running of the facilities. Tem- The guidelines and recommen- integration. plates for informed consent and Ma- dations are applicable to biobanks This book also includes sections terial and Data Transfer Agreements operating in different geographical on sample sharing, ELSI, and harmo- are available in the Annexes section. locations, and although the book’s nization guidelines important to sup- This new book also benefits focus is on biobanks dedicated to port collaborative research efforts from the experience and knowl- cancer research, the principles and that make use of biological materi- edge gained by IARC from coordi- guidelines outlined here are also als. In particular, the section on open nating the LMICs Biobank and Co- applicable to non-cancer biobanks. access deals with the principles of hort Building Network (BCNet) and Table 1 presents a list of the sharing and provides recommenda- managing an international biobank, main sources of information used tions for biobanks in relation to sam- which contains diverse collections to develop the recommendations ple and data sharing, which is key to of specimens and data drawn from presented in this book. Whenever establishing research collaboration. studies across the world, including appropriate, the book indicates ref- The section on governance provides the European Prospective Inves- erences and links to more extensive guidelines on governance structures tigation into Cancer and Nutrition documentation and protocols. for biobanks for transparent and ef- (EPIC) collection.

Table 1. Guidelines, procedures, and documentation on biobanks

Title Authors/origin

Tissue banking for biomedical research National Cancer Centre Singapore

Biorepository protocols Australasian Biospecimen Network (ABN)/Australia

Standardizing tissue collection and quality control procedures for a European Human Frozen Tumour Tissue Bank (TuBaFrost) European virtual frozen tissue bank network Human tissue and biological samples for use in research: operational Medical Research Council (MRC)/United Kingdom and ethical guidelines 2012 Best practices for repositories: collection, storage, retrieval, and International Society for Biological and Environmental Repositories distribution of biological materials for research (ISBER)/International NCI best practices for biospecimen resources National Cancer Institute (NCI)/USA

Guidance on regulations for the transport of infectious substances World Health Organization (WHO)/International United Nations recommendations on the transport of dangerous goods, United Nations Economic Commission for Europe (UNECE)/ model regulations, 19th revised edition International Recommendation Rec(2006)4 of the Committee of Ministers to Member Council of Europe Committee of Ministers States on research on biological materials of human origin Collection, transport, preparation, and storage of specimens for Clinical and Laboratory Standards Institute (CLSI)/USA molecular methods: approved guideline The Human Proteome Organization Human Proteome Organization (HUPO)

Case studies of existing human tissue repositories: “best practices” for RAND Corporation/USA a biospecimen resource for the genomic and proteomic era Biological resource centres: underpinning the future of life sciences and Organisation for Economic Co-operation and Development (OECD)/ biotechnology International OECD best practice guidelines for biological resource centres Organisation for Economic Co-operation and Development (OECD)/ International Standard operating procedure for the collection of fresh frozen tissue European Organisation for Research and Treatment of Cancer samples (EORTC)

viii Abbreviations

ACD acid citrate dextrose BBMRI-ERIC Biobanking and BioMolecular resources Research Infrastructure–European Research Infrastructure Consortium BBMRI-LPC BBMRI–Large Prospective Cohorts BCNet LMICs Biobank and Cohort Building Network BRIF Bioresource Research Impact Factor BRISQ Biospecimen Reporting for Improved Study Quality CEN European Committee for Standardization

CO2 carbon dioxide CSF cerebrospinal fluid DBS dried blood spot DEPC diethylpyrocarbonate DIN DNA integrity number DMSO dimethyl sulfoxide DNA deoxyribonucleic acid DR disaster recovery dsDNA double-stranded DNA DTA Data Transfer Agreement EDTA ethylenediaminetetraacetic acid ELSI ethical, legal, and social issues EPIC European Prospective Investigation into Cancer and Nutrition ESBB European, Middle Eastern and African Society for Biopreservation and Biobanking EU European Union FBS fetal bovine serum FFPE formalin-fixed, paraffin-embedded GA4GH Global Alliance for Genomics and Health gDNA genomic DNA HBV hepatitis B virus HIV human immunodeficiency virus IARC International Agency for Research on Cancer IATA International Air Transport Association ICAO International Civil Aviation Organization

Abbreviations ix ISBER International Society for Biological and Environmental Repositories ISO International Organization for Standardization IT information technology LIMS laboratory information management system LMICs low- and middle-income countries

LN2 liquid nitrogen MIABIS Minimum Information about Biobank Data Sharing miRNA microRNA MTA Material Transfer Agreement NCI United States National Cancer Institute NIH United States National Institutes of Health OCT optimal cutting temperature OECD Organisation for Economic Co-operation and Development P3G Public Population Project in Genomics and Society PCR polymerase chain reaction QA quality assurance QC quality control QMS quality management system qPCR quantitative PCR R&D research and development RIN RNA integrity number RNA ribonucleic acid rRNA ribosomal RNA RT-PCR reverse transcription PCR SOPs standard operating procedures SPREC Sample PREanalytical Code ssDNA single-stranded DNA TNM tumour–node–metastasis TuBaFrost European Human Frozen Tumour Tissue Bank UNECE United Nations Economic Commission for Europe UV ultraviolet WHO World Health Organization

x SECTION 1 SECTION

section 1. Glossary and definitions

Unless otherwise defined in an- Aliquot usually detected by staff of the area other context in this book, important Aliquoting is a process in which a in which the event occurred, which terms are defined below. specimen is divided into separate may result in non-compliance with Some of the definitions are ac- parts, which are typically stored as the quality management system or cording to the 2012 International So- individual samples. The term “ali- with the requirements of the user. ciety for Biological and Environmen- quot” may also be used as a noun tal Repositories (ISBER) guidelines to denote a single sample. It is ad- Anonymization (ISBER, 2012). visable to store aliquots in separate The process in which identifying It should be noted that the Inter- containers, to minimize loss due to information or details are re- national Organization for Standard- unexpected equipment failure. moved from the data collected with ization (ISO) standards that are cur- a sample, so that the sample donor rently under development and will be Analyte remains anonymous. released within 2 years (ISO/TC 276 A substance or chemical constituent Biotechnology) will include a section that is determined in an analytical Associated data on biobanking definitions. procedure. The clinical, pathological, and epidemiological information related to pa- Adverse event Annotation tients who provided a sample. The Any event that caused harm or had Additional information associated information relates to characteristics the potential to cause harm to any with a particular point in a document of the sample, the study participant, biobank personnel or visitors, in- or other piece of information. and biological experiments that can cluding but not limited to breach of be used to generate knowledge. security of the premises and its con- Anomaly tents, or harm to biospecimens or An unexpected event occurring with- Autopsy data integrity or linkage. in the quality management system, The postmortem examination of

Section 1. Glossary and definitions 1 organs and tissues of a body, to de- that can affect human health. It can Container termine cause of death or pathologi- also include substances harmful to An enclosure for one or more units cal conditions. animals. of a specimen or specimens.

Biobank Biological resource Controlled areas Infrastructure for the collection, ar- A collection of biological specimens Restricted work areas of low micro- chiving, and storage of biospeci- and associated data that are ac- bial and particulate content in which mens and their associated data, and quired for a defined purpose. The non-sterile materials are prepared. the procedures and related servic- custodian of the collection is re- es connected to the biospecimens sponsible for the management of the Custodian and associated data. The services biological resource. Biological re- The person responsible for the include informing individuals who sources may be stored in a biobank management of a biological re- are approached to participate in a or laboratory and in databases, de- source. The custodian works with study, obtaining their consent, col- pending on the number of samples, other key stakeholders in the man- lecting and processing specimens the volume of information, and the agement of the resource, including for secure long-term storage, ac- governance structure of the biobank. the tracking of all relevant documen- cessing and retrieving specimens tation for the resource, and is re- appropriate for analysis, processing Biological safety hood sponsible for ensuring that policies for preparation of biomaterials (e.g. A cabinet designed to provide a mi- on access to the resource are in DNA, RNA, proteins), quality con- crobe-free work environment, which place and are implemented accord- trol, and packaging and shipping of enables work on samples in an ing to appropriate guidelines. specimens. Many types of biobank isolated area. are relevant to cancer research. Database They include, among others, tumour Biorepository A structured collection of records and tissue biobanks for specimens See “Biobank”. or data that is stored in a computer and data obtained in the course of system so that a computer program normal clinical procedures; special- Coding or a person using a query language ized collections of specimens and Substituting a code for personally can consult it to answer queries. data developed in the context of identifying information in such a way clinical trials, mechanistic studies, that linkage is only possible through Dehydration or diagnostic or prognostic studies; a key. The removal of water from a tissue. and collections of specimens and data developed in epidemiologi- Cold chain De-identification cal studies and biomarker studies. A temperature-controlled supply chain. A process that ensures that a per- Biobank samples include tissues, son’s identity cannot be connected blood, cell lines, DNA, and pro- Cold ischaemia with information or samples donated teins derived from individuals with a The condition of a tissue sample af- by them. history of hereditary or familial ter its removal from the body until its cancer. Biobanks are also known as stabilization or fixation. Desiccant biorepositories. A desiccant is a hygroscopic sub- Collection stance that induces or sustains a Biobanking The practice or technique of collect- state of dryness (desiccation) in its The process of storing material or ing a specimen, or a specific sam- vicinity. Commonly encountered specimens and associated data for ple or group of samples, that has pre-packaged desiccants are solids future use. been isolated for future research that absorb water. purposes. Biohazard Deviation An organism, or a substance de- Consignee An intentional or unintentional event rived from an organism, that poses Any individual, agency, institution, that departs from a set procedure or a threat to (primarily) human health. or organization that receives speci- normal practice. This can include medical waste and mens and assumes responsibility for samples of a microorganism, virus, storing, dispensing, and tracking the Dewar or toxin (from a biological source) disposition of specimens. A specialized container that holds

2 liquefied gases. A dewar may also Incident at −196 °C. Samples stored in the be referred to as a dewar flask or Any unplanned occurrence that vapour phase of liquid nitrogen are dewar vessel, or a liquid nitrogen deviates from standard operating −190 °C and warmer, depending on tank. procedures (SOPs) or applicable the distance from the liquid phase. government laws and regulations 1 SECTION Distribution during specimen retrieval, process- Liquid nitrogen tank A process that includes receipt of ing, labelling, storage, or distribution See “Dewar”. a request for specimens, selection that may affect subsequent use of of appropriate specimens, and those specimens. Lyophilized final inspection, in conjunction with Dehydrated for storage by conver- subsequent shipment and delivery Individual sion of the water content of a frozen of specimens to another biobank, The person who is the subject of pro- specimen to a gaseous state under specimen collection centre, or tected health information. vacuum. Also called “freeze-dried”. laboratory. Informed consent Material Transfer Agreement (MTA)/ Donor A decision to participate in research, Data Transfer Agreement (DTA) A person who donates or gives an taken by a competent individual An agreement or contract that gov- organ, blood, or blood products to who has received the necessary in- erns the transfer of research materi- another person. formation; who has adequately un- als and/or data between two organi- derstood the information; and who, zations, when the recipient intends to Dry ice after considering the information, use them for research purposes. It

Solid-phase carbon dioxide (CO2). has arrived at a decision without defines the rights and obligations of

CO2 solidifies at −78.5 °C. having been subjected to coercion, the provider and the recipient with undue influence, inducement, or respect to the use of the materials End user intimidation. and/or data. A health-care practitioner, scientist, or laboratory staff member who Institution Monitoring system performs an appropriate procedure, The body responsible for speci- A system that monitors the temper- test, or archival function. men collection and archiving that ature and environmental conditions, commits itself to the development, including alarms, in conjunction with Error management, and long-term main- remote access, security features, A deviation from a standard operat- tenance of a biobank. Although the and electronic data storage. ing procedure (SOP) during speci- organizational nature of such insti- men retrieval, processing, testing, tutions may vary widely, they are Participant quarantining, labelling, storage, or primarily clinical cancer centres, A person who takes part in a trial. distribution that might adversely academic medical centres, research Participants must usually meet cer- affect the specimen. institutes closely associated with tain eligibility criteria. clinical centres, or central organiza- Ethical, legal, and social issues tions dedicated to the management Patient (ELSI) of biobanks. A person who receives medical at- The ethical, legal, and social issues tention, care, or treatment. associated with the development Institutional review board (IRB) and operation of a biobank. See “Research ethics committee Pre-analytical data (REC)”. Factors that may have an impact on Identifier the integrity of the sample during the Information (e.g. name, social se- Label collection, processing, and storage curity number, medical record Any written, printed, or graphic mate- processes. These data include infor- number, or pathology accession rial on or affixed to a specimen con- mation on the treatment of the sam- number) that would enable the iden- tainer or package. ple, including the conditions and the tification of the subject. For some duration of the treatment. specimens, this information might Liquid nitrogen (LN2) include the taxon name and the Coolant used to cool and store Preservation collection number. samples. Nitrogen becomes liquid The use of chemical agents, alterations

Section 1. Glossary and definitions 3 in environmental conditions, or oth- Re-identification Snap-freezing er means during processing and A reversible process that allows The process by which the temper- storage to prevent or retard bio- data from which identifiers have ature of samples is lowered very rap- logical or physical deterioration of a been removed, and replaced by idly to below −70 °C using dry ice or specimen. a code, to be re-identified and liquid nitrogen. linked to a specific individual by, for Procedure example, using the code or linking Specimen A series of steps that, when followed different data sets. A specific tissue sample, blood sam- in order, are designed to result in a ple, and so on taken from a single specific outcome. Removal subject or donor at a specific time. See “Retrieval”. Processing Standard operating procedures Any procedure used after specimen Repository (SOPs) collection but before distribution, An entity that receives, stores, pro- A set of detailed written instructions including preparation, testing, and cesses, and/or disseminates speci- to achieve uniformity of the perfor- releasing the specimen to inventory mens, as needed. This term encom- mance of a specific function. and labelling. passes the physical location as well as the full range of activities associ- Storage Pseudo-anonymization ated with its operation. A repository Maintenance of specimens under The process whereby identifiable may also be referred to as a bio- specified conditions for future use. personal information is anonymized, repository or a biobank. but in such a way that the per- Subject sonal identifiers are replaced by one Research ethics committee (REC) A living or deceased individual who pseudonym, which can be linked A board, committee, or other group is the source of the specimen in ac- across multiple data records without formally designated by an institution cordance with established medical revealing the identity of the person. to review the ethical, legal, social, criteria, procedures, and privacy reg- scientific, and financial implications ulations. In some countries, the term Quality of biomedical research involving “Donor” or “Individual” may be used Conformance of a specimen or pro- humans as subjects, to approve in the same context as “Subject”, cess with pre-established specifica- the initiation of the research, and to especially in the context of human tions or standards. conduct periodic reviews of such re- specimens. search. In some countries, this body Quality assurance (QA) is known as an institutional review Traceability An integrated system of manage- board (IRB) or a research ethics The ability to locate a specimen dur- ment activities involving planning, board (REB). ing any step of its donation, collec- implementation, documentation, as- tion, processing, testing, storage, sessment, and improvement to Retrieval and disposition. ensure that a process or item is of The removal, acquisition, recov- the type and quality needed for the ery, harvesting, or collection of Warm ischaemia project. specimens. The condition in which the tissue is deprived of its normal blood Quality control (QC) Safety supply, containing oxygen and nu- The system of technical activities that Processes, procedures, and tech- trients, while the tissue is at body measures the attributes and perfor- nologies to ensure freedom from temperature. mances of a process or item against danger or harm. defined standards, to verify that the stated requirements are fully met. Sample A single unit containing material Quality management system (QMS) derived from one specimen. The organizational structure, procedures, processes, and resourc- Shipping manifest es needed to implement quality A written description of the contents management. of a shipped package.

4 section 2. Role of biobanks in cancer research SECTION 2 SECTION

The role of biobanks in biological 2.1 Importance of biobanks mechanisms involved in causing can- research in general and their impact cer or in determining its progression, on medical, societal, and economic 2.1.1 Biobanks are critical for resistance or response to treatment, issues have been discussed in two cancer research and clinical outcome (Riegman et al., reports from the Organisation for 2006a). Economic Co-operation and Devel- Human biological specimens have Biobanks are the foundation of opment (OECD) (OECD, 2007, 2009). been used for many decades for three rapidly expanding domains of The OECD publications address the translational purposes in cancer re- biomedical science: importance, justification, and sustain- search, to investigate disease patho- • molecular and genetic epidemiolo- ability of developing biobanks for re- genesis, to test scientific hypotheses, gy (aimed at assessing the genetic search. In 2014, the Biobanking and and to assess biomarkers identified and environmental basis of cancer BioMolecular resources Research in experimental studies. The advent causation in the general population Infrastructure–European Research of new technologies opens unprec- as well as in families); Infrastructure Consortium (BBMRI- edented opportunities to assess the • molecular pathology (aimed at de- ERIC), an umbrella organization for status of the human genome and its veloping molecular-based classifi- biobanking in Europe, was estab- expression, the complex networks of cation and diagnostic procedures lished to provide a focal point for interactions between biomolecules, for cancers); and biobanking activities in Europe and and the functional and clinical con- • pharmacogenomics/pharmacopro- to provide fair access to quality-consequences of their alteration (NCI, teomics (aimed at understanding trolled human biological samples and 2016). the correlation between an in- associated data for cross-biobanking Therefore, studies on human dividual patient’s genotype or research (van Ommen et al., 2015; specimens are also becoming critical phenotype and response to drug Mayrhofer et al., 2016). for the process of discovering new treatment).

Section 2. Role of biobanks in cancer research 5 2.1.2 Biobanks are important ter individual prevention, diagnosis, lection of higher-quality samples for developing personalized prognosis, treatment, and monitoring. and data, enable larger research medicine and/or precision projects to take place, and reduce medicine 2.1.3 Biobanks have an duplication of effort (Yuille et al., impact on biotechnological 2008; Harris et al., 2012). For can- With conventional diagnostic meth- and medical innovation cer biobanks, networking can en- ods, risk factors of importance, as able the study and classification In the continuum from laboratory dis- of rare cancers; a cancer type is well as the opportunity to prevent covery to medical application, bio- considered rare if fewer than 5 cas- diseases that may emerge later, are banks play a key role in life science es are diagnosed in a population of often overlooked when the focus is on research and development (R&D). 10 000, and rare cancers make up the symptoms manifested. Collecting Progress in medicine depends on at least 20% of new cancer cases and analysing biological specimens innovation, development, and the (ESMO, 2010; van Ommen et al., is a necessary procedure for pathol- translation of laboratory findings into 2015; Mayrhofer et al., 2016). ogy-based diagnosis and to enable clinical practice. Access to human Networking implies a multidirec- patients to benefit from the applica- biological specimens and associat- tional flow of information, expertise, tions of molecular and genetic cancer ed data is often a prerequisite for and biological materials between research. such R&D advances. cancer centres and research insti- Personalized medicine and pre- Therefore, the development of tutions and requires the adoption cision medicine are transforming di- high-quality biobanks with innovative of common technical standards for agnosis in medicine and are leading research platforms has accelerated specimen collection, storage, and towards patient-centred and multifac- and facilitated this translational pro- annotation, and for data collection eted diagnostics (Hall et al., 2011). cess. This is due mainly to techno- and management. Biobanks have logical advances and reductions in an important role in facilitating such Personalized medicine is an the cost of information technology exchanges and in providing logis- emerging practice of medicine that (IT), used for data storage and for the tics and infrastructure for multi- uses an individual’s genetic and en- assembly, evaluation, and analysis of centre research projects involving vironmental profile to guide decisions large numbers of samples, as well as cancer centres, academic medical made about the prevention, diagno- increases in analytic capabilities and centres, and diagnostic and health- sis, and treatment of disease. This the drastically reduced costs of DNA care facilities. Biobank networks concept has been refined and its sequencing, with results available involved in the collection, process- scope expanded to include the ap- within a shorter time frame. Simi- ing, storage, and dissemination of proaches, decisions, and practices in lar advances in mass spectrometry biological specimens can range medical facilities, resulting in the new have drastically lowered the cost and from small operations with single term “precision medicine”. expanded the ability to characterize projects in research or university Precision medicine is defined proteins and the metabolites present laboratories to large operations in by the United States National Insti- in biological samples. hospital, academic, or commercial tutes of Health (NIH) as “an approach biobanks. National, regional, and to disease treatment and prevention 2.1.4 Importance of international networks are also de- that seeks to maximize effectiveness networking and exchanges veloping to provide resources from by taking into account individual var- between biobanks diverse populations. For example, the Low- and Middle-Income Countries iability in genes, environment, and Cancer is a burden faced by people (LMICs) Biobank and Cohort Building lifestyle” (Precision Medicine Initiative across the globe. Occurrence and Network (BCNet), coordinated by the Working Group, 2015). In precision mortality rates vary in different parts International Agency for Research medicine, genomic and epigenomic of the world. In addition, studies of on Cancer (IARC), has established analyses with associated data can be many rare forms of cancer are limited a virtual catalogue to document the used to define individual patterns of by the difficulty of recruiting a suffi- resources of its members. disease and susceptibility. Perform- cient number of cases within any sin- The operational model and gov- ing molecular-based assessments gle collection centre, or even within ernance of networks depend on their may become a systematic require- one country. focus and mission. One such model is ment at different stages of patient Networking, or harmonizing, of the federated model, where the bio- follow-up, potentially leading to bet- biobanks can encourage the col- banks maintain their samples and

6 contribute to a common network death (Bergmann et al., 2013) as norms (CEN/TS 16826, 16827, and project when necessary. Another well as dietary intake in relation 16835) (CEN, 2015) and with the model is the project-based model, to mortality among people who new ISO 276 standards, which will where the biobanks collect samples develop different types of cancer, become available within 2 years. for a specific project (Vaught et al., such as colorectal cancer (Alek- • The CEN norms deal with the stan- 2009). sandrova et al., 2014) and prostate dardization of the entire process Several factors can contribute to cancer (Rohrmann et al., 2013), of sample handling, from primary the success of a biobank network. and other diseases, such as is- sample collection to analysis. They They include: chaemic heart disease (Crowe et are based on studies undertaken to • well-defined goals, effective coor- al., 2012). determine the important influenc- dination, and funding mechanisms; ing factors. The Technical Specifi- • efficient communication between 2.1.4.1 Tools for effective cations draw on the effort to codify the relevant medical disciplines and networking and standardize the different steps the global scientific community; in the pre-analytical phase. • standard operating procedures Several important tools have been (SOPs), compatible informatics developed in recent years for effec- 2.1.4.2 Visibility and systems, and harmonized informed tive networking and resource sharing standardized citation schemes consent and material transfer poli- between biobanks. Some examples cies and procedures; and are the following (see also Sec- Being part of an international network • tools to enable de-identified, up- tion 3.8). and contributing to a global catalogue SECTION 2 SECTION to-date follow-up and retrieval of • The Minimum Information about of available resources, with the pos- information and clinical data on Biobank Data Sharing model sibility of creating population-based participants. (MIABIS 1.0 and MIABIS 2.0). MIABIS biobanks, provides opportunities These tools are key to the suc- 1.0 recommends the minimum data for biobanks to benefit from the excess of biobank networks. items and the format of the items periences and tools developed for The European Prospective In- required to enable the exchange networks. Increased participation in vestigation into Cancer and Nu- of biological samples and data, research will result in an increase trition (EPIC) study, a popula- and required to initiate collabora- in the visibility of biobanks and their tion-based study that was initiated tions between biobanks (Norlin et recognition as an important part of in the 1990s and coordinated by al., 2012). MIABIS 2.0 provides an research infrastructure. These at- IARC, is an example of an effec- ontology that represents the admin- tributes can serve to augment the con- tive networked project. The project istrative entities and includes data fidence of researchers and donors in involved partners from 10 European about the biobanks where specific the institutions and countries that the countries and 23 EPIC centres, and specimens of interest are stored; established resources are managed each centre collected biospecimens this ontology can be helpful to an- effectively and used optimally. and data. Blood samples and as- swer research-relevant questions, Recently, a programme of guide- sociated data, including lifestyle such as those about the scope and lines for reporting bioresource use and dietary information, were col- curation status of the specimens and standardized citation schemes lected at baseline. Blood samples and the contact information for cu- has been established to formal- from participants in eight out of the rators of biobanks (Brochhausen et ly recognize the efforts involved in 10 European countries are kept in al., 2013). generating, maintaining, and sharing the IARC central biobank. For two • The Sample PREanalytical Code high-quality bioresources. Scandinavian countries, blood sam- (SPREC) (Lehmann et al., 2012) Two current initiatives aim to put ples are kept locally. identifies and records the main in place standardized procedures for Although EPIC has a central pre-analytical factors that may have formally recognizing the contributions biobank for the baseline samples, an impact on the quality of sampled of biobanks in research through ci- the tissue samples from individu- clinical fluids and solid biospeci- tations in scientific publications: the als who develop cancer are kept at mens and their simple derivatives Citation of BioResources in Journal the centre, and this forms the EPIC during collection, processing, and Articles (CoBRA) guidelines for the federated biobank. storage. However, the SPREC tool reporting of bioresource use in re- The EPIC study has provided may be less important with the research articles (Bravo et al., 2015) opportunities for researchers to lease in 2015 of the European Com- and the Bioresource Research Im- investigate lifestyle and cause of mittee for Standardization (CEN) pact Factor (BRIF), a standardized

Section 2. Role of biobanks in cancer research 7 citation scheme. Biobanks joining • European Union (EU) legislation, in- international solidarity. The public the BRIF citation scheme will have cluding the General Data Protection sector (local and national govern- increased visibility and will benefit Regulation (European Commission, ments and international bodies and from participation in network projects 2016). organizations) has a responsibility (Cambon-Thomsen et al., 2011). Another useful approach derives to contribute to the funding of the The formal recognition of the role rights and responsibilities from a set basic infrastructure of biobanks, be- of biobanks in scientific research will of four ethical principles guiding bio- cause of the important contribution encourage sharing of biological re- medical research: respect for autono- of biobanking to research on global sources and will increase the visibility my, non-maleficence (to do no harm), health and diseases. In contrast, the of biobanks both nationally and inter- beneficence (to do good), and justice responsibility for the development nationally. (Beauchamp and Childress, 2013). and maintenance of sustainable and Protecting the rights of individuals usable resources lies primarily with 2.2 Issues in developing arising from these principles includes the institutions. biobanks and using stored the development of appropriate Institutions and the public sector specimens methods to obtain informed consent should make provision for: from a potential participant and the • infrastructure Developing and using the resources development of research protocols • maintenance of infrastructure in a biobank requires the active in- that are fully compatible with the • equipment volvement of many professionals and principles of beneficence, non-ma- • running costs has ethical and legal implications. leficence, and justice. The institu- • trained personnel Section 3.1 is dedicated to putting tions and investigators that develop • data management systems these ethical, legal, and social issues and manage biobanks also have a • quality management systems (QMSs) (ELSI) into perspective. However, it responsibility to protect personal • procedures to deal with ELSI. is useful to highlight some of the key data, ensure biological and environ- In addition, users of the biobank- documents and principles that can mental safety, and make collections ing infrastructure facilities should con- guide decision-making when estab- accessible and available for reuse for tribute through cost reimbursement, lishing a biobank. Key documents research purposes under (the con- for the financial and structural sus- include the following: sented) defined conditions. Access tainability of biobanks. Thus, biobanks • the WMA Declaration of Taipei on requests should take into account the should establish user fees for access ethical considerations regarding non-renewable nature of the speci- to human specimens, data, and ser- health databases and biobanks mens in setting priorities for scientific vices, to cover the costs of collecting, (WMA, 2016); use, and the distribution of specimens annotating, storing, retrieving, and • the WMA Declaration of Helsinki, for research should be governed by processing the delivered biospeci- which provides the general frame- the use of clear and documented Ma- mens. However, human biospecimens work in which questions relating to terial Transfer Agreements (MTAs). should not under any circumstances medical research can be addressed These rights and responsibilities are be commercialized. Regardless of the (WMA, 2013); further defined and addressed in the role of industry in core funding, which • the more specific guidance issued remainder of this book. is a matter of debate with serious im- by the OECD: Guidelines on Human plications, the legal responsibility and Biobanks and Genetic Research 2.3 Principles for sustainable custodianship of the specimen collec- Databases (OECD, 2009) and Best biobanks tion and storage must remain within Practice Guidelines for Biological institutions. This is because people Resource Centres (OECD, 2007); Developing a biobank is expensive. who agree to provide their samples • best practice principles outlined Added to the maintenance and run- donate to the institution and not to by organizations such as the Unit- ning costs, this can place financial researchers or individuals, and the ed States National Cancer Insti- strain on underresourced institutions. samples will remain in the primary tute (NCI) (NCI, 2016) and ISBER These constraints are a significant institution after the research project (ISBER, 2012); obstacle to developing biobanks ends or the researcher leaves the • guidance from the Global Alliance in low- or middle-income countries organization. To ensure continuity in for Genomics and Health (GA4GH) and for the long-term sustainability the management of the samples, the (GA4GH, 2016) and the Public Pop- of biobanks worldwide. Overcoming institution should nominate another ulation Project in Genomics and So- these obstacles requires a signifi- person who will assume primary re- ciety (P3G) (P3G, 2016); and cant concerted effort of national and sponsibility for the samples.

8 In defining mechanisms for sus- 2.4.1 Institutional commitment data owners, which are guaranteed tainability or stability, there is a need by EU law. to develop safeguards for preserva- Many factors contribute to the deci- However, there are conflicting tion of participant confidentiality and sion to establish and run a biobank. In data protection rules in different protection against improper use of practice, the process often starts with countries, which need to be observed human biospecimens and data. In the willingness of medical doctors during international exchanges. addition, the stability of biobanks re- and scientists to develop a resource Therefore, common EU rules have lies heavily on the value of the stored useful for diagnosis, prognosis, and been established to ensure that per- resources, in terms of their quality research purposes. However, the sonal data have a high standard of and scientific relevance and the use establishment of a biobank must not protection everywhere in the EU. The of the samples. rely only on individual action but also EU Data Protection Directive also Financial forecasts have demon- requires a clear commitment by the provides specific rules for the trans- strated that the actual costs associ- host institution, which also needs to fer of personal data outside the EU, to ated with biobanking are significantly ensure that collections are developed ensure the best possible protection of higher than recognized by researchers within appropriate legal, ethical, clin- data when they are exported abroad. and funding bodies (Matharoo-Ball ical, scientific, and technical guide- ELSI and governance recom- and Thomson, 2014). Cost recovery lines, to provide historical continuity in mendations relating to governance is essential for biobank sustainability specimen management and record- structures, informed consent, data and stability. Although each institu- keeping. Finally, the biobank should protection, return of results and inci- tion will have to decide on the cost-re- ensure that the stored materials can dental findings, and data and sample SECTION 2 SECTION covery model that will best serve its be made available for research. sharing are presented in Section 3.1. purposes, common elements to be The purpose of the biobank must An important governance issue considered include costs related to be clearly formulated and document- to highlight when establishing and personnel, equipment, supplies, and ed. In case of loss of funding or other maintaining biobanks relates to pub- service contracts. adverse events that may prevent the lic engagement programmes and The models should be consid- institution from maintaining its com- the establishment of clear channels ered in the context of relationships mitment, it is the responsibility of of communication with partners and between the users, funding agen- the institution to take the necessary stakeholders. Therefore, transparen- cies, academia, and universities, steps, depending on the applicable cy in procedures and operations is and possibly also industry partners. legal/ethical requirements. There may critical, and clear descriptions of the Contingency plans in case of unex- be an obligation to destroy the sam- roles and responsibilities of person- pected incidents and inadequate ples or to transfer the collected spec- nel should be communicated to part- supporting infrastructure, such as imens and data to another institution ners and stakeholders. Given that flood or fire disasters, interruption that will take over the commitment participation is voluntary and that most in electricity supply, and poor Inter- for the long-term maintenance of the biobanks operate on a non-economic net connectivity, should be included resources. There may be specific basis, biobanks need public trust in any model. obligations related to such a transfer. and support. It has become common practice for large-scale population 2.4 General considerations 2.4.2 Ethical, legal, and social biobanks to engage in consultation for establishing a biobank issues (ELSI) and governance with the public and other stakeholders before the biobank is established Several factors must be taken into ac- ELSI considers local, national, and (UK Biobank Ethics and Governance count when setting up and running international cultural, legal, social, Council, 2015, 2016). Methods of a biobank. A detailed description of and ethical norms. For example, the communication could include, for ex- these requirements is provided in the EU Data Protection Directive states ample, consultation with community 2012 Best Practices for Repositories: that under EU law, personal data can representatives, focus group meet- Collection, Storage, Retrieval, and be gathered legally only under strict ings, workshops, interviews, public Distribution of Biological Materials conditions, for a legitimate purpose meetings, polls, and surveys. Public for Research, developed by ISBER (European Commission, 1995). Fur- consultation is particularly important (ISBER, 2012). Some aspects of thermore, people or organizations when ethnic or cultural minorities are particular importance in setting up that collect and manage personal in- approached to participate in biobank a biobank for cancer research are formation must protect it from misuse collections. Section 3.1 provides fur- highlighted here. and must respect certain rights of the ther information on transparency and

Section 2. Role of biobanks in cancer research 9 communication with key stakehold- regulations, and has a critical role in adequate educational backgrounds, ers, and Section 3.1.2.5 describes receiving, processing, and respond- experience, and training to ensure community engagement in relation ing to requests for access to stored that assigned tasks are performed to the consent process. specimens. The manager can act in accordance with the biobank’s as a technical advisor to the access established procedures. Updated 2.4.3 Biobank management committee during the review of ac- training should be conducted on a and staffing cess applications. periodic basis for personnel, in ac- Running a biobank requires ded- cordance with applicable regulations Biobanks should be adequately icated staff members for specimen and roles within the biobank. staffed, and the personnel selected processing and storage and for data Other personnel who are not nec- for these tasks must be well quali- management. The job description, essarily staff members of biobanks fied and have an appropriate level tasks, and reporting system of all but should be aware of the purpose of specialized training. The biobank supervisory and technical staff mem- and goals of obtaining high-quality should be placed under the overall bers must be documented. This is bioresources are clinicians, research- supervision of a biobank manager of particular importance in instanc- ers, technicians, nurses, surgeons, with sufficient training, experience, es where biobank staff members pathologists, and anaesthetists. The and seniority to fulfil the scope of the also perform other tasks within the involvement of a pathologist in this activities of the biobank. The manag- institution (e.g. pathology service process is crucial to ensure that er is responsible for operations, in- or service activities in molecular patient care is not compromised cluding compliance with appropriate biology). Staff members must have (NCI, 2016).

10 section 3. Recommendations for biobanks

3.1 Ethical, legal, and social operates (Laurie, 2011). A good inter- and data (Section 3.1.5; see also issues (ELSI) and governance nal governance system should: Annex 1). • ensure that the biobank remains Further sections consider quality This section provides advice on faithful to its purpose, encour- (Section 3.4) and records manage- developing an internal governance aging trust between the various ment (Section 3.6). system for biobanks. It references stakeholders; Good governance includes en- recommendations and best prac- • be guided by a set of overarching gaging with the public during the tices of international organizations, principles when making decisions, establishment of a biobank and 3 SECTION including OECD (2007, 2009), ISBER including being transparent, ac- throughout the life-cycle of the bio- (2012), GA4GH (2016), and NCI countable, consistent, proportion- bank. Therefore, the approach to (2016), among others. However, the ate, efficient, coordinated, equita- public engagement must be con- background of law and guidance is ble, and fair; and sidered from the outset. In addition continually developing and should be • be dynamic and able to adapt over to engaging with participants, the monitored. For example, the new EU time. biobank may need to engage with General Data Protection Regulation The internal governance ap- the scientific community, research- (European Commission, 2016) has proaches introduced in this section ers, patient groups, and/or the wid- implications for patients’ rights in are based on a good governance er public using a variety of meth- medical research, CEN norms, and structure or framework (Section 3.1.1) ods, for example by consultation ISO standards. and documentation on: on study designs and policies, in- Governance, in the context of bio- • informed consent (Section 3.1.2); volvement on committees, or publi- banks, is not one-size-fits-all. During • data protection, confidentiality, and cation and outreach. Good biobank the establishment of a biobank, gov- privacy (Section 3.1.3); governance also includes a strong ernance systems should be designed • return of results and incidental find- commitment to researchers, ensur- to take into account the biobank’s ings (Section 3.1.4); and ing quality, efficiency, and trans- scope and the context in which it • access to and sharing of samples parency of service. Therefore, the

Section 3. Recommendations for biobanks 11 following recommendations should larger biobanks will need to develop many committees or policies, or if be put into practice in collaboration a detailed protocol and procedures. they are ill-defined, this can impede with project principal investigators. The policies are usually stipulat- procedures and cause delays. ed in a governance document that 3.1.1 Governance framework describes the objectives and scope 3.1.1.1 Governance organization of the biobank, the organizational A good governance framework structure, the scientific and eco- The biobank should have a structure should define the organizational nomic strategy of the biobank (which of committees and appropriately quali- structure of the biobank, for daily will be articulated in an annually up- fied personnel in relevant roles to over- management and oversight of its dated business plan), and contingen- see its governance. The size, type, strategic policy. This framework usu- cy plans in the event of closure. The and number of committees and their ally includes lists and descriptions governance document also includes composition will vary depending on the of the biobank’s personnel, commit- policies on data protection and pri- size and purpose of the biobank. Care- tees, and policies that are required vacy as well as the procedures gov- ful consideration should be given when to enable the correct functioning of erning specific operational activities participants, patient groups, or public the biobank. The level of policies of the biobank. representatives are asked to serve and procedures governing the bio- Defining the structure and man- on biobank committees. Their roles bank should be scalable to its na- date of committees and describing on the committee should be clearly ture, size, and available resources. policies is an effective way to en- communicated, and training should For example, smaller biobanks may sure adherence to proper gover- be provided. The following types of have more limited policies, whereas nance. However, if there are too committee may be considered (Fig. 1).

Fig. 1. Sample committee structure for internal biobank governance.

S E

ssential Stronl recoene tional

IE Executive committee or steering Operations or management In terms of personnel, the bio- group committee bank should have clear reporting lines and accountability, with doc- All biobanks should have an execu- The role of the operations or man- umented levels of authority and tive committee or steering group. The agement committee is to support the responsibility associated with each responsibilities of this committee may executive committee for the strate- role. Clear responsibilities for staff include overall management, defin- gic decisions of the biobank and to members enable the biobank man- ing strategic objectives, monitoring provide expertise in all aspects of agement to ensure that the biobank’s progress, revising and/or adopting biobanking operations (e.g. safe- activities comply with ethical and policies, and developing a commu- ty; quality and efficiency, including legal requirements (OECD, 2009). An nications strategy. This committee processing, storage, and distribution organizational chart and list of staff may also conduct an annual review of biospecimens). members and their responsibilities meeting to consider the QMS. should be developed, alongside an Larger biobanks may require organizational plan, which defines the Ethics oversight (or advisory) additional committees, such as the organization and management of the committee following. biobank and its relationship to external parties. Roles and responsibilities The ethics oversight committee ad- Scientific oversight (or advisory) should be clearly defined, to establish vises the executive committee on committee who has legal responsibility in relation strategy, developments, and proce- to the biobank, who has day-to-day op- dures relating to ethical oversight, in- This committee would provide scien- erational responsibility, and who is act- cluding legal and policy issues. The tific feedback to the executive com- ing as the custodian of the resources. committee could include, for exam- mittee, advise on scientific strategy Specific roles within the biobank ple, ethicists, scientific researchers, and current developments, consider will depend on the institutional con- medical experts, lawyers, social sci- the pertinence of new collections, or text but may include the following. entists, and members of the public advise on procedures. Membership • A designated director, who is re- or participant organizations. In some should include relevant profession- sponsible for implementing biobank cases, this committee may be part of als. In some biobanks, this commit- policies. The roles and responsibili- a larger infrastructure, such as a local tee could be combined with an ethics ties of this person in their institution hospital ethics committee. In some oversight committee. In some coun- should be clearly defined. countries, this committee may be a tries, this committee may be a legal • A biobank coordinator or manager, legal requirement. requirement. who reports directly to the steering group. To eliminate conflicts of in- Laboratory safety and biosecurity Public engagement committee terest, it is recommended that the committee biobank manager is not an active in-

This committee could help biobank vestigator or a biobank user. The bi- 3 SECTION All biobanks should establish, or have personnel and associated research- obank manager may also be desig- access to, a committee on laboratory ers to better understand public opin- nated the custodian of the resource, safety, which may also consider gen- ion. For some larger biobanks, ad- with the following responsibilities: eral health, safety, and security issues. visory panels of study participants - establishing procedures; meet regularly and provide feedback - ensuring that ethical guidelines are Data and sample access committee on new projects and review study adopted and respected; materials, newsletters, and ques- - implementing the decisions of the Biobanks should consider establish- tionnaires. Examples are the Avon relevant committees in relation to ing a data and sample access com- Longitudinal Study of Parents and the control, access, and use of the mittee, to oversee access requests, Children (ALSPAC) teenage advisory material; monitor related procedures, and en- panel (UK Biobank Ethics and Gov- - maintaining close collaborations sure that participants’ interests are ernance Council, 2009) and the NIH with principal investigators; protected and biobank protocols Precision Medicine Initiative Cohort - distributing information about the are followed. In some cases, this Program subcommittee, which has biobank and related research; committee is external to the biobank significant participant representation and and is composed of independent (Precision Medicine Initiative Work- - other responsibilities, which members. ing Group, 2015). should be defined in advance.

Section 3. Recommendations for biobanks 13 • A biobank quality manager, who is • Researchers should submit re- Additional policies to consider responsible for the QMS and for ports annually and at the end of include: periodic review of all SOPs, and their projects, including informa- • a governance policy, containing in- has overall responsibility for quality tion on publications and patent formation about the biobank’s gover- control (QC) and quality assurance applications (OECD, 2009). nance structure and the responsibil- (QA). • The biobank should maintain a sys- ities of management (OECD, 2009); • A data steward, who is responsible tem for reporting adverse events, • a retention policy, covering bio- for data protection and privacy. anomalies, and non-compliance specimen availability and wheth- with the QMS; this reporting sys- er collections can be shared or 3.1.1.2 Documentation: plans, tem supports corrective and pre- destroyed; policies, and procedures ventive actions and enables any • a policy on storage options; relevant documents to be updated • a safety policy for staff and visitors; Documentation requirements in- (CCB, 2014). • a policy on transportation of clude plans, policies, and specific A critical document is the bio- material; SOPs. The documents should be bank programme document (or • a policy on disposal of material and compatible with international stan- biobank protocol), which contains biosafety and biosecurity; dards such as the ISO standards information about the scientif- • policies covering ethical issues, for biobanking and the CEN norms ic rationale, scope, design, and including information on the pro- that articulate how activities of the strategy for the biobank. Other tection of the confidentiality and biobank are to be performed (see biobank plans, policies, and proce- privacy of participants (see Sec- Section 3.4 for more details about dures should be developed in line tion 3.1.3), informed consent, return ISO and CEN). Some general prin- with this protocol. The biobank’s of results and incidental findings, ciples in relation to these docu- mission should be clearly outlined and so on; ments should be followed: in terms of its purpose, the types • a policy on the intellectual proper- • Documents should be developed of research or other users sup- ty generated from the use of the in the context of a QMS, which in- ported (scope), and the types of resources and research results; cludes document version control. samples and data collected. Ad- • a publication policy, governing pub- • Documents should be developed ditional considerations include lications arising from the use of the in the context of an up-to-date risk which services are provided (e.g. biobank; and assessment undertaken alongside specific research assays, storage of • policies on how the termination of a procedure that takes into account samples) and whether legacy sam- the biobank would be handled. risks to the health and safety of ples can be incorporated into the Guidelines recommend that ac- people. biobank. This protocol and associ- companying SOPs should be put in • Documents should include a time ated key biobank documents should place to govern all biobank activities: frame for review and revision; 2 be approved by a research ethics recruitment; consent; staff training; years is a recommended time committee, and renewed approval biosafety; the collection, receipt, frame (NCI, 2016). should be required if the documents processing, and storage of samples; • To facilitate cooperation between are amended (OECD, 2009). sample QC; laboratory QA; partici- biobanks, documents should ad- An annually updated business pant de-identification; data collection, here to internationally accept- and continuity plan or model is es- recording, storage, and management; ed technological standards and sential, especially if the biobank is data protection; the monitoring, cali- norms, ensuring that these are planning to charge for use of the bration, maintenance, backup, and clearly referenced (OECD, 2009). resources (Vaught et al., 2011). repair of equipment; the procurement • High-level policies, including data The business plan should include a and monitoring of supplies (dispos- and sample access policies and strategy for both medium-term and ables and reagents); the distribution terms of reference of committees, long-term sustainability. A budget- and tracking of samples; records should be publicly and freely avail- ing or costing exercise will assist and documentation; reporting of able, for example on a website. in the development of such a plan. non-conformity and complaints; and • Biobanks should consider imple- All biobanks should also devel- disaster management. menting monitoring strategies op a quality management policy All staff members should be with scheduled audits to ensure and a policy on access to samples trained in the procedures at the that policies and procedures are and data from the biobank (see biobank, and this should be followed. Annex 1). documented.

14 Key points: biobank governance • Good governance involves considering structures and documentation from the outset. • The biobank should, at a minimum, have an executive committee or steering group and have (or have access to) a laboratory safety and biosecurity committee. • A scientific oversight committee, an ethics oversight committee, an operations or management committee, and a data and sample access committee are strongly recommended. • Other committees are optional, depending on the size and scope of the biobank, including a public engagement committee and a quality management committee. • In terms of personnel, it is critical that clear reporting lines and accountability exist, with documented levels of authority and responsibility associated with each role. An organizational chart should be made and communicated to all biobank staff members. • Key biobank personnel may include a director of the biobank. • Other personnel should include a biobank coordinator or manager, who reports directly to the steering group. A biobank quality manager and a data protection officer are also strongly recommended. • A critical document is the biobank protocol, which includes information about the scientific rationale, scope, design, and strategy for the biobank. The protocol and associated documents should be approved by an independent research ethics committee. • A business plan or model that considers long-term sustainability and provides a continuity plan is essential, especially if the biobank is planning to charge for use of the resources. • All biobanks are strongly advised to develop a quality management policy and a biobank access policy, based on the model of the biobank. • Extensive guidance is provided on other policies and SOPs that may be implemented, depending on the context of the biobank.

3.1.2 Informed consent research area would benefit from ticipants to consent to a broad range community engagement in relation of uses of their data and samples. The approach to informed consent is to the consent process; Although broad consent allows for a a key consideration when establishing • what to do if the potential partici- broad range of research activities, it is a new biobank, and a policy should pant does not fully understand the regarded by research ethics commit- be developed (see Section 3.1.1.2). language of the researcher who is tees as specific enough to be consid-

Requesting appropriate informed administering the consent; ered “informed”, because guidance is 3 SECTION consent has become a cornerstone • what to do if the potential partici- provided on the nature of the future for the collection of samples and data pants do not have the legal capacity undetermined research uses (e.g. for use in research, and is supported to consent for themselves; research on breast cancer and as- by relevant guidance and legislation. • considerations when including sam- sociated conditions). It is important to This section presents recommenda- ples or data from deceased partici- note that broad consent forms usually tions to assist a biobank in developing pants in the biobank; contain a series of statements spe- a consent policy and associated doc- • the continuing nature of consent; cific to the biobank, and not state- umentation, and covers the following • when participants might need to be ments related to specific research areas (see also Annex 2): re-contacted to request new or up- projects. Table 2 outlines the differ- • types of consent; dated consent; and ent types of consent associated with • what information to provide to po- • how to approach withdrawal of biobanks and sample collections, tential participants; consent. together with key points about each • potentially ethically or legally chal- approach and notes on information to lenging issues; 3.1.2.1 Types of consent be provided to participants. • what to consider during the process Further guidance on designing of requesting consent; Many biobanks use a broad consent, and implementing a broad informed • what to consider if the country or the which allows patients or research par- consent is provided in Annex 2.

Section 3. Recommendations for biobanks 15 Table 2. Types of consent and key considerations

Type/subtype of Uses Key points Information to be provided to consent participants

Consent waiver Existing collections An ethics committee agrees that existing samples None and anonymous data can be used for research or biobanking without a new/updated consent. Consent waivers should be an exceptional measure for high-value collections. If a similar collection can be prospectively obtained, this should be done.

Opt out Leftover clinical This approach needs specific review by an ethics Information on the biobank should samples from committee. be available to the participant treatment when Part of the participant’s routinely taken sample and population, with details of how expected uses are anonymous data can be used for research, unless to opt out (e.g. information low-risk the participant takes action to opt out. sheets given directly to patients, leaflets distributed with hospital New uses of existing This approach should not be used for collection of collections appointments, and clearly visible additional/new samples for research projects or posters). biobanking.

Opt in, with subtypes

Specific consent Research projects Consent forms usually contain a series of Information is provided that refers involving sample statements specific to the project. to one research project or a linked collection that are Restricts samples and data to the specific research group of projects. complicated for project described. the participant to understand, including Ethics approval is needed. clinical trials

Specific and Used for specific The consent form for a specific project or trial Information on the intended broad consent projects or activities includes provision on the addition of participant biobanking activity should be (e.g. surgical treatment data and samples to a biobank. included in the project information or clinical trials) The consent form for surgical treatment should sheet, plus information in other involving sample include a clause on adding any remaining samples relevant sections of the information collection when there and anonymized clinical data to a biobank. sheet, if possible. is a future plan for For surgical treatment, information biobanking May restrict use for biobank to anonymized samples and data. about the biobank should be provided (see advice for “Opt out” Ethical and scientific approval will be required above, including posters, etc.). for future biobanking or research with samples collected via this route. An existing biobank must have ethics approval for samples to be accepted via this route and should have standard approved wording to include on the consent forms and information sheets.

Broad consent Used when samples This approach provides information and choice to Topics for a biobank information are taken for the participants about the biobank’s activities. sheet are included in Annex 2. purpose of a biobank The consent forms usually contain a series For multiple sampling of statements specific to the biobank, and not events and multiple statements related to specific research projects. projects Ethical approval is mandatory for this approach. Ethical and scientific review is usually needed before distribution of samples and data to researchers.

Dynamic consent Used when (multiple) The consent process and continuing communication Through the use of an IT system, samples are taken with the participant usually happen via an IT-based the participants themselves can for the purpose of a infrastructure. The platform can be used for other choose how much information they biobank, or a research communications relating to the study. wish to receive, i.e. in-depth or brief project If the biobank enables this, the participant can opt information. When the scope of the in or out of parts of the biobank’s planned research The information can cover both the biobank or project may and amend this over time, and find out which biobank’s scope and information on change over time projects their samples have been used in. the governance of the biobank. When the biobank Ethical approval is needed for this approach. More in-depth information could be envisages regular provided on potential uses of the contact with samples, to enable participants to participants opt in or out of certain uses.

IT, information technology.

16 3.1.2.2 What information to it may be involved in any potentially • The person requesting consent provide to potential participants challenging uses and include infor- should not coerce the potential mation about these in the informa- participant in any way. Information about the biobank and tion sheet and/or the consent form • The person requesting consent biobanking activities is usually pro- as appropriate, in addition to the should encourage open discus- vided to potential participants using core elements usually included as sion and give the potential par- a participant information sheet in part of a consent form. The consent ticipant the opportunity to ask conjunction with a consent form (in form should provide the participant questions. some cases, these two documents with a means to opt out of uses that • The person requesting consent together are called the informed con- the participant feels are ethically should ensure that the potential sent form). The information provided questionable. The consent form may participant is informed about their will vary depending on the nature of also require specific opt-in provisions right to withdraw consent, about the the biobank and the type of consent if they are legally required by national risks and benefits of participating in requested. Further details are provid- or regional laws; an example is the project, and about any other im- ed in Table 2 and Annex 2. transfer of data outside of Europe, portant issues. according to the EU Data Protection 3.1.2.3 Potentially ethically or Directive (European Commission, 3.1.2.5 What to consider if the legally challenging issues 1995). A means to opt out of certain country or the research area uses should be provided by the bio- would benefit from community The following potential uses of sam- bank only if this is recordable (i.e. in a engagement in relation to the ples and data are examples of issues database), actionable (i.e. when dis- consent process that may be considered ethically or tributing the samples for research), legally challenging: and practicable (e.g. given the num- The consent process needs to be • transfer of samples or data across ber of participants or the number of appropriate for the local cultural con- national borders; it is important to be samples distributed). text, and in some cases this means aware of regional and national reg- that wider community engagement ulations, such as the EU Data Pro- 3.1.2.4 What to consider during is appropriate (H3Africa, 2013). In tection Directive of 1995 (Article 26) the process of requesting cases where wider community en- (European Commission, 1995) and consent gagement is needed, consultation on the EU-U.S. Privacy Shield adopted the biobank’s consent processes and by the EU Commission on 12 July It is important to consider the fol- documents should take place with the 2016 (http://ec.europa.eu/justice/ lowing aspects during the consent wider community, local leaders, and data-protection/international- process. professionals. The requirement for transfers/eu-us-privacy-shield/ • Where possible, the information community involvement in the con- index_en.htm); sheet should be distributed ahead sent process may also be specified

• use of samples in experiments in- of the meeting with the potential in local ethical or legal guidance. In 3 SECTION volving animals; participant. some of these cases, prior consent, • creation of cell lines from the sam- • The potential participant must be assent, or permission may need to ples, including stem cell lines; given adequate time to read and be obtained from community, tribal, • use of samples and data by com- consider the information sheet and or family leaders (Nuffield Council mercial researchers; should be offered the option to de- on Bioethics, 2002). In all cases, the • research linked to reproduction, cide and give consent at a later visit potential research participant must including use of embryos; if required. be approached for consent and must • return of individual research results • The person administering the con- have the right to refuse participation. and incidental findings (this is an im- sent process must be convinced of portant topic that warrants exten- the capacity of the potential partici- 3.1.2.6 What to do if the sive discussion, which is beyond the pant to give consent. If they are not potential participants do not scope of this document); and convinced, Section 3.1.2.6 (on par- have the legal capacity to • research into high-penetrance ticipants without the legal capacity consent for themselves genes linked to disease. to consent) may be applicable. Al- When information sheets and ternatively, the potential participant This category of participant is of- consent forms are being developed, may require assistance in reading ten called “vulnerable people”, and the biobank should consider whether the form. careful consideration must be given

Section 3. Recommendations for biobanks 17 to how recruitment will be conduct- participate (rather than consent). In- plants, which may differ markedly ed (WMA, 2013, 2016). Recruitment formation and consent materials can from country to country. of “vulnerable” participants must re- be designed for different age groups spect the requirements in the Decla- to aid understanding of the research. 3.1.2.8 The continuing nature of ration of Helsinki that all vulnerable Any objection from the child should consent groups and individuals should receive be respected (Hens et al., 2011). specifically considered protection, The assent process is based on the If the participant has given prior writ- that the research is responsive to the age and maturity of the child and on ten consent, they should always be health needs of this group and can- any applicable local laws or ethical asked to confirm (verbally and/or tac- not be carried out in a non-vulnerable guidance on the matter. In addition itly, as appropriate) their agreement group, and that this group will benefit to the assent of the child, the child’s to donate samples to the biobank, from the research. parent(s) or an appropriate legal rep- and they should always have the Three types of participant com- resentative must provide consent on opportunity to ask questions, before monly identified as vulnerable are: the child’s behalf. It is also good prac- additional sampling (e.g. blood, biop- • mentally incapacitated adults; tice to re-contact child participants sy, aspirate, bronchial brushings) or • adults in emergency care situations; once they reach the local legal age of data collection is performed. Where and maturity, to request consent, if possi- possible, the verbal consent should be • minors/children. ble (CIOMS, 2002; Hens et al., 2011). recorded electronically or noted and In the case of mentally incapaci- stored with the original consent form. tated adults, a legally authorized rep- 3.1.2.7 Considerations when The participant may decline to provide resentative can provide consent on including samples or data from further samples or data at any time. their behalf. If the participant made deceased participants in the This does not invalidate the consent legally approved provisions about re- biobank to use any previous samples or data search participation before they were given to the biobank, unless notice of incapacitated or if they assigned a Consent requirements will vary withdrawal of consent is given. legal representative, these should depending on whether the biobank be respected. The participant should intends to request consent for sam- 3.1.2.9 When participants might be involved as much as possible in ples and data from potential partici- need to be re-contacted to the decision to participate, and any pants before their death (for example, request new or updated consent resistance or objections should be for a brain biobank) or request the respected. samples and data after the partici- Several situations may arise where In the case of research taking pants’ death. Local legislation will the biobank may need to re-contact place in an emergency clinical sit- dictate the applicable consent and the participants to request new or uation where consent has not been legal requirements. Some legal or updated consent, apart from con- obtained, requirements will differ by practical constraints may exist for tact to request additional data and/ country and may include: biobanks accessing medical records or samples for the purposes of the • the local ethics committee explicitly after the participants’ death. Uses same project. These situations may approving the recruitment pathway; of the samples and data, collected include children reaching the age of • another medical professional au- before or after death, that fall outside maturity and temporarily incapacitat- thorizing the involvement of the the scope of the original consent will ed participants regaining legal capac- participant; require approval by a research ethics ity (see Section 3.1.2.6), and in such • the known wishes or objections of committee (Tassé, 2011). cases full informed consent should the participant being respected; and Where samples are to be col- be requested (Burke and Diekema, • a maximum time limit being im- lected for research after death, local 2006). Another situation is when the posed for participant involvement institutional, ethical, and legal guide- information provided in the initial con- without consent. lines to obtain consent must be fol- sent form and information sheets is Consent should be requested lowed, and the individual’s wishes modified or updated (e.g. if the scope from the participant if the participant expressed before death, if they are of the biobank changes). In this case, regains legal capacity. known, should be respected. The re-contact of participants to request In the case of research involving consent procedure may be built into an updated consent may be required, children, they should take part in the existing procedures for postmortems given the changing conditions of consent process in accordance with or for clinical use of postmortem their participation (Wallace et al., their age and maturity, and assent to samples for organ or tissue trans- 2016). An appropriate research ethics

18 committee should decide whether biobank to present withdrawal op- and data already collected and can re-consent is required or whether a tions to participants in the consent continue to access the participant’s waiver can be applied. form or information sheets. This may medical records if necessary. A general guideline is that be- not mean guaranteeing to destroy • “No further access” option: the bio- fore re-contact is established, a all samples and data; for example, bank will not contact the participant participant’s options with respect to the withdrawal options may stipulate or access the participant’s medical re-contact should be checked, be- that samples and data already re- records but can continue to use cause participants should be given leased or used in analyses are not samples and data already collected. the option not to be re-contacted retrievable. Examples of withdrawal The biobank should also clearly (see Annex 3). options include the following. communicate to participants when it • “No further use” option: the bio- is impossible to destroy parts of the 3.1.2.10 How to approach bank will destroy all samples and samples or data. Examples include withdrawal of consent data from the participant and will not being unable to destroy: contact the participant again. • samples and data already distribut- At any time, participants can with- • “No further contact” option: the ed for research or used in analyses; draw consent for the biobanking and biobank will no longer contact the and use of their samples or data without participant directly by any means • data needed for audit purposes or giving a reason. It is crucial for the but can continue to use samples already archived.

Key points: informed consent • Consider local legal or ethical requirements that are applicable to the consent process. • Distribute the consent materials to the participant in advance whenever possible. The form should be written in a language that is understandable to the participant. • Give participants adequate time to read the form, understand the information, and consider possible participation. • The person requesting consent should ensure that the participant fully understands what is required of them. • The person requesting consent should encourage open discussion with the potential participant and should not coerce them to participate in the project. • The rights of the participant and the risks and benefits of participating in the project should be explained to potential participants. • The withdrawal options should be explained. SECTION 3 SECTION 3.1.3 Data protection, tection for individuals in the EU. The data collected alongside the samples confidentiality, and privacy processing of personal data outside in line with the commitment undertak- the EU is also an important com- en with participants. This section briefly outlines recom- ponent of EU privacy and human Methods to ensure data protec- mendations about the protection of rights law. tion, confidentiality, and privacy are biobanks’ data and about the con- Other examples of privacy and discussed in Section 3.3.4 and Sec- fidentiality and privacy of the parti- security policies are those of the tion 3.6. The biobank should consider cipants’ data. Legislation and guid- Confederation of Cancer Biobanks using de-identification methods, such ance on these issues vary between (CCB, 2014) and GA4GH (GA4GH, as coding or pseudo-anonymization countries and, where they exist, may 2015b). associated with a procedure to store also be complemented by local site At a European level, the changing codes. Explanations of these terms requirements. data protection regulations and re- are provided in Section 1 and in Ap- In the EU, the General Data Pro- quirements in relation to the EU-U.S. pendix 1 of the privacy and security tection Regulation (European Com- Privacy Shield should be taken into policy of GA4GH (GA4GH, 2015b). mission, 2016) replaces the Data account. The biobank must develop Examples of particular issues for Protection Directive (European Com- a strategy and have an IT framework data protection and privacy for bio- mission, 1995) and unifies data pro- and policies in place for managing banks include the following.

Section 3. Recommendations for biobanks 19 • Access to medical records. When how data will be shared, and how fidential data should have a duty possible, staff members should their privacy and the confidentiality of professional secrecy (OECD, be bound by a professional code of the data will be protected. 2007). Staff members, consultants, of practice with high standards of • Research involving genetic data or committee members without ethical behaviour. The participant and next-generation sequencing such a duty must be asked to sign should be asked for permission to data may lead to concerns about a confidentiality agreement. Ac- access their medical records and (i) whether data can identify individ- cess to personal data should be should be informed where these uals and/or family members, and limited, and access to any data data are held in an encrypted, (ii) whether to return results should be restricted to those data non-identifiable format at the bio- from this type of analysis (see needed for the research project or bank (CCB, 2014). Section 3.1.4). other use. Data can be separated • Data protection mechanisms when • The inclusion of medical images in into different databases according biobanks share data with other biobanks (e.g. scans and histology to type. The biobank should keep biobanks or provide data for trans- slides) poses specific challenges specimen metadata in a linked lational research. Privacy and for de-identification, because iden- but separate database from the confidentiality of data must be guar- tifying data are usually embedded patients’ medical records and de- anteed, while facilitating access. within the images, which by them- mographic information, to keep • Participants should also be in- selves may not be identifying. data safe and confidential. Regular formed, in the informed consent, In terms of confidentiality, all audits of the data systems must be about what data will be shared and staff members with access to con- implemented. Key points: data protection and privacy • Inform participants about any data protection and privacy issues (e.g. sending information abroad, intention to share data). • Use a method to protect privacy, such as de-identification, coding, or pseudo-anonymization, and consider how this affects re-contact and return of results. • Develop a policy or procedure that describes the process of re-identifying participants. • Coded data and codes should be stored separately. • Put in place robust data systems and audit trails. • Manage, limit, and trace rights of access to information systems. • Limit physical access (e.g. store paper documents in rooms with limited access), and implement electronic security procedures where possible. • Respect participants’ consent options during access, use, and transfer of data. • Consider what data or combinations of data will not be made available, because of confidentiality or privacy reasons.

3.1.4 Return of results and balance between the duty of care participants, if required, and whose incidental findings to participants, the ethical and legal responsibility this is. requirements to return results, and One toolkit is the framework on This section presents the issues the logistical and technical ability of the feedback of health-related find- with respect to research results: the biobank to return results in an ings in research (Medical Research summary results, individual results appropriate manner. Factors to con- Council and Wellcome Trust, 2014). from baseline assessment, and in- sider include whether the biobank dividual research results. The prin- no longer has contact with the pa- 3.1.4.1 Generalized, non- cipal investigator and the biobank tient, the ease of re-identifying the individual study results have collective responsibility for participants and finding out whether deciding whether to return research they have chosen to be informed, According to best practices, re- results to participants. The deci- the potential cost implications of search results can be published sion-makers should consider the providing re-testing or counselling to on the biobank website or via a

20 newsletter (CCB, 2014). These are 3.1.4.3 Individual research ences is during the consent pro- summary results of research using results cess. The information sheet and samples and/or data from the bio- consent form should provide poten- bank and cannot be connected back Individual research results fall into tial study participants with informa- to a specific individual. two categories. tion and give them the opportunity The participant should be given • Results that can be anticipated be- to choose whether they wish to re- the option during the consent pro- cause they are in line with the aims ceive individual research results. cess to receive these publications, of the research. The method for The protocol must provide a way and researchers using samples and handling these can be considered for participants to later change their data should commit in the MTA to during the evaluation of the sample preferences. providing the report of research re- request. sults to the biobank. • Incidental findings that are not linked 3.1.4.4 Results of genetic tests to the aims of the research. The and next-generation sequencing 3.1.4.2 Individual results from method for returning these to the bio- tests conducted during sign-up bank can be addressed in the MTA. Returning the results of genetic tests or registration In both cases, the biobank or next-generation sequencing should will need procedures for evaluat- involve offering a clinical-grade vali- Some biobank studies request paring the validity of such results, as dation and making available clinical ticipants, after they give consent, well as the period of validity, and expertise or genetic counselling. Rec- to undergo initial testing (baseline for returning these results to the ommendations about which genetic assessments), such as blood pres- participants, including re-iden- test results to return are provided, for sure measurements, lung function tification and re-contact of the example, in the American College tests, and vision tests. In addition, participant if the participant has of Medical Genetics and Genomics biological samples may be routinely indicated in the consent form (ACMG) recommendations for report- tested for infectious diseases, such that they wish to be re-contacting of incidental findings in clinical as HIV, hepatitis B, and hepatitis ed (UK Biobank Ethics and Gov- exome and genome sequencing C, before storage in the biobank. ernance Council, 2015). The scope (Green et al., 2013) and in the Geno- Biobanks should consider whether of the results to be returned and mics England project (https://www. they will return the results of these how they are to be returned should genomicsengland.co.uk/taking-part/ tests, and this should be clearly in- be defined in advance with relevant results/). dicated in the participant consent experts and the ethics committee materials. These tests should not (Thorogood et al., 2014), taking into 3.1.4.5 Results of imaging be used as incentives for the par- account that biobank participants studies and scans ticipants to sign up, and it should be have the right to choose not to know made clear that they are not part of research results. The ideal time to Imaging biobanks are defined by the health checks. ask about an individual’s prefer- European Society of Radiology as 3 SECTION

Key points: return of results

• The return of research results to the biobank by researchers using samples and/or data should be addressed in the MTA. Return of research results to the participant should be covered in the consent form. • Individual research results should be validated using clinical techniques before being returned to the participant. • Individual research results should be returned to the participant only if a relevant clinical support structure can be made available to the participant (e.g. in the case of genetic results, a genetic counsellor should be made available). • Decisions about whether to return individual research results to participants should consider the balance between the validity of the results, the duty of care to participants, and the logistical and technical ability of the biobank to return results in an appropriate manner. • Biobank participants should be given the opportunity to choose whether they wish to receive research results, and they should give consent for the return of results.

Section 3. Recommendations for biobanks 21 “organised databases of medical one of the largest directories for and the policy should be publicly images and associated imaging bio- biobanks in Europe. The directory available (CCB, 2014). See Annex markers (radiology and beyond) currently contains more than 6 mil- 1 for the IARC access policy; oth- shared among multiple research- lion samples with associated data, er examples include those of the ers, and linked to other bioreposi- which can be accessed for collabo- National Cancer Research Institute tories” (European Society of Radi- ration (BBMRI-ERIC, 2016). (NCRI, 2009) and P3G (Harris et ology, 2015). Specialized facilities Researchers requesting ac- al., 2012). and biobanks that also conduct cess to the biobank’s resources Evaluation of requests should be imaging studies such as scans are should do so by applying to the based on the notion of proportional- particularly likely to discover inci- biobank and following its access ity, balancing risks against benefits, dental findings. The Royal College policy and access procedures (see and ensuring that the intended use of Radiologists provides guidance Section 3.1.5.1). Furthermore, the follows the biobank’s protocol and on the management of incidental biobank should assess and review priorities and the consent provided findings detected during research the type of data requested by the by the participants (Mallette et al., imaging (RCR, 2011). researcher. For example, the bio- 2013). In general, samples should bank cannot, without explicit prior be shared in a fair, transparent, and 3.1.4.6 Results about children consent, disclose participant-iden- equitable manner (Chen and Pang, tifiable data to researchers. This 2015). In the case of scarce sam- If the biobank includes biological sam- should be addressed in any agree- ples, a decision could be made to ples from children, the biobank needs ment between the researcher and provide samples to projects more to evaluate whether it has a stronger the biobank (such as an MTA or closely aligned with the aims and responsibility to return results in this Data Transfer Agreement [DTA]; strategy of the biobank. The re- case because the participants are see Section 3.1.5.5). In all cas- searcher should sign an MTA/DTA children (Hens et al., 2011). It must es, a section stipulating that the (see Section 3.1.5.5), which will also consider what action to take if researcher may not attempt to include the obligations of the re- the results become available after the re-identify any participants should searcher, before receiving the sam- child comes of age, because the orig- be included. In general, the policy ples and/or data. inal consent was not the child’s, and on disclosing data must consider whether the parents have the right to which identifiers will be removed 3.1.5.2 Principles for international receive all information about the child from the participant’s record to en- specimen exchanges (see Section 3.1.2.6). sure that privacy is protected. Par- ticular care should be taken with The legal aspects of sample shar- 3.1.5 Access to and sharing of regard to data that may not direct- ing vary between countries, and an samples and data ly lead to re-identification but, in assessment should be made to en- combination with other data, could sure that the relevant legal regimes A catalogue of biological material do so. are compatible with those of the should be published, to optimize biobank and the consent. Where ap- the use of resources and ensure 3.1.5.1 Access to stored plicable, the participant should also the transparency of biobank activi- materials and data for research have given consent for the transfer ties. Optimally, each sample should purposes of data between countries. Exam- be listed, with associated access ples of legal requirements are the conditions and consent elements The biobank should develop an EU-U.S. Privacy Shield principles, (OECD, 2009). access policy and access pro- which deal specifically with transfer In some cases, funders may re- cedures, in line with its protocol of data from Europe to the USA (see quire specific data sharing policies (Section 3.1.1). The policy and pro- Section 3.1.2.3), and the new EU to be designed and implemented cedures should describe the admin- General Data Protection Regulation (Kaye and Hawkins, 2014; Kosseim istrative and approvals process for (see Section 3.1.3). et al., 2014). Intended sample and applying for and obtaining access Finally, if there are any doubts data sharing should be included on to samples or data, comprising in relation to privacy implications the participant information sheets an overview of applicable restric- when samples or data are to be and consent forms (GA4GH, 2015a). tions and obligations. A procedure transferred internationally, a data To facilitate data and sample should exist to ensure that the ap- privacy impact assessment can be sharing, BBMRI-ERIC has created plicants are bona fide researchers, performed before such transfer

22 (GA4GH, 2015b). For further infor- 3.1.5.3 Collaboration with the 3.1.5.4 Intellectual property and mation on the legal requirements private sector ownership related to international sample sharing, researchers can use the Collaboration with the private sector Intellectual property policies vary Human Sample Exchange Regula- must adhere to the same require- across institutions, but the bio- tion Navigator (hSERN) tool, avail- ments and obligations with respect to bank should define an intellectual able at http://www.hsern.eu/. data and sample sharing. It is impor- property policy. Special attention should be given tant for the possibility of sharing sam- Aspects of this policy should to the transfer of samples to or from ples and data with the private sector be defined in the MTA/DTA (see countries with poor or non-existent to be specifically mentioned in the in- Section 3.1.5.5), as well as own- regulatory frameworks (Chen and formed consent and information sheet ership of biological samples. Pang, 2015). (European Commission, 2012a).

Key points: data and sample sharing • As a general rule, no ownership of biological samples exists, and the biobank should assign ownership or custodianship based on national and institutional guidelines. • The biobank should develop a procedure for sharing samples and data that is in line with its protocol and with the consent provided by the participants. • The biobank should develop a policy on potential benefit sharing (sharing of benefits received by the biobank through the sharing of samples and/or data) or collaboration with the contributing community. • The biobank should develop an intellectual property policy.

3.1.5.5 Material Transfer The agreements should include cation describing the biobank; and Agreement (MTA)/Data Transfer specific aspects relating to the bio- • respect intellectual property terms. Agreement (DTA) bank’s policies and provisions that An example of an MTA is pro- bind the researcher to: vided in Annex 4. Other examples An MTA, a DTA, or a similar agree- • use the samples and data in line with include those of Knoppers et al. ment should be put in place before the biobank access approval given; (2013) (online supplementary ma- the transfer of samples and/or data • adhere to applicable laws, regula- terial), NCI (NCI, 2016), the Na- between organizations (ISBER, tions, and guidance; tional Cancer Research Institute 2012). An MTA/DTA is a legally bind- • not further distribute the samples (NCRI, 2009), the Association of ing document that governs the condi- or data; Research Managers and Adminis- 3 SECTION tions under which the samples and/ • dispose of, or return, the samples trators (ARMA, 2016), and Belgian or data can be used (see Annex 4). and data after use; Co-ordinated Collections of Micro- The MTA/DTA outlines the type • guarantee confidentiality and data organisms (BCCM, 2016). of samples and/or data to be trans- protection; ferred, the purpose of the transfer, • not attempt to re-identify partici- 3.2 General safety precautions and all restrictions or obligations pants; required for working in a that relate to the use of the samples • inform the biobank of any issues biobank and data (NCI, 2011; ISBER, 2012; with the data or samples; NCI, 2016). These restrictions and • provide traceability of samples; The primary, basic requirement of obligations must be in line with the • return research results in the form a biobank is general safety. This in- conditions of the informed consent, of individual results, raw data, an cludes protection of people and of ethics approval, and biobank gov- interim/final report, relevant publi- the environment against biological ernance attached to the samples cations, or patent applications; and chemical hazards. The man- and/or data. The agreement may in- • cite or acknowledge the biobank in agement of these risks should be clude a statement that the samples publications, patents, or other doc- based on a general implementation and data have received appropriate uments, or include a citation in any of a precautionary principle similar ethics approval and consent. published work to a specific publi- to those used in laboratories and

Section 3. Recommendations for biobanks 23 clinical settings, and should be em- of LN2 from several relief valves, handling and means of protection, bodied in a general safety manage- causing white-out conditions in a must be given to personnel before ment plan. matter of a few seconds. This leads they work in a biobank, and should to a drop in visibility to almost zero, be repeated on a regular basis. 3.2.1 General laboratory and the oxygen level in the area de- There are also risks associated safety creases below what is necessary to with the use of chemical fixatives sustain life. Personnel must evacu- and solvents used in tissue process- In addition to biosafety, biobanks ate immediately. ing. In addition, electrical safety is an must follow strict general safety reg- Oxygen-level sensors should al- important concern. Freezers must be ulations and procedures in relation ways be used when LN2 containers properly wired to adequate sources to chemical, physical, and electrical are used in a biobank. LN2 expands of electrical supply, and grounded. safety. The use of liquid gases such to 650 times its original volume at Work in a biobank also entails as liquid nitrogen (LN2) for cryopre- room temperature, causing a form several occupational hazards typ- servation poses a serious source of explosion hazard if evaporation ical of the laboratory environment. of hazard. Where LN2 refrigeration is restricted. Storage areas must These risks must be taken into ac- is used, an adequate supply of re- be well ventilated. Plastic and glass count before setting up a biobank, frigerant must be maintained. The containers can easily explode if liq- and their prevention must be inte- supply maintained on-site should be uid is trapped when the container is grated into all aspects of the SOPs at least 20% more than the normal removed from the LN2. of the biobank. refill use, to allow for emergency Protective safety equipment must situations. be worn when handling LN2. Heavy 3.2.2 Biological hazards

Handling LN2 has serious safety gloves, a face shield, and a protec- implications. Skin contact with LN2 tive garment should always be worn Laboratory biosafety requires the can cause severe frostbite. (Fig. 2). Protective shoes are also implementation of good laboratory When bulk storage and pip- recommended. Safety notices and practices and procedures as well as ing systems are used, blockage of protocols must be clearly displayed in the proper use of safety equipment relief valves and/or overpressure the biobank area. Appropriate train- and facilities, to prevent unintention- may lead to simultaneous leakage ing on the risks of LN2, including safe al exposure to microorganisms and toxins, or their accidental release. All biological specimens should be considered as potentially infec- Fig. 2. Equipment for safe handling of liquid nitrogen: (a) individual oxygen tious. They should always be han- detector, (b) knitted gloves, (c) cryogenic gloves, and (d) face shield. dled with great care to avoid potential exposure. Their collection and a b processing represents a source of hazard both for the person who is the source of the specimens and for the staff members involved in these processes. It is recommended that potentially infectious samples should be handled under a biological safety hood to minimize exposure of laboratory staff. The risk group of the samples held in a c d biobank should be determined, and the biobank should comply with the biosafety levels corresponding to the risk group of the samples. Immunization of biobank staff members is recommended when appropriate vaccines are available. In particular, immunization against hepatitis B virus (HBV) is mandatory

24 for staff members involved in col- 2006, the World Health Organiza- • reporting protocols; lecting and processing human blood tion developed the publication Bio- • investigation reports; and or tissues. Other significant risks are risk Management: Laboratory Biose- • recommendations and remedies. posed by exposure to hepatitis C vi- curity Guidance, which defines the Adoption of these security re- rus (HCV) and HIV as well as to the scope and applicability of “labora- quirements is important for bio- prion that causes Creutzfeldt–Jakob tory biosecurity” recommendations, banks that store pathogenic or toxic disease. Other pathogens can also narrowing them strictly to human, biospecimens. represent a serious hazard. veterinary, and agricultural laborato- Further sources of biological risk ry environments (WHO, 2006). 3.3 Infrastructure and storage have been identified. Recommen- Laboratory biosecurity mea- facilities dations for laboratory practices in sures should be based on a compre- a safe working environment have hensive programme of accountabil- The biobank infrastructure and stor- been provided by the United States ity for valuable biological material age system depend on the type of Centers for Disease Control and that includes: material being stored, the required Prevention (CDC) in Guidelines for • assessment of biosecurity risks; storage conditions, the anticipated Safe Work Practices in Human and • restricted and controlled access; period of storage, the intended use Animal Medical Diagnostic Labora- • containment-in-containment archi- of the materials, and the resources tories (Miller et al., 2012). tecture; available for purchasing the stor- • regularly updated inventories with age equipment. The storage infra- 3.2.3 Biosecurity storage locations; structure also depends on the avail- • identification and selection of per- able resources and support to the Laboratory biosecurity describes sonnel with access; biobank (Mendy et al., 2013). The the protection of, control of, and ac- • plan of use of valuable biological storage system is fundamental to countability for valuable biological material; maintaining high sample quality. materials, to prevent their unautho- • clearance and approval process- The data and databases re- rized access, loss, misuse, theft, or es; and lated to biospecimen annotation, intentional release. • documentation of internal and quality, storage location, and use, The scope of laboratory biose- external transfers within and be- including the patients’ clinical and curity is broadened by addressing tween facilities and of any inactiva- epidemiological information, are the safekeeping of all valuable bio- tion and/or disposal of the material. important attributes of biobank in- logical materials, including not only Institutional laboratory biosecu- frastructure. pathogens and toxins but also sci- rity protocols should include how The collection, storage, uses, entifically, historically, and econom- to handle breaches in laboratory and management of data linked to ically important biological materials, biosecurity, including: biospecimens are discussed in Sec- such as collections and reference • incident notification; tion 3.6 and Section 3.8.2. strains, pathogens and toxins, vac- 3 SECTION cines and other pharmaceutical products, food products, genetically Key points: creating a biobank modified organisms, non-pathogen- • Type, number, aliquots, and sizes of biospecimens. ic microorganisms, extraterrestrial samples, cellular components, and • Storage containers. genetic elements. • Storage temperature and conditions. Biosecurity can also refer to precautions that should be taken to pre- • Frequency of access to biospecimens. vent the use of pathogens or toxins • Requirements for identification of biospecimens. for bioterrorism or biological war- fare. Securing pathogens and toxins • Availability of storage space. at research and diagnostic laboratories cannot prevent bioterrorism but • Requirements for temperature monitoring. can make it more difficult for poten- • Associated data. tial terrorists to divert material from a legitimate facility so as to build a • Financial and operational sustainability. biological weapon (OECD, 2007). In

Section 3. Recommendations for biobanks 25 3.3.1 Storage conditions available on the principles of cryopre- for morphological analysis, mor- servation (Cryo Bio System, 2013) phology-related methods, and im- Biospecimens should be stored and on the optimal temperature munohistochemistry. It may also under stabilized conditions to meet for selected biomarkers and me- be used as an alternative method the requirements of potential future tabolites (Hubel et al., 2014). The to preserve tissues at relatively low use in research. In selecting the bio- process of thawing may also influ- cost when adequate freezing proce- specimen storage temperature, it ence cellular structure or metabolite dures and storage facilities are not is essential to consider the type of analyses. available. Paraffin blocks and histo- biospecimen, the intended period of Specimen freezing can be per- logical slides may be stored in light- storage, the frequency of use of bio- formed, for example, by placing and humidity-controlled facilities at specimens, the biomolecules and the specimen in a sealed (but not 22 °C (Figs. 3 and 4). analyses of interest, the intended airtight) container and immersing Tissue fixed according to strict purpose of the sample, and whether the container in the freezing me- protocols may be used for DNA ex- the goals include preserving viable dium. The ideal medium for rapid traction. The DNA is usually frag- cells. Other factors that should be freezing is isopentane that has mented but remains suitable for poly- considered include the humidity lev- been cooled to its freezing point merase chain reaction (PCR)-based el, the light intensity in the facilities, (−160 °C). To achieve this, the analysis of short DNA fragments. access to a continuous power sup- vessel containing the isopentane However, fixed tissue is of limited ply, and backup systems in case of should be placed in a container usefulness for RNA extraction. freezer breakdowns, loss of power, of LN2. The freezing point approx- RNAlater is a commercial aque- and other emergencies. imately corresponds to the mo- ous, non-toxic tissue storage reagent ment when opaque drops begin to that rapidly permeates tissues to sta- 3.3.1.1 Cryopreservation appear in the isopentane. Direct bilize and protect cellular RNA at room

contact of the specimen with LN2 temperature. RNAlater eliminates the Cryopreservation is the recommend- should be avoided because this need to immediately process tissue ed standard for preservation of human can damage tissue structure. samples or to freeze samples in LN2 biological samples for a wide range of for later processing. Tissue pieces research applications. The challenge 3.3.1.2 Other fixation and can be harvested and submerged in of tissue preservation is to be able to preservation methods RNAlater for storage for specific pe- block, or at least slow down, intracellu- riods without jeopardizing the quality lar functions and enzymatic reactions Formalin or alcohol fixation and par- or quantity of RNA obtained after while at the same time preserving the affin embedding is the best method subsequent RNA isolation. physicochemical structures on which these functions depend. Cryopreservation is a process in Fig. 3. Paraffin-embedded tissues. which cells or whole tissues are preserved by cooling to ultra-low subzero temperatures, typically −80 °C (freezer) or −196 °C (LN2 phase). At these low temperatures, most biological activity is effectively stopped, including the biochemical reactions that would lead to cell autolysis. However, due to the particular physical properties of water, the process of cryopreservation may damage cells and tissue by thermal stress, dehydration and increase in salt concentration, and formation of water crystals. Specific applications (e.g. proteomics or storage of primary cell cultures) may require more complex cryopreservation procedures. General information is

26 Fig. 4. Histological slides. LN2 vapour-phase containers

with LN2 in the base of the tank can

maintain samples below Tg (the critical glass-transition temperature,

i.e. −132 °C), and submersion in LN2 guarantees a stable −196 °C temperature environment for all samples. Vapour-phase storage is preferred over liquid-phase storage, because it avoids some of the safety hazards inherent in liquid-phase storage, including the risk of transmission of contaminating agents (Fig. 6). The design of the tank is critical to main-

tain a sufficient amount of LN2 in the vapour phase. Liquid-phase storage needs less

frequent resupply of LN2 and thus af- fords better security in case of a cri-

sis in LN2 supply. Closed LN2 tanks can maintain samples at below PAXgene tissue fixation is in- 3.3.2.1 Liquid nitrogen storage −130 °C for several weeks without creasingly used for tissue preser- the need to refill the LN2 tank. The vation. PAXgene tissue systems LN2 facilities contain LN2 in liquid- initial investment and the availability are formalin-free solutions for the phase tanks (Fig. 5) and vapour-phase and cost of LN2 can be major draw- simultaneous preservation of histo- containers (Fig. 6). Cryogenic storage backs. Also, safety hazards inherent morphology and biomolecules and using LN2 is an effective long-term in the use of LN2, such as burning the purification of high-quality RNA, storage system, because its ex- or oxygen deficit risks, should be

DNA, microRNA (miRNA), pro- treme ultra-low temperatures slow managed. When LN2 tanks are teins, and phosphoproteins from the down most biological, chemical, and used, oxygen-level sensors must same sample. Tissue specimens physical reactions that may cause be used, and they should be cali- are collected, fixed, and stabilized biospecimens to deteriorate. brated every few years. The use of with the PAXgene tissue fixation and stabilization products. PAX- gene-fixed tissue can be processed Fig. 5. Liquid nitrogen facility with LN2 tanks. and embedded in paraffin similarly 3 SECTION to formalin-fixed tissue, and biomolecules can be extracted (Gündisch et al., 2014).

3.3.2 Biospecimen storage infrastructure

Two types of storage systems are used for biospecimen storage: ultra-low-temperature (or low-temperature) storage systems and ambient-temperature storage systems. “Ultra-low temperature” can be defined as temperatures below −80 °C

(e.g. LN2), and “low temperature” as temperatures between 0 °C and −80 °C.

Section 3. Recommendations for biobanks 27 Fig. 6. Tank for storage in vapour-phase liquid nitrogen. ever, the compressor technology requires constant electrical power to maintain subzero temperatures, so a backup power system and an emergency response plan are needed. Whether samples warm up significantly during power outages or freezer breakdowns depends on the temperature, type, and volume of the stored biospecimen, the ambient conditions of the environment where the freezers are stored, and the design and maintenance of the freezer. Ambient temperature and humidity influence temperature stability considerably if doors are left open for prolonged periods, for example for sample loading, or if frost forms in the freezer, racks, or samples. Overheating of compressors may shorten their lives. Mechanical freezers and refrigerators should protective equipment – in particu- as low as −140 °C. Mechanical freez- be positioned with sufficient air flow lar, face shields, cryogenic gloves, ers, which generally require a lower around the units and preferably in and individual oxygen detectors – initial investment than LN2 tanks and rooms that are air-conditioned or should be mandatory, and this provide easy access to biospeci- have equipment for extraction of equipment should be easily acces- mens, can be installed if appropriate the hot air generated by the com- sible (Fig. 2). Appropriate training electrical power is available. How- pressors. Regular cleaning and in the safe handling of LN2 must be provided, and this should be included in an SOP describing the po- Fig. 7. Freezer facility. tential health hazards and required safety precautions.

3.3.2.2 Mechanical freezers

Mechanical freezers are used for a variety of storage systems with temperatures ranging from low- temperature to ultra-low-temperature conditions, including −20 °C, −40 °C, −70 °C to −80 °C, and −150 °C, and come in a wide range of sizes and configurations (Figs. 7 and 8). Ice crystals may form in biological samples at temperatures between 0 °C and −40 °C, and protein activity may persist until −70 °C or −80 °C; therefore, freezer temperatures should preferably be below −80 °C. Cascade compressor technologies may produce temperatures

28 Fig. 8. Freezer racks. the longevity of biospecimens being stored is enhanced if they are stored below ambient temperature, due to biomolecular degradation that can occur at high ambient temperatures. Storage at 4 °C can be a temporary storage solution as an in- termediate step before preparation for ultra-low-temperature storage or before sample processing. For refrigerators, as for mechanical freezers, it is important to maintain and monitor the temperature in the required operating range and to have a backup power system.

3.3.2.4 Ambient-temperature storage

If a biobank does not have mechanical freezers or cryogenic storage equipment, because of practical or financial reasons, then specific biological storage matrices may be used for long-term maintenance of some biological components at room temperature. Formalin-, PAXgene-, or ethanol-fixed, paraffin-embedded tissues and lyophilized samples can be stored at ambient temperatures. Dried samples, such as blood spots on filter paper, can be stored at ambient temperature (Figs. 11 and 12). There are also some new tech-

niques for storage of DNA at am- 3 SECTION bient temperature, for example in mini-capsules after dehydration. A mini-capsule consists of a glass vial containing the sample, enclosed in a stainless steel shell with a cap. The mini-capsule is sealed maintenance of freezers should breakdown and/or to alert person- by a laser, which welds the junction be planned; this should consist, at nel in case this happens. Some of between the shell and the cap un- a minimum, of cleaning filters and the freezers (approximately 10%) der an anhydrous and anoxic inert removing ice around the door and should be kept empty and cool to atmosphere. seals. Freezers should be equipped be used as a backup system. Biological storage matrices with alarms set at about 20 °C should be evaluated before use to warmer than the nominal operat- 3.3.2.3 Refrigerators ensure that they are appropriate for ing temperature of the unit. An in- downstream applications. Temper- dependent temperature monitoring Refrigerators are commonly used ature, humidity, and oxygen levels system should be in place (Figs. 9 for samples that can be maintained should be controlled to avoid mould and 10), to prevent freezer failure or at ambient temperature. However, growth and microbial contamination.

Section 3. Recommendations for biobanks 29 Fig. 9. Temperature monitoring Fig. 10. Graph of temperature log obtained from monitoring system. system.

3.3.3 Storage services, traceability and for the updating of a system should have the capacity to access, and security biobank catalogues. run for a sufficient time to allow the All biobanks require a constant restoration of the power supply (typ- Biobanks should have dedicated source of electrical power. Given that ically 48–72 hours) and should be storage facilities that are not shared the commercial electrical power grid tested regularly (Fig. 16). Enough with other activities, for the safety is likely to fail at some point, a backup fuel should be available on-site to and security of biospecimen col- power system is required. This backup run the generator for several days. lections. Sufficient air conditioning system should operate independently The fuel should also be tested to en- must be provided for air circulation from the grid and from any other facil- sure its quality. and to maintain the ambient tem- ities. The most common type of back- Biobanks with LN2 facilities perature at 22 °C or below, to pre- up power is a diesel generator. Such should have an LN2 supply stock vent excess freezer wear and early failure. Rooms that contain LN2 Fig. 11. Room-temperature storage Fig. 12. Box of samples stored at tanks should be equipped with ap- facility. room temperature. propriate air flow systems to avoid the accumulation of N2 in case of leakage, coupled with an oxygen- level alarm system, to monitor N2 release from the tanks. In general, storage facilities and equipment should be monitored by appropriate alarm systems (Figs. 13 and 14). Biobanks should be equipped with a system that adequately limits access to authorized staff members and protects against intrusion by unauthorized individuals (Fig. 15). In principle, only people assigned to biobank activities should have access to the storage facility and biospecimens, and all materials added or withdrawn should be documented. The documentation of sample movement is important for

30 Fig. 13. A tank fitted with a monitoring device, which shows the level of Fig. 14. Video monitoring in liquid liquid nitrogen inside the tank. nitrogen facilities.

men-associated clinical data (Sec- tion 3.8) that have been input into a separate system. Although it is not essential for the specimen-asso- from which to refill the LN2 tank will enable the preservation of a set ciated data to be in the same data- (Figs. 17 and 18). Adequate back- of samples in the case of adverse base as the biobank-specific data, it up capacity for low-temperature events in one location. For multicen- is important for the clinical data to units must be maintained. The total tre studies, it is recommended that be easily accessible via a link or a amount of backup storage required each recruitment centre retain a set regular import. There may be logis- for large biobanks must be deter- of aliquots at the place of collection, tic concerns in directly accessing mined empirically but will typically with the second set transported to a hospital IT systems, and careful be 10% of the total freezer capacity central location that is accessible to attention should be given to this for mechanical freezer storage. Be- all recruitment centres. during the planning of the biobank IT cause LN2 storage is safer than us- infrastructure. ing mechanical freezers, the backup 3.3.4 Basic informatics The IT infrastructure should capacity for LN2 storage could be infrastructure also be part of the QMS, and the less than 10% (ISBER, 2012). records stored in the system should

Every facility should use basic The biobank informatics infrastruc- be checked for veracity. QC checks 3 SECTION security systems; these must be ture needs to contain hardware and should include the verification of monitored and alarms must be re- software that are sufficient to address biospecimen locations to assess the sponded to 24 hours a day, 7 days the functional requirements of the concordance between physical stor- a week by people who can take the biobank, record and store the infor- age and database location. necessary action to respond to an mation acquired during each biobank alarm within a time frame that pre- process (see Section 3.8), and pro- 3.3.4.1 IT functionality vents or minimizes loss or damage vide an electronic method for records to biospecimen collections. Sys- management (see Section 3.6). It is The biobank management software tems should allow for calls to other important that the hardware and soft- must guarantee the management of key staff members from a list of staff ware infrastructure is designed in such different functions and data related telephone numbers if the first per- a way that it not only meets these ca- to biobanking activities (see Sec- son fails to acknowledge the alarm. pacity and traceability requirements tion 3.8). It is fundamentally impor- Whenever possible, it is recom- but also meets the requirements for tant that there is a method to track mended to consider splitting stored security, data protection, and privacy each sample throughout the bio- biospecimen collections into two (see Section 3.1.3). bank process and to document the sets of aliquots, with each set stored One challenge that persists actions that have been carried out in a different location. This strategy for IT solutions is importing speci- on the sample.

Section 3. Recommendations for biobanks 31 Fig. 15. Controlled access in a secured room. tabase containing this information should be updated in real time as a biospecimen is moved within or out of the biobank. In addition to IT software to record the information at each point of the biobanking process, there need to be software solutions to document information about monitoring of storage infrastructure and to report alarms about adverse events. It is also recommended that the biobank software record information about operations and opera- tors. This should include information about the standard and regular measures taken to calibrate and repair biobank instruments. The management of these functions is fundamental to provide Fig. 16. Power generator. high-quality samples.

3.3.4.2 Software solutions

As biobanking evolves in terms of the types of samples that are collected, archived, and stored and the downstream use of the samples, there continues to be a need to develop informatics tools for the management of biobanks. Different options may be considered depending on the needs, financial resources, and IT resources of the specific biobank. For the rapidly growing field of biobanking, commercial software solutions are increasingly available. Recently, open-source systems have emerged, and some have been selected by European biobanks (Kersting et al., 2015). However, commercial and open- source solutions mainly cover par- Documentation related to sample corded in the IT system are correct- ticular aspects and require adapta- collection (informed consent, partic- ly tracked and maintained, and are tion to respond to the requirements ipant information sheet, sample col- recoverable in the event of erroneous of the individual biobank. lection protocol), sample processing, modifications. An alternative to commercial and sample sharing (MTA and DTA), and Semantic interoperability, in par- open-source systems may be the de- shipment (proof of shipment and deliv- ticular, presents a significant chal- velopment of a dedicated in-house ery) must be appropriately referenced lenge for biobanking and IT support. system, noting that the internal cost in the IT system (see Section 3.6). The specific location of every of maintaining a development team The IT system requires a backup stored aliquot relating to a sample for modifications and maintenance process to ensure that all data re- should be tracked. The biobank da- can be considerable (Voegele et al.,

32 Fig. 17. Liquid nitrogen supply stock tank. they must also guarantee the confidentiality of sample records. Data security systems should be adequate to ensure confidentiality and safety. Electronic records should be adequately protected through regular backups on appropriate media. Intrusion-proof management systems should include solutions such as dedicated servers, secure networks, firewalls, data encryption, and user authentication through verification of user names and passwords. All computers used by biobank personnel should be password-protected and have automatic timeout mechanisms. The biobank management software should also be password-protected and should have different user profiles to permit different levels of access. Each biobank staff member should have an Fig. 18. Liquid nitrogen piping. individual user ID, to provide complete traceability of all actions performed on biobank data. The protection of personal information and individual data associated with specimen collection is a fundamental requirement of a biobank. This should be achieved through the use of safe, structured bioinformatics systems. Personal identifiers should be replaced by codes, and all individual data stored in the biobank management system should be protected with

the same stringency as patient clinical 3 SECTION files. This also applies to data that are considered to be sensitive. Commu- nication to third parties of data files containing personal information and identifiers should be strictly prohibited unless it is required by law or explicit permission to do so was granted. Examples of methods of coding 2010). On a larger scope, a laborato- engineers, and technicians (Voegele are provided in Appendix 2 of the ry information management system et al., 2013). privacy and security policy of GA4GH (LIMS) enables the management not (GA4GH, 2015b). only of the biobank but also of the 3.3.4.3 Data management and entire sample life-cycle workflow. informatics security 3.3.4.4 Biobank networking Electronic laboratory notebooks are infrastructure also a solution for the management Biobank management systems must of procedures performed in a labora- permit access to sample data in or- The facilitation of scientific net- tory, and can be used by scientists, der to stimulate collaboration, but working is an important aspect of

Section 3. Recommendations for biobanks 33 IT infrastructure. Networking can biobank develop a website to pre- banks adhere to standards for use of increase biobank use and therefore sent its operations to the scientific samples and data to ensure seman- is an important element of biobank community, in addition to an online cat- tic interoperability between different sustainability. Publication of data alogue with information on the nature, systems and different biobanks, and on the Internet can greatly increase characteristics, and quality of its biolog- this in particular presents a significant the visibility of the biobank and its ical samples. Networking to facilitate challenge for biobanking and IT sup- ability to participate in biobank net- exchange and access to an increased port (see Section 3.8, Section 3.5, and works. It is recommended that a number of samples requires that bio- Section 2.1.4).

Key points: IT systems • IT systems must correspond with biobanking activities and processes. • IT systems must ensure complete traceability of samples and data. • Data security systems should be adequate to ensure confidentiality and safety. • Access to IT systems must be managed so that they can be accessed only by authorized personnel. • Data and combinations thereof should only be made available based on consent and requirement. • IT systems should have a method of coding to de-identify individual data to protect privacy. • IT systems must also include biobank monitoring. • The biobank management system must permit some level of data publication, such as an online catalogue, to stimulate collaboration. • Cost, functionality, maintenance, and interoperability must be considered when evaluating the selection of software solutions: commercial, open-source, or developed in-house.

3.3.5 Basic storage disaster key personnel, facilities, and data original specimen to produce two recovery – monitoring, recovery. DR plans are not a one- identical aliquots (in the presence backup, and additional size-fits-all solution; in order for DR of tumour heterogeneity, this is storage plans to work, they need to address questionable for tumour tissue the needs of the specific biobank. samples). Biobanks require a disaster recov- The best possible DR planning • Additional logistics are involved in ery (DR) plan to protect their assets, for biological materials and data regular transportation of the fresh biological material, and associated is to ensure that there are dupli- and/or frozen samples to ensure data. The ability to respond to a cated aliquots stored in two or that the biobank has the same con- disaster and protect the integrity more locations. The more distinct tent at each location. of the samples and data directly these locations are in terms of ge- • Retrieval of samples from the dupli- affects their quality. ographical area and reliance on the cate locations involves increased In its most simple terms, DR same utilities (power, generator, costs and time delays. entails taking all necessary steps LN2, carbon dioxide [CO2] supply, Retrieval of samples from du- to ensure that, in the event of a ambient-temperature control, and plicate locations is hampered by disaster, the loss caused by the other elements that pertain to the increased distances (preferable disaster is kept to an acceptable functioning of the biobank storage for the DR plan) and transportation level and operations can return to infrastructure), the better the ability facilities (couriers, transportation in- normal as smoothly and as quick- of one of the locations to withstand frastructure). Preventive measures ly as possible. DR encompasses a particular disaster. Although this such as different methods of stor- all processes, policies, and proce- strategy will avoid unnecessary age or reducing the specimen to its dures for recovery or continuation loss in case of adverse events in basic derivative components, such of infrastructure operation after a one location, this approach has as nucleic acids, will provide oppor- natural or human-caused disas- three difficulties. tunities for innovative storage meth- ter, and must include planning for • There needs to be enough of the ods. Also, nucleic acids are more

34 stable once extracted from tissue, • Automatic LN2 filling systems are needed to collect the lost material and therefore are more resistant to most affected by faulty sensors again, considering the availability temperature fluctuations and permit and faulty transfer pipes. of such samples and their asso- longer response times. • Monitoring systems are most af- ciated data as well as the effort A similar situation relates to fected by electricity supply, Inter- required by personnel, the equip- biobank data: saving the data con- net connectivity, wireless connec- ment to be used, and the consum- temporaneously at two distinct sites tions, and telephone lines. ables. Samples from longitudinal would guarantee the same safe- Events such as a power outage studies acquire more value over guards to the data. This is potentially or power fluctuations can be low time as their associated samples more feasible than storing samples priority if there is a way to mitigate and data accumulate, and there- in separate locations, because du- or avoid the problem by providing fore the cost of replacing them in- plicating and transferring data is an either an uninterrupted power sup- creases with time. easier task and does not necessar- ply or a backup diesel generator. • Carry out a risk analysis to eval- ily require physical transportation. The backup generator should be uate the potential disasters, the However, where continual data able to start automatically, needs to probability of each type of disas- transfer is not feasible, periodic have the capacity to run for a suf- trous event occurring, and the im- backups should be carried out, with ficient time to allow the restoration pact each event would have on the backups stored off-site to reduce of the power supply (typically 48–72 biobank. The risk analysis makes loss of data. hours), and should not be affected it possible to prioritize the events Each biobank infrastructure DR by the adverse event that caused that need to be addressed. Then, plan should contain an evaluation the power outage. based on the resources available, of the events and elements that can It is always important to consider it can be decided how to address affect the biobank, the probability of the cascading effect of a single event. each event. these occurring, and the means to An example is a fault in the air con- • Calculate the response times in address them. These can be either ditioning system that causes the bio- the event of a disaster. Response natural events (e.g. earthquakes, bank’s ambient temperature to rise. times are critical because they di- hurricanes, storms, floods, fires, This temperature rise, in turn, caus- rectly affect the potential loss of plane crashes, excess temperatures es the mechanical freezers to need samples, and they must be cal- and humidity) or human-caused CO2 to maintain their temperature of culated based on the acceptable events (e.g. breakdown of a sin- −80 °C. If the CO2 supply is depleted loss and the time needed to either gle freezer, breakdown of multiple by the time the ambient temperature return to normal functioning or mit- freezers, power outage or power returns to an acceptable level, then the igate the problem caused by the fluctuations, CO2 outage, air con- temperature of the mechanical freez- adverse event. ditioning breakdown, air extraction ers will also rise, potentially leading • For each type of disaster, calculate breakdown, inaccessible room due to damage of the samples they a maximum response time to en- to gas leak). Only those elements contain. sure the integrity of the conserved 3 SECTION that affect the biobank, either direct- A complete DR plan requires the samples, such as either fixing a ly or indirectly, should be considered following steps. broken freezer so that it returns to in the individual plan. • Categorize the stored samples its desired temperature before it Apart from faults with a single in order of priority. In case of an has reached critical temperature, container (caused by blown fuses, emergency, high-priority samples or moving the samples to a dif- battery discharges, blocked refill will be moved to an external facility ferent location before their quality valves, broken compressors, bro- before lower-priority samples. is compromised. This calculation ken covers or doors, or worn seals), • Evaluate the acceptable downtime must take into consideration the external events will affect each bio- (the time during which the biobank different reactions of the contain- bank to a different extent. is inaccessible). ers and the different effects of • Biobanks with −80 °C freezers are • Evaluate the acceptable loss (the temperature change on each most affected by electricity supply, number of samples and their as- sample type stored (tissue, blood,

CO2 supply, biobank room temper- sociated data that can be lost). plasma, serum, DNA, RNA). ature, dusty conditions, humidity, The acceptable loss should be • Assign people to be on call to re- and air conditioner faults. considered in terms of delays to spond to any alarms at all times

• LN2 biobanks are most affected by research, and by evaluating how (24 hours a day, 7 days a week);

LN2 supply. much time and money would be it is essential that they are able to

Section 3. Recommendations for biobanks 35 respond and carry out the DR plan units must be maintained (10% lists must be presented in the form within the allocated time. is the best practice). The total of SOPs, so that in the event of • Carry out simulation exercises amount of backup storage required a disaster, action can be taken to ensure effective training of the for large biobanks must be deter- immediately. people assigned to respond. mined empirically. Typically, the The DR plan should be part • Specify methods for transporting minimum should be the capacity of the QMS and should be re- samples without affecting their of a single container (where there viewed annually to guarantee that quality and integrity, in case the are different sizes, this should be it responds adequately to the bio- samples need to be moved. calculated based on the capacity bank’s evolution. The DR plan • Ensure that backup facilities are of the largest freezer) or, for large must be tested as extensively as available, in case samples need biobanks, 10% of the total contain- possible using simulated scenar- to be moved from the current er capacity (NCI, 2016). ios and should be updated regu- biobank or freezer. Adequate back- • Prepare a detailed list of actions larly as the biobank infrastructure up capacity for low-temperature for each evaluated event. These changes.

Key points: disaster recovery plan • Categorize the stored samples in order of priority, to facilitate the relocation process if the samples or equipment need to be moved to an external facility in case of an emergency. • Calculate the acceptable downtime and the response times in the event of a disaster. • Carry out a risk analysis to evaluate the potential disasters and the acceptable loss. • List the actions for each evaluated event, and design SOPs as part of the QMS, along with adequate simulation exercises, training, and review. • Prepare an on-call list of people on standby in case of an emergency. • Ensure that adequate backup storage capacity is available, in case samples need to be transferred.

3.4 Quality ture and resources – such as storage specific to biobanking processes facilities, pre-analytical processing and procedures. However, in 2015 Biobanks are key for the develop- tools, trained personnel, robust gov- CEN published a series of Technical ment of clinically useful biomarkers ernance, and policy management – Specifications for molecular in vitro of disease and disease progression, is central to maintaining quality and diagnostic examinations – Specifica- for discovering and monitoring new determines the relevance and suc- tions for pre-examination processes, drugs, and for understanding the cess of a biobank. which are relevant for diagnostic lab- mechanisms of cancer and related The key components that can af- oratories as well as biobanks. See diseases. All of these possibilities fect the quality of samples and data Table 3 for a list of CEN Technical are underpinned by the availability are presented in Fig. 19. Specifications. It is recommended of high-quality, well-annotated sam- In general, biobanks should im- that these standards are used. ples of diseased and control tissue, plement systems that specify QC In addition, ISO is developing blood, and other biological materials and QA for sample collection, pro- standards for biobanks and biore- and associated data. cessing, storage, shipment, and dis- sources. The Technical Committee The availability of high-quality position. Such systems are essential of ISO 276 (standardization in the samples is also important to demon- for maintaining a fit-for-purpose bio- field of biotechnology) will include: strate to funders of biobanks and bank for cancer research. The ISO • biobanking terms and definitions; to the research community that the 15189 standard currently referred • biobanks and bioresources; facility provides a good return on to by biobanks (ISO, 2012) is based • analytical methods; their investments in sample and on ISO/IEC 17025 and ISO 9001, • bioprocessing; and data collection, which will accelerate which provide general requirements • data processing, including annota- progress in cancer research. for the competence of testing and tion, analysis, validation, compara- The scientific and technical man- calibration laboratories and for the bility, and data integration (Furuta agement of the biobank infrastruc- QMS, respectively. They are not and Schacter, 2015).

36 Fig. 19. Overview of the key issues related to quality in biobanking.

ESEC

Sharinaccess T Sale collection nalsis nnotation ata ott T ESI TININ TECNIC EETISE IT E T Sale storae E S reeetha C Sale rocessin Safet ccess

INSTCTE SECTION 3 SECTION Table 3. CEN Technical Specifications for molecular in vitro diagnostic examinations

Technical Specification Title

CEN/TS 16826-1:2015 Specifications for pre-examination processes for snap frozen tissue. Part 1: Isolated RNA

CEN/TS 16826-2:2015 Specifications for pre-examination processes for snap frozen tissue. Part 2: Isolated proteins

CEN/TS 16827-1:2015 Specifications for pre-examination processes for FFPE tissue. Part 1: Isolated RNA

CEN/TS 16827-2:2015 Specifications for pre-examination processes for FFPE tissue. Part 2: Isolated proteins

CEN/TS 16827-3:2015 Specifications for pre-examination processes for FFPE tissue. Part 3: Isolated DNA

CEN/TS 16835-1:2015 Specifications for pre-examination processes for venous whole blood. Part 1: Isolated cellular RNA

CEN/TS 16835-2:2015 Specifications for pre-examination processes for venous whole blood. Part 2: Isolated genomic DNA

CEN/TS 16835-3:2015 Specifications for pre-examination processes for venous whole blood. Part 3: Isolated circulating cell free DNA from plasma

CEN, European Committee for Standardization; FFPE, formalin-fixed, paraffin-embedded;TS, Technical Specification.

Section 3. Recommendations for biobanks 37

IE Biobanks should have appropri- reported on the identification of 3.4.2 Quality of tissue and ate QA and QC programmes with evidence-based biospecimen QC derivatives respect to equipment maintenance markers (Betsou et al., 2013). The and repair, staff training, data man- findings are summarized in Table 4. The procurement of tissue, both agement and record-keeping, and Although the report provided evi- diseased (neoplastic, pre-neoplastic, adherence to principles of good dence for several quality biomark- and inflammatory) and normal, must laboratory practice. All biobank op- ers, their level of applicability and always be carried out by, or under erations must be subject to regu- accessibility varies. In Table 4, the supervision of, a pathologist. lar audits. The timing, scope, and only markers that scored highly for This permits a more accurate mac- outcome of these audits should be applicability and accessibility are roscopic sampling followed by a documented. included. These markers provide microscopic confirmation. This is QC tools for assessing biospeci- standard QA for tissue procurement 3.4.1 Biospecimen quality mens in relation to pre-analytical (Hainaut et al., 2009). biomarkers conditions. NCI’s Biorepositories and Biospecimen Research Branch 3.4.2.1 Quality control of tissue Biospecimen quality biomarkers has initiated the Biospecimen (e.g. frozen section) are useful to assess the quality of Research Network (http://biospeci material before it is included in ex- mens.cancer.gov/researchnetwork/ QC should be done during sampling perimental platforms and to avoid projects/default.asp), which aims in the grossing room on surgical the unnecessary use of biospec- to stimulate original research and samples using the frozen sec- imens. In 2013, the ISBER Bio- disseminate available data in bio- tion method. This is done by sam- specimen Science Working Group specimen science. pling the area of suspected cancer

Table 4. Identified biospecimen molecular diagnostic biomarkers, with QC scope and evaluation

Analyte Sample Applicability Accessibility Delay QC tool QC scope Reference type type grade grade Consequence

Transferrin Protein Serum Pre-centrifugation 1 1 8 h blood pre-centrifugation De Jongh et al. receptor delay delay (1997) 90% increase K+ Ion Serum Pre-centrifugation 1 1 1 day pre-centrifugation delay Heins et al. delay at 4 °C (1995) 200% increase 7 day pre-centrifugation delay at 4 °C 500% increase GM-CSF, IL-1α, Protein EDTA Pre-centrifugation 1 1 2 h pre-centrifugation delay Ayache et al. G-CSF plasma delay at RT (2006) ± PI 11–20-fold increase without PI 7–10-fold increase with PI sCD40L Protein Serum Exposure to RT 1 1 12 h at 37 °C or 48 h at RT Lengellé et al. Complete degradation (2008) Vitamin E Vitamin EDTA Storage conditions 1 1 > 24 months at −20 °C Ockè et al. plasma > 90% decrease (1995) MMP-7 Protein Serum Freeze-thawing 1 1 30 freeze–thaw cycles Chaigneau et al. Loss of MMP-7 (2007) DUSP1 RNA Fresh Warm ischaemia 1 1 Warm ischaemia Lin et al. expression prostatic time 14-fold upregulation (2006) tissue p-Tyr, ERBB2 Protein Breast Cold ischaemia 1 1 24 h of cold ischaemia De Cecco et al. (alias HER2; tissue time Complete denaturation of (2009) alias Neu)- phosphorylated epitopes Tyr1248, PTK2 (alias FAK) ±, with or without; EDTA, ethylenediaminetetraacetic acid; G-CSF, granulocyte colony-stimulating factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; IL-1α, interleukin 1 alpha; K+, potassium; MMP-7, matrix metalloproteinase-7; PI, protease inhibitors; QC, quality control; RT, room temperature; Tyr, tyrosine. Source: Adapted from Betsou et al. (2013), Copyright (2013), with permission from Elsevier.

38 macroscopically, performing a rou- by the nucleic acid to the absor- The qualification process con- tine frozen section, preparing a bance of the contaminants. Aromatic sists of the quantification of dsDNA stained slide, and documenting the amino acids absorb light at 280 nm, and the assessment of its suitability review data on the sample collec- so absorbance measurements at for downstream applications, such tion sheet. The following information that wavelength are used to estimate as high-throughput next-generation should be provided, which defines the amount of protein in the sample. sequencing. Microarray experiments the quality of the tissue sample: Measurements at 230 nm are used may require nucleic acid samples • frozen section performed (yes or no); to determine the amount of other with specific values of concentra- • pathologist who performed frozen contaminants that may be present in tion, purity, and integrity, whereas section review; the samples, such as guanidine thio- quantitative PCR (qPCR)-based as- • tumour confirmed; cyanate, which is common in nucleic says may accept samples with lower • percentage of tumour cells; acid purification kits. Typical require- quality scores because the ampli- • percentage of stromal and inflam- ments for A260/A280 ratios are 1.8– cons are small (typically < 100 bp). matory cells; 2.2; A260/A280 of pure DNA is ~1.8, Correctly interpreting data obtained • percentage of surface occupied by and A260/A280 of pure RNA is ~2. from quantification and QC analysis necrosis; and Requirements for A260/A230 ratios is essential. • other comments. are generally > 1.7. The A260/A230 ratio may also predict sample ampli- 3.4.3.1 Methods for evaluating 3.4.2.2 Methods for quality fiability (the ability of the extracted quality of nucleic acids from control of tissue sections for sample to be amplified by PCR). tissue DNA/RNA extraction Acceptable ratios for purity vary with the downstream application. Spectrophotometers can measure Regardless of whether a frozen A230 is often constant for nucle- absorbance and provide values for section is performed at the time of ic acid purified using a specific kit, wavelengths of 260 nm, 280 nm, and sampling, microscopic pathology whereas the amount of nucleic acid 230 nm. However, they lack the sen- review should be performed on the can vary depending on the sample sitivity to measure small quantities tissue sections taken for nucleic source. Thus, the A260/A230 ratio of DNA. All nucleic acids (dsDNA, acid extraction. It is recommend- often decreases when small amounts RNA, and ssDNA) absorb at 260 nm, ed that this is performed every 20 of nucleic acids are isolated. and this method cannot distinguish sections of 5 µm, because of the Integrity represents intactness between the various forms of nucle- potential heterogeneity in the sam- or state of degradation. This is often ic acid. For example, the amount of ple. This is also recommended for presented as the DNA integrity num- genomic DNA (gDNA) present in an sections taken from formalin-fixed, ber (DIN) and the RNA integrity num- RNA preparation or the amount of paraffin-embedded (FFPE) blocks. ber (RIN). The higher the RIN value, RNA present in a gDNA sample can- the better the integrity of the RNA. not be determined. These contam-

3.4.3 Quality control of RNA is considered to be of high qual- inants contribute to the absorbance 3 SECTION nucleic acids from tissue ity when the RIN value is ≥ 7. RNA value, resulting in an overestimation with RIN values of 5 and 6 may be of nucleic acid concentration. In The quality of a nucleic acid is based considered acceptable. Care must addition, if samples are degraded, on quantity, concentration, purity, be taken when using instruments to single nucleotides will also contrib- and integrity. determine these values, because the ute to the 260 nm reading, and thus Concentration is calculated for concentration of the sample can af- the nucleic acid concentration will be DNA, RNA, and proteins using the fect the resulting value. overestimated. ultraviolet (UV) absorbance read- The quality of nucleic acid ex- Fluorescent dye-based quantifi- ing at a wavelength of 260 nm and tracted from tissue can vary de- cation uses dyes that only fluoresce a conversion factor based on the pending on the sample source and when bound to specific molecules, extinction coefficient for each nu- the extraction method applied. dsDNA, ssDNA, or RNA, and thus cleic acid (A260 of 1.0 = 50 µg/mL Quality requirements can be very the concentration of the specific for double-stranded DNA [dsDNA], different depending on the dow molecule can be measured. This 40 µg/mL for RNA, and 33 µg/mL for stream application. Nucleic acids makes the measurement more single-stranded DNA [ssDNA]). that are unsuitable for one applica- accurate for samples that contain Purity is calculated from the tion may provide perfectly accept- nucleic acid contaminants or sam- ratio of the absorbance contributed able results in another application. ples that are partially degraded.

Section 3. Recommendations for biobanks 39 Although this method provides a 3.5 Contents of standard reporting of accidents, errors, more accurate concentration of the operating procedures (SOPs) complaints, and adverse events; sample for the molecule of interest, • policies, procedures, and schedules it does not give an indication of the Biobanks should develop, docu- for equipment inspection, mainte- contamination of the sample. ment, and regularly update policies nance, repair, and calibration; Gel electrophoresis verifies the and procedures in a standardized • emergency procedures in case of integrity of DNA and RNA mole- written format incorporated into an failure of a refrigerator, freezer, or cules by separating their fragments SOP manual that is readily avail- LN2 tank; based on size and charge and thus able to all laboratory personnel. • procedures for disposal of medical estimating the size of DNA and RNA The SOP manual is a key part of waste and other hazardous waste; fragments. the overall QMS of the biobank, is and The RIN is an algorithm for as- important to the success of biobank- • policies and procedures describing signing integrity values to RNA ing, and is a major contributor to the the requirements of recruitment measurements. The integrity of RNA development of biomedical practice and training programmes for bio- is a major concern for gene expres- worldwide. bank staff. sion studies and traditionally has The SOP manual should specif- been evaluated using the 28S/18S ically include: 3.6 Records management ribosomal RNA (rRNA) ratio. The • procedures for obtaining informed RIN algorithm is applied to electro- consent and withdrawal of consent The importance of an adequate re- phoretic RNA measurements and is from participants; cords management strategy cannot based on a combination of different • records management policies, be overstated. features that contribute information including access control, a back- Documentation related to sam- about the RNA integrity to provide up system, clinical annotation, ple collection, sample processing, a robust universal measure. If RNA and document maintenance and sharing of samples (MTA and DTA), is purified from FFPE samples, the archiving; and shipment of samples (proof of 28S/18S rRNA ratio and the RIN val- • policies and procedures for spec- shipment and delivery) must be ap- ue are not useful for assessing RNA imen handling, including supplies, propriately maintained and archived quality. methods, and equipment; in a traceable and secure manner. A The DIN determines the level of • laboratory procedures for speci- backup system must be implement- sample degradation using an algo- men processing (e.g. collection, ed to guarantee appropriate mainte- rithm to evaluate the entire electro- transportation, processing, ali- nance of all documents. phoretic trace. The higher the DIN quoting, tests, storage, and QC); All documents and documen- value, the better the integrity of the • procedures for sharing and trans- tation must be kept centrally and gDNA sample. ferring specimens (access policy, should include: qPCR can be a useful technique MTA); • the SOP manual; in the QC of gDNA for downstream • procedures for a business model • quality certifications; sequencing, because it simultane- and cost recovery, when applicable; • personnel training records; ously assesses DNA concentration • policies and procedures for ship- • templates of forms and spread- and suitability for PCR amplification. ping and receiving specimens; sheets; However, this technique is labour- • QA and QC policies and proce- • documentation of biobank audits; intensive and has higher costs. dures for supplies, equipment, in- • documentation of adverse events; Sequential use of spectropho- struments, reagents, labels, and • instrument calibration records; tometric and fluorescence-based processes used in sample retrieval • maintenance and repair records; methodologies permits the cost-ef- and processing; • signed informed consents; fective assessment of DNA quality • procedures for security in biobank • signed collaboration agreements; for high-throughput downstream facilities; • sample request forms; applications. This combination also • policies and procedures relat- • signed MTAs and DTAs; and enables the detection of impuri- ed to emergencies and safety, • shipping notes. ties, and thus their removal from including reporting of staff inju- Similarly to SOPs, each form samples. This is particularly useful ries and exposure to potential should have a unique number and for samples such as FFPE sam- pathogens; title. All changes made to forms ples that are available in limited • policies and procedures for the should be noted, dated, and signed amounts. investigation, documentation, and to provide a trace of all modifications.

40 All hard copies of records must be shelves, racks, and boxes as cide the period for record retention archived in a secure manner, to be ac- well as each location within the depending on the type of record. cessed only by authorized personnel. container. Records pertaining to samples that no All stored records should be stored in An IT solution (see Section 3.3.4) longer exist may be destroyed if the a manner that provides easy access can provide a centralized system to records are considered to no longer for inspection by authorized personnel. maintain traceable records of sam- be valuable. Records pertaining to Each container, tank, freez- ples. Where possible, hard copies of samples that were withdrawn should er, refrigerator, or room-tempera- records should be scanned into an IT be destroyed in a secure manner. ture storage cabinet should have a system to provide a backup. Records pertaining to instruments may unique identifier. The hierarchy of All records should be archived be destroyed once the instrument has each storage unit should be clearly for a period in line with institution- been retired. The destruction of records defined, to enable stored samples al or local regulations, where they should be carried out in a manner in to be located easily. A convention exist. Where there are no such reg- line with the security requirements of should be established for numbering ulations, the biobank should de- the record.

Key points: records management system • Evaluate the available systems: commercial, open-source, or developed in-house. • Biobanking activities and processes must be documented. • Data security systems should be adequate to ensure confidentiality and safety. • Records management should be audited regularly (QA/QC). • Biobank management systems must also allow access to sample data, to stimulate collaborations. • Semantic interoperability is an important consideration. • Systems must ensure full traceability of samples, data, and documentation. • Documentation must be archived in a traceable and secure manner.

3.7 Specimen collection, tices to facilitate multidisciplinary 3.7.1.1 Blood processing, and storage collaboration. This section provides general The following general guidelines Many types of biological material can advice about the collection of: should be considered. be stored for cancer research pur- • whole blood and derivatives • All blood should be treated as po- 3 SECTION poses. The methods used to collect • solid tissues tentially infectious. Blood samples biospecimens will vary depending on • urine for research purposes should be what the intended end use is and how • buccal cells and saliva collected at the same time as rou- the specimens will be processed. • bronchoalveolar lavage tine clinical blood samples, so as The recommendations present- • bone marrow aspirate to limit discomfort to individuals. ed here are derived from multiple • cerebrospinal fluid Blood should be collected from sources, such as international publi- • semen fasting individuals (i.e. after ab- cations and articles (Eiseman et al., • cervical and urethral swabs stinence from food, alcohol, and 2003), including the biorepository • hair caffeine-containing beverages for protocols of the Australasian Bio- • nails. 8–12 hours). specimen Network. Although this • Blood should not be collected after book focuses on cancer research, 3.7.1 Collection of blood or prolonged venous occlusion. the research community realizes blood-derived products • Tubes into which the blood is that samples may also be used collected should be clearly labelled in other areas of research; the Detailed instructions and protocols (Fig. 20). key issue is the importance of har- for the collection of blood or blood • For blood collection, the recom- monization of techniques and prac- derivatives are provided in Section 4. mended order of draw is the following

Section 3. Recommendations for biobanks 41 Fig. 20. Blood sample. be used if DNA will be extracted heel-stick blood from newborns for or lymphoblastoid cell lines will metabolic disease screening. The be derived. Lithium heparin is not 903 paper is manufactured from recommended for establishment of 100% pure cotton linters with no lymphoblastoid cell lines. wet-strength additives. The critical • EDTA tubes are recommended if parameters for collection of new- protein studies will be performed. born screening samples are blood The use of EDTA tubes results in absorbency, serum uptake, and less proteolytic cleavage com- circle size for a specified volume pared with the use of heparin tubes of blood. Blood spots archived for or ACD tubes. as long as 17 years, sometimes at • For the preparation of plasma, the room temperature, have also pro- blood should be centrifuged as vided valuable sources of ampli- soon as possible. For the prepa- fiable DNA (Makowski et al., 1996) ration of serum, the blood should (Fig. 21). be processed within 1 hour of Modified cards (IsoCode cards collection. or FTA cards) have been devel- • The amount of blood collected oped. These consist of filter paper should be justified when applying impregnated with a proprietary mix for ethical clearance. of chemicals that serves to lyse • A reduced volume of blood in a cells, to denature proteins, to pre- (Calam and Cooper, 1982; CLSI, tube containing additives should vent growth of bacteria and other 2007): be recorded to avoid confounding microorganisms, and to protect 1. blood culture tube; the results. nucleic acids from nucleases, oxi- 2. coagulation tube; • The time and date of blood collec- dation, and UV damage. Room-tem- 3. serum tube with or without clot tion and the time of freezing should perature transportation of such activator, with or without gel; be recorded, as well as any devia- cards in folders or envelopes (by 4. heparin tube with or without tions from the standard processing hand or by mail) has been common plasma separating gel; protocol. for years. The papers protect DNA 5. ethylenediaminetetraacetic acid • Blood should be transported at in the samples for some years under (EDTA) tube with or without sep- room temperature or on melting ambient conditions. The main vari- arating gel; ice depending on the particular ap- able is expected to be the quality 6. glycolytic inhibitor. plications. Samples to be used for of the storage atmosphere, particu- • For the preparation of plasma, proteomics assays should be pro- larly the content of acid gases and blood may be collected into an cessed immediately at room temper- free-radical-generating pollutants, EDTA tube, an acid citrate dex- ature, because cool temperatures although FTA paper can protect trose (ACD) tube, or a lithium hep- can activate platelets and release against such conditions (Smith and arin tube. peptides into the sample ex vivo. Burgoyne, 2004). Sample integrity • Ideally, blood should be processed • Blood spot collection should be is optimized when FTA cards are within 1 hour of collection. After considered as an alternative to stored in a multi-barrier pouch with that time, cell viability decreases whole blood for validated tech- a desiccant pack. Whatman Protein rapidly, resulting in poor cell struc- niques when conditions necessi- Saver Cards are commonly used to ture and degradation of proteins tate easier collection and cheap collect dried blood spots for molecu- and nucleic acids. room-temperature storage. Differ- lar and genomic studies and for the • Lithium heparin is generally used if ent types of collection cards are isolation of viruses (Mendy et al., cytology studies will be performed, available (e.g. Guthrie cards, “fast 2005) and bacteria (see Section 4). but it is not recommended for pro- transient analysis” [FTA] cards, teomics work. IsoCode cards) (see Section 4). 3.7.1.3 Buffy coat • PCR was clearly interfered with when heparinized blood (heparin 16 U/mL 3.7.1.2 Blood spots For DNA testing, if DNA cannot blood) was used as a source of be extracted from blood within 3 template DNA (Yokota et al., 1999). Guthrie cards (Schleicher & Schuell days of collection, the buffy coat • Either EDTA or ACD tubes can 903 filter paper) are used to collect may be isolated and stored at

42 Fig. 21. Card with dried blood spots. tions of the tumour and adjacent apparently normal tissue and other areas of interest. Where possible, two or more samples of the tumour tissue should be taken, represent- ing different areas, i.e. different macroscopic patterns in the body of the tumour. Normal tissue can be taken from a non-diseased re- sected organ, but where the normal tissue is required for use as matched control, it should be taken preferably > 10 mm from the diseased tissue. • If applicable, involved lymph nodes and metastases will also be collected. Tissues must be sliced with sterile forceps and scalpel blades, and staff members must use sterile gloves. The use of the same scalpel blade for normal and neo- −70 °C or below before DNA iso- • The collection of samples for re- plastic areas should be avoided. If lation. Buffy coat specimens that search should never compromise this is not possible, normal tissue are being used for immortaliza- the diagnostic integrity of a spec- should be collected before tissue tion by Epstein–Barr virus should imen. Only tissue that is excess to from tumour areas. be transported frozen on dry ice diagnostic purposes should be col- • Standard diagnostic processes usu-

(solid-phase CO2). RNA should be lected for research. It is the responsi- ally place surgical specimens in for- isolated from buffy coat within 1–4 bility of the pathologist to decide this. malin after excision. Where fresh, hours of specimen collection; al- • The intact surgical specimen or vitally cryopreserved, or fresh fro- ternatively, RNA stabilization solu- biopsy sample should be sent to zen samples are required, samples tion (e.g. RNAlater) should be used pathology. must be transferred as fresh spec- (see Section 4). • Tissue bank staff members must imens. In this case, fresh speci- be present in pathology, to collect, mens should be placed in a closed 3.7.2 Collection of solid freeze, or fix the tissue as quickly container in a sterile cloth on wet tissues as possible. ice for transportation from surgery

• All materials and instruments to pathology. An alternative, which 3 SECTION Solid tissues for research are col- should be prepared in advance. If also permits a delay in the need for lected by biopsy or after surgical a fresh sample is to be obtained, immediate processing, is to vacu- excision. Detailed procedures are transport medium (RPMI 1640, um-pack the tissue. presented in Section 4. 10% fetal bovine serum [FBS], • Transfer of specimens on wet ice The following important points 100 U/mL penicillin/streptomycin, must be carried out as soon as should be considered when plan- 100 U/mL amphotericin) should be possible, to minimize the effect of ning tissue collection for research. prepared. If a sample is to be vital- hypoxia on gene expression and • The collection of samples should ly cryopreserved, cryopreserving degradation of RNA, proteins, and be carefully planned with sur- solution should be prepared (RPMI other tissue components. Transfer geons, clinical staff, and patholo- 1640, 10% dimethyl sulfoxide of vacuum-packed specimens is gists. Collection of solid tissue for [DMSO], 20% FBS). less time-critical; the samples may research from surgically excised • A pathologist should supervise be stored for up to 115 hours in a tissue should always occur in the the procurement of the tissue for 4 °C refrigerator before and/or after grossing room unless the standard research purposes. The patholo- transportation from the operating procedure for clinical care permits gist will examine the sample and, theatre, until processing. The tem- collection in the operating theatre allowing adequate tissue for diag- perature of the specimen during or nearby pathology suite. nostic purposes, will remove por- transfer should be documented.

Section 3. Recommendations for biobanks 43 • It is recommended that surgical be immersed directly in LN2, be- • Each specimen conservation re- specimens or biopsy samples be cause of the potential formation ceptacle (tube) must be clearly preserved within 1 hour of exci- of cryo-artefacts. When dry ice or labelled before it is placed in the

sion. However, tissue subject to a LN2 is not readily available, tissue biobank (see Figs. 24–26). delay up to 2 hours should still be collection in RNAlater is a good collected (Eiseman et al., 2003). alternative, provided that this tis- 3.7.3 Collection of other Detailed records should be kept of sue is not required for diagnostic specimens the timing of events from excision purposes and that permission has (or arterial clamping, in the case been given by the pathologist. Al- 3.7.3.1 Urine of larger specimens) to fixation or ternatively, PAXgene can be used freezing. as a fixative that preserves nucle- Urine is easy to collect and is a • All tissue should be treated as ic acids and morphology for histo- suitable source of proteins, DNA, potentially infectious; the collec- pathological analyses (Viertler et and metabolites. Urine should be tion process should be carried out al., 2012). routinely stored at −80 °C. Ambi- under the most aseptic conditions • Where possible, it is advisable for ent-temperature storage before possible. a cryostat section to be taken, to freezing should be kept to a mini- • Each specimen collection recepta- prepare a haematoxylin and eo- mum (see Section 4). cle must be clearly labelled when sin (H&E)-stained slide for review multiple samples are being collect- by the pathologist for confirmation 3.7.3.2 Buccal cells ed for the biobank. and QC of the tissue sample be- • Fresh tissue required for xeno- ing conserved. An indication of the The collection of buccal cells is not grafting or for creation of cultures cancer cellularity is important for difficult and does not require highly or cell lines must be placed in tissue banking because it predeter- trained staff. Buccal cell collection transport medium (RPMI 1640, mines the need for microdissection is considered when non-invasive, 10% FBS, 100 U/mL penicillin/ of tissue for nucleic acid extraction self-administered, or mailed collec- streptomycin, 100 U/mL ampho- in next-generation sequencing. tion protocols are required for DNA tericin). If this tissue is to be vitally • FFPE tissue can be used for tar- analysis (Steinberg et al., 2002). How- cryopreserved, it should be placed geted immunohistochemistry, fluo- ever, buccal cells will yield only limit- in freezing medium (RPMI 1640, rescence in situ hybridization ed amounts of DNA compared with 10% DMSO, 20% FBS). Because (FISH), and next-generation se- blood. Different methods of self-col- DMSO requires slow freezing, the quencing and validation studies. lection are available, depending on tissue can be placed into a house- RNA can also be extracted from the end-points and the analyses to be hold −20 °C freezer for 30 minutes FFPE tissue for gene fusion stud- performed (Mulot et al., 2005). and then placed into −80 °C stor- ies, next-generation sequencing, age overnight before final storage or quantitative reverse transcrip- Cytobrush

in LN2. A specific system to reduce tion PCR (RT-PCR). The same the temperature of the tissue by procedure as for diagnostic tissue With this method, buccal cells are 1 °C per minute can also be used may be followed, with the samples collected on a sterile cytobrush by before the tissue is transferred. placed in containers of different twirling it on the inner cheek for 15 • Tissue required for expression colours to identify them as sam- seconds. The operation is repeat- profiling and other molecular pro- ples for research purposes. ed three times, on the two cheeks. filing, such as whole-genome se- • Care should be taken in the evalua- The swabs are separated from the quencing or epigenetic studies, tion of biopsy material for research, stick with scissors and transferred must be snap-frozen. Each tissue because the sample has a much to a cryotube. The duration of the sample should be placed on card smaller quantity of tissue and most collection can influence the DNA and covered with optimal cutting of it may be needed for diagnostic yield. García-Closas et al. (2001) temperature (OCT) compound be- purposes. When needed for diagno- reported that cytobrushes produce fore vapour-freezing the sample sis, the biopsy sample should follow DNA with good quality. Howev-

by holding it over LN2. The sam- the standard diagnostic process er, King et al. (2002) concluded ple can also be frozen by placing and be formalin-fixed and paraf- that the mouthwash method of it into a container immersed in fin-embedded. After the diagnostic collecting buccal cells is superior freezing medium (e.g. precooled process, any leftover material can for reactions that require long isopentane). Tissue should never be recovered for research. fragments.

44 Mouthwash the lowest efficiency for DNA yield, 3.7.3.5 Bone marrow aspirate because of the small quantity of With this method, buccal cells are collected saliva. Moreover, some The following paragraphs on bone collected by rinsing the mouth for 10 proteins are left in the solution of marrow aspirate and cerebrospinal seconds with 10 mL of sterile water extracted DNA. Therefore, the DNA fluid are derived from the Austral- and expectorating the rinse into a cannot be kept for long-term con- asian Biospecimen Network recom- 50 mL centrifuge tube. This oper- servation. However, an advantage mendations (see Table 1) and the ation is repeated three times. The of this method of saliva collection is publication Guidelines on Standard effect of lag time of storage at room its low cost, because of the absence Operating Procedures for Microbiol- temperature is observed for mouth- of an extraction step. ogy (Kumari and Ichhpujani, 2000). washes, whereas cytobrushes are Bone marrow is the soft tissue less sensitive to the lag time at room 3.7.3.4 Bronchoalveolar lavage found in the hollow interior of bones. temperature. In adults, the marrow in large bones Cytobrushes and mouthwashes The airways, and particularly the al- produces new blood cells. There are generally considered unsuitable veoli, are covered with a thin layer of are two types of bone marrow: red for children, because cytobrushes epithelial lining fluid, which is a rich marrow (also known as myeloid tis- are abrasive. Mouthwashes require source of many different cells and sue) and yellow marrow. In cancer participants to expectorate and may of soluble components of the lung research, red bone marrow from the be aspirated or swallowed. that help protect the lung from infec- crest of the ilium is typically examined. tions and preserve its gas-exchange Bone marrow should be collected 3.7.3.3 Saliva capacity. Bronchoalveolar lavage by a doctor who is well trained in this performed during fibre-optic bron- procedure. Bone marrow should be Saliva is used as a biological fluid choscopy is the most common way aspirated by sterile percutaneous as- for the detection of different bio- to obtain samples of epithelial lining piration into a syringe containing an markers, such as proteins, drugs, fluid (Reynolds, 2000). The cellular EDTA anticoagulant, and the speci- and antibodies. Saliva meets the and protein composition of the epi- mens should be chilled immediately. demand for a non-invasive, acces- thelial lining fluid reflects the effects Heparin is not recommended as an sible, and highly efficient diagnostic of the external factors that affect the anticoagulant for molecular testing. If medium. The collection of saliva is lung, and changes in this composi- a specimen contains erythrocytes, it non-invasive (and thus not painful), tion are of primary importance in the should be processed to remove the and a sample can easily be collect- early diagnosis, assessment, and erythrocytes before freezing. The ed without a need for various de- characterization of lung disorders bone marrow samples should be vices. Whole saliva is collected by as well as in the search for disease fresh frozen and stored at −80 °C. expectoration into a provided tube, markers (Griese, 1999). whereas for the collection of sub- Bronchoalveolar lavage is clas- 3.7.3.6 Cerebrospinal fluid (CSF) mandibular saliva and sublingual sically performed by instillation of 3 SECTION saliva, different ducts need to be buffered saline solution divided into Cerebrospinal fluid (CSF) originates blocked by cotton gauze. For the three or four aliquots (typically a from the blood. The choroid plexuses collection of parotid saliva, a parotid total volume of 100–150 mL) through in the first, second, and third ventri- cup should be used (see Section 4). a flexible fibre-optic bronchoscope, cles of the brain are the sites of CSF after local anaesthesia. The first production. CSF is formed from Treated cards 10 mL should be processed separate- plasma by the filtering and secretory ly and is denoted as bronchial lavage. activities of the choroid plexus and These cards are treated to inhibit The rest of the lavage, denoted as the lateral ventricles. CSF circu- the growth of bacteria and kill virus- bronchoalveolar lavage, should lates around the brain and the spinal es, thereby minimizing degradation be pooled into a sterile siliconized cord. It nourishes the tissues of the of nucleic acids. Saliva is expecto- bottle and immediately transported central nervous system and helps rated into a sterile cup. The tip of the on ice to the laboratory. At the labo- to protect the brain and the spinal triangle of treated card is placed into ratory, the total volume of the lavage cord from injury. It primarily acts as the saliva, which is wicked onto the is measured, and cells and proteins a water shock absorber. It totally matrix. The treated card is air-dried are separated by centrifugation. The surrounds the brain and the spinal and placed in a bag with a desiccant lavage fluid should be frozen and cord, and thus absorbs any blow to pack. Treated cards correspond to stored at −80 °C until use. the brain. CSF also acts as a carrier

Section 3. Recommendations for biobanks 45 of nutrients and waste products Fig. 22. Hair sample. Fig. 23. Nail clippings. between the blood and the central nervous system. CSF is a very delicate biological material. Often, only small volumes of CSF are available for analysis, because of the difficulty of collecting CSF, and therefore it should be handled with care. Only a physician or a specially trained nurse should collect the specimen. After collection, the specimen should be transferred into a clean penicillin vial containing about 8 mg of a mixture of EDTA and sodium fluoride in the ratio of 1:2. Centri- fuging CSF is recommended before freezing if the sample contains red blood cells or particulate matter. The specimen should be frozen and stored at −80 °C or in LN2. Do not be added to the sample, to avoid delay freezing the CSF, because digestion by powerful proteases cells are rapidly lysed once the present in seminal fluid. To ensure drug use and to conduct criminal CSF is removed from the body. complete separation of cell debris investigations (see Section 4). Hair or occasional spermatozoa from should be kept in a sealable plastic 3.7.3.7 Semen seminal plasma, the sample can bag, stored in the dark at room tem- be centrifuged a second time. The perature (Fig. 22). Seminal fluid, which is the liquid sample should be stored at −80 °C. component of sperm, provides a 3.7.3.10 Nails safe surrounding for spermatozoa. 3.7.3.8 Cervical and urethral At pH 7.35–7.50, it has buffering swabs Nail clippings may contain analytes properties, protecting spermato- of interest that were deposited dur- zoa from the acidic environment of The quality of collected cervical ing the growth of the nail. Nail spec- the vagina. Seminal fluid contains and urethral specimens depends imens can be collected for drug, a high concentration of fructose, on appropriate collection methods. nutritional, poisons, and toxicity test- which is a major nutriment source Swabs, brushes, or other collection ing (see Section 4) (Fig. 23). for spermatozoa during their journey devices should be placed in a trans- in the female reproductive tract. The port medium, or transported dry in 3.8 Specimen annotations complex content of seminal plas- a sealed tube and resuspended in and data sets ma is designed to ensure the suc- the transport medium upon arrival. cessful fertilization of the oocyte by The transport fluid may either be Data associated with the biological one of the spermatozoa present in stored at −70 °C or below or immedi- specimens provide added value to the ejaculate. Seminal plasma is a ately centrifuged, and the pellet pro- the samples and increase the types mixture of secretions from several cessed for DNA or RNA extraction of research for which the biospeci- male accessory glands, including (see Section 4). mens can be used. Specimen an- the prostate gland, seminal vesicles, notations provide basic information epididymis, and Cowper’s glands 3.7.3.9 Hair such as sample type, quantity, and (Pilch and Mann, 2006). current form (how the sample was After collection, the fresh ejac- Currently, hair analysis is used for stabilized and conserved), which ulate should immediately be spun purposes of assessing environmen- can be used to evaluate the use down at 4 °C to separate the sem- tal exposures, such as exposure to of the sample in a specific assay. inal fluid from the spermatozoa. mercury from eating fish. Hair anal- Specimen annotation also provides Protease inhibitors should then ysis is also used to test for illegal parameters that define the quality of

46 the specimen and thus the quality of to classification systems, the version lected, stabilized, and preserved. It the downstream assay. to which the value applies is also in- also contains clinical data associ- For biobanks wishing to share dicated. As versions change, these ated with the patient. samples in large studies and for re- values can be correctly interpreted • Tier 2 comprises 19 elements of search that requires samples from or adjusted. One such example is beneficial data, covering patient different sources, it is important the staging score used for defining demographic information, times that, as with all other elements of a the stage of a cancer. The require- and temperatures, and methods of biobank, the data are standardized ment to indicate the scoring system enrichment. or at least harmonized to permit also applies to values that may be • Tier 3 comprises 16 elements of effective aggregation. retrieved using different assays. An nice-to-have data, pertaining to Information to annotate the example of this is the concentration environmental conditions such as sample should be collected at each value taken using a spectrophotome- ischaemia, therapy, exposures, phase of the biobank/biospecimen ter or a fluorescent dye-based quan- disease state, and storage con- processes: tification. Other fields for which the tainers and shipping parameters. • consent; situation may be similar are units of Tier 1 is now required for many • donor/patient ID, sample ID; time (e.g. time to stabilization, time journals. • collection (technique, date, time); from diagnosis to collection, time MIABIS 2.0 represents the mini- • processing/stabilization; from diagnosis to follow-up), which mum information required to initiate • conservation/storage; may be recorded in minutes, hours, collaborations between biobanks. • for tissues: organ of origin; days, months, or years, as well as This standard currently comprises • for tissues: disease features (e.g. units of measurement of size (e.g. aggregated descriptive data, and tumour, non-neoplastic); millimetres, centimetres) or weight not sample-specific data, to permit • quality parameters; (e.g. nanograms, milligrams). a harmonized exchange of sam- • donor/patient-related data; Systems already exist to address ples and data among biobanks. The • distribution/use; and the need to standardize biobank- MIABIS standard pertains to de- • returned data. and sample-associated information. scriptive data of a biobank, col- It is important to determine a The SPREC tool, in particular, lection, and study, which include minimum data set, because this es- addresses the pre-analytical data collection types and contact infor- tablishes a basic quality of all sam- required and contains seven data mation. It also includes aggregated ples collected in the biobank (see fields and defined values for the data such as sex, age range, materi- Table 5). This should not, however, definition of sample type and the al type, data categories, and diseas- compromise the ability to collect ad- processes of collection, stabiliza- es. MIABIS is the only standard to ditional data for particular sample tion, and storage. There is a SPREC provide indications for this collective sets that may be useful in the future. available for fluids and one for sol- type of information. This information The minimum data set must be as ids, to address the different collec- is useful when creating biobank cat- completely defined as possible, in- tion and stabilization processes alogues and inventories to provide 3 SECTION dicating values for each of the fields required. However, the SPREC sys- visibility to available resources. in the data set, to reduce the het- tems will be replaced by CEN norms erogeneity of sample-associated and ISO standards. 3.8.1 Annotations on patients/ data and thus improve its quality. The Biospecimen Reporting for individuals One potential problem of data Improved Study Quality (BRISQ) values involves different systems standard covers pre-acquisition, It is important for the biobank to an- that use different date formats: DD/ acquisition, stabilization/preserva- notate the consent that is collected MM/YYYY or MM/DD/YYYY or tion, storage/transportation, and QA for the samples and data that be- YYYY/MM/DD. Another problem for measures (Moore et al., 2011). The long to the patient. This information sample annotation is unfilled fields. elements in the BRISQ list are pri- should include whether the consent It is important that a value for “not oritized into three tiers according to or a waiver was used to permit the available” is defined, because blank the relative importance of their be- use of the sample or data in re- fields can potentially be interpreted ing reported. search. It is important to indicate as zero and can provide incorrect • Tier 1 comprises 15 elements of the scope of the permission, the evaluations when used in research. necessary data, covering all sam- type of research that can be per- During the creation of a data set, ple types and including the manner formed, information such as what it is important that for data that refer in which the specimens were col- types of entities can access the

Section 3. Recommendations for biobanks 47 sample (public, private), and wheth- Not all of these data categories system functionality or through a er there are geographical restric- of participant-associated data are parent ID field that relates initially tions (local, national, international) required for all studies, and even to the donor data. This avoids re- on shipment of samples and data. within a single category, different peating each donor data annota- In the era of personalized medicine data fields will be required depend- tion for each sample. and open access, it is also impor- ing on the type of sample being col- • It is important to have a method tant to record which participant- lected and the intended use of the to indicate participants for which related data can be associated with sample. different sample types are avail- the sample (clinical data, patho- able. This should be done either logical data, follow-up data) and, 3.8.2 Annotations on stored within the database system func- in particular, whether genetic data specimens tionality or through a field to indi- can be used and whether these cate the availability of other types data can be placed in public data- Obtaining and storing information of samples related to the same bases (publication or research). It about the stored specimens – in case. is vital to indicate whether a donor/ particular, the pre-analytical variables • For all classification systems (on- patient wishes to be re-contacted related to the collection, transpor- tologies) that are used to annotate for further studies, whether they tation, ischaemia times, stabiliza- samples, the version should be wish to be informed of incidental tion, and conservation of the spec- indicated. findings, and what should be done imens – is mandatory in CEN and • All numerical values indicated if any findings have hereditary ISO. The data categories to consid- should have associated units of implications. er for sample-specific annotations measurement (e.g. months, days, For all samples, it is vital to are: hours, nanograms, microlitres). have the diagnosis and pathological • pre-acquisition; • All null values (not inserted) should data. It is preferable that accepted • collection; have default values that are not nomenclature is used for diagno- • processing/stabilization; zero. sis and classification systems are • conservation/transportation; and • Values lists for data fields avoid the used for all pathology data, because • quality. introduction of error and are pref- they provide standard comparable erable to free-text fields. parameters. One such example is 3.8.3 General recommendations See Table 5 and Annex 5. the tumour–node–metastasis (TNM) for data sets system for classification of malig- 3.8.4 Specimen labelling and nant tumours. • Wherever possible, the biobank aliquoting Participant-associated data are should collect its data from existing important, to provide additional val- clinical databases for patient-relat- Each specimen should be labelled ue because they permit an extended ed data. This avoids the need for in such a manner that the labelling evaluation of downstream assays. duplicate input and reduces the will survive all potential storage con-

The more information can be col- possibility of human error. If the ditions, in particular dry ice and LN2 lected during the patient’s clinical data are collected through a link and potentially water bath. care path, the more valuable the between the biobank database Ink used on the label should be sample becomes. Some of these and the clinical database, this may resistant to all common laboratory data categories are: also permit tracking of additional solvents. A minimum requirement is • demographic information; clinical data over time. to print labels with a barcode (linear • family history; • Because it is not always possible to or two-dimensional), thus providing a • environmental exposure; set minimum data sets common to direct link to database software and • lifestyle; multiple sample or disease types, preventing human error in identifica- • diagnosis; macro fields should be set to in- tion. However, it is also essential to • clinical data/medical history; dicate the presence of such data include human-readable indications • complete pathology report, includ- (e.g. clinical data, epidemiological of contents in case no barcode ing immunohistochemical and mo- data, follow-up data). reader is available (Figs. 24–26). lecular biology markers; • All donor/patient-related data The barcode template should be • treatment; should be associated with each documented. The software used for • follow-up/outcome; and sample collected. This should be labelling should enable data import • molecular/genetic characterization. done either within the database and export in standard formats and

48 Table 5. Example of IARC minimum data set for a study or collection in a biobank

Attribute Standard

1 Study details 1.1 Study ID MIABIS 2.0

1.2 Study name MIABIS 2.0

1.3 Description/objective MIABIS 2.0

1.4 Responsible unit

1.5 Responsible/principal investigator MIABIS 2.0

1.6 Sample manager

1.7 Study design MIABIS 2.0

1.8 Cancer type WHO name or ICD-O code

1.9 Other chronic disease BRISQ

2 Collaborators details 2.1 Contact person (collaborators) MIABIS 2.0 – First name – Last name – Telephone number – Email – Contact institution – Contact department – Contact address – Contact country

3 Collection details

3.1 Collection start date

3.2 Collection end date

3.3 Collection centres – Centre name – Centre country

4 Ethical, legal, and social issues (ELSI)

4.1 Ethical approval – Date SECTION 3 SECTION – Reference

4.2 Informed consent

4.3 Participant information sheet

4.4 Material Transfer Agreement – Date – Reference

4.5 Other contract – Date – Reference

5 Donor/patient-related data

5.1 Sample ID

5.2 Parent sample ID (for aliquots and derivatives)

Section 3. Recommendations for biobanks 49 Table 5. Example of IARC minimum data set for a study or collection in a biobank (continued)

Attribute Standard

5.3 Informed consent – YES/NO/NI (implying waiver) – Type of consent – Area of research – Re-contact – Return of results – Access to medical data – Possibility of publishing data – Access to genetic data

5.4 Sex

5.5 Age at collection

5.6 Country and region of origin

5.7 Basic diagnostic parameters (e.g. for cancer: individual TNM codes where possible; if not, then stage and always grade – for all, the version should be indicated)

5.8 Associated diagnostic parameters (CA125, CA19-9, etc.)

5.9 Other diseases

5.10 Disease status

6 Biospecimen-related data

6.1 Biospecimen type

6.2 Anatomical site: organ of origin or site of blood draw

6.3 Collection mechanism: how the biospecimens were obtained

6.4 Type of stabilization: the initial process by which the biospecimens were stabilized during collection

6.5 Biospecimen size

6.6 Delay to preservation: SPREC – Time between biospecimen collection and processing – Time between biospecimen processing and cryopreservation – Warm ischaemia time for tissue: period between circulatory arrest and beginning of cold storage

6.7 Temperature before preservation: – Storage temperature before processing – Storage temperature before cryopreservation

6.8 Type of long-term preservation: the process by which the biospecimens were SPREC sustained after collection

6.9 Constitution of preservative: the make-up of any formulation used to maintain the biospecimens in a non-reactive state

6.10 Storage temperature for short-term storage: the temperature, or temperature range, at which the biospecimens were kept until distribution or analysis

6.11 Storage temperature for long-term storage SPREC

6.12 Freeze–thaw cycles: this field is for low-temperature storage and should account for the number of times the sample underwent a freeze–thaw cycle for processing; it should also account for any anomalies to the container containing the samples

50 Table 5. Example of IARC minimum data set for a study or collection in a biobank (continued)

Attribute Standard

7 Categories of associated data collected

7.1 Medical history data (e.g. history of other diseases, medications, family history of same cancer to first and second degree, family history of other cancers, family history of other diseases): – Available or not? – Which kind of data? – Where are data kept? – Who manages data?

7.2 Epidemiological and survey data (e.g. age, sex, exposure, anthropometric data, reproductive history, physical activity, tobacco status, alcohol consumption, occupational history, socioeconomic status, previous illness): – Available or not? – Which kind of data? – Where are data kept? – Who manages data?

7.3 Clinical data (e.g. clinical diagnosis, clinical presentation, comorbidities, biochemical data, immunophenotypic data, neoadjuvant therapy, disease status of patients, vital status of patients, clinical diagnosis, pathology diagnosis): – Available or not? – Which kind of data? – Where are data kept? – Who manages data?

7.4 Pathology data (e.g. pathology diagnosis, histological type, TNM, stage, grade, nuclear component, immunohistochemistry): – Available or not? – Which kind of data? – Where are data kept? – Who manages data?

7.5 Follow-up data (e.g. bioassays, treatment, disease progression, relapse, status – disease-free, alive with disease, dead from disease, dead from other causes): – Available or not? – Which kind of data? – Where are data kept? – Who manages data?

8 Shipment data saved for each sample SECTION 3 SECTION 8.1 Date of deposition

8.2 Number of biospecimens shipped

8.3 Shipment conditions

8.4 Carrier

8.5 Date of next shipment

8.6 Number of biospecimens to be shipped

8.7 Expected carrier

BRISQ, Biospecimen Reporting for Improved Study Quality (Moore et al., 2011); ICD-O, International Classification of Diseases for Oncology; MIABIS 2.0, Minimum Information about Biobank Data Sharing 2.0 (Brochhausen et al., 2013); SPREC, Sample PREanalytical Code (Lehmann et al., 2012); TNM, tumour–node–metastasis classification of malignant tumours; WHO, orldW Health Organization.

Section 3. Recommendations for biobanks 51 should be able to link with the bio- space saving in the biobank storage Experts on the Transport of Dan- bank management system. facility. Consideration and attention gerous Goods, a committee of the Ideally, all specimens should should be given to the composition United Nations Economic and Social be labelled with at least two hu- of plastic, potential interaction with Council (UNECE, 2015). man-readable forms of identification some analytes, and resistance to ul- The International Civil Aviation without revealing the identity of the tra-low storage temperatures. Organization (ICAO) Technical In- donor. The anonymity of the donor structions for the Safe Transport must be guaranteed in all cases. Ra- 3.9 Specimen shipping of Dangerous Goods by Air (ICAO, dio-frequency identification (RFID) 1986) are legally binding interna- is another option but is not in wide- Human biospecimens are con- tional regulations. The Dangerous spread use for biobanking. sidered to be “dangerous goods”, Goods Regulations incorporate the Information on the label should defined by the International Air ICAO provisions and may add fur- include the biobank’s unique iden- Transport Association (IATA) as ther restrictions. The ICAO rules tifier number, the name of the proj- “articles or substances which are apply on all international flights. For ect, the type of biospecimen, and/ capable of posing a risk to health, national flights, i.e. flights within one or the number of the location within safety, property or the environment”. country, national civil aviation au- the storage system, with the same According to United Nations regula- thorities apply national legislation. information repeated in the barcode tions, dangerous goods meet the This is usually based on the ICAO if available. criteria of one or more of nine Unit- provisions but may incorporate vari- After primary samples are pro- ed Nations hazard classes (DGI, ations. State and operator variations cessed, derived products should be 2016). The relevant class for biolog- are published in the ICAO Technical stored in appropriate and optimized ical specimens is Class 6, Division Instructions and in the IATA Dan- containers. As technologies for 6.2: Infectious substances (IATA, gerous Goods Regulations (IATA, analysing biospecimens improve, 2015b). 2015a; WHO, 2012). smaller volumes of sample are The shipping and dispatch of Each person involved in the required. Therefore, the volume of biospecimens is subject to inter- transportation of biospecimens aliquots should be adapted to avoid national regulations. These regu- classified as dangerous goods by unnecessary freeze–thaw cycles. lations, applicable to any mode of IATA should undergo an initial train- A wide range of tubes of differ- transport, are based on the recom- ing session followed by a refresher ent sizes, with or without a preprint- mendations of the Committee of course every 2 years. This training ed barcode, are now available and affordable. Coloured caps can be used to distinguish between differ- Fig. 25. Printed two-dimensional bar- Fig. 26. Pre-labelled tube with two- dimensional barcode. ent types of samples and to facilitate code. the retrieval of samples. More and more analysis platforms are using robots, and sample storage in SBS format containers is also important to consider, to facilitate downstream analyses. Otherwise, specific boxes must be used for appropriate storage of SBS format tubes, allowing

Fig. 24. Printed linear barcode.

52 is for staff members involved in the Fig. 27. The triple packaging system. preparation of documentation and also for those involved in packaging biospecimens.

3.9.1 Regulations

Infectious substances fall into two categories: Category A and Category B. Category A comprises any infectious substance that is transported in a form that, when exposure to it occurs, is capable of causing permanent disability or life-threatening or fatal disease in otherwise healthy humans or animals. Catego- ry A specimens include, but are not restricted to, specimens contaminated by highly pathogenic viruses • The primary receptacle is a water- The triple packaging system also (Ebola, Hantaan, Marburg, Lassa, tight, leakproof receptacle contain- applies to “Exempt Human Speci- etc.) or cultures of viruses such as ing the specimen, packaged with mens”, such as Guthrie cards (which dengue, HIV, or HBV. The proper enough absorbent material to ab- should be transported in watertight shipping name for such substances sorb all fluid in case of breakage. plastic bags) and histopathological is UN 2814: “Infectious substances • The secondary packaging is a du- slides (which need to be cushioned affecting humans” or UN 2900: “In- rable, watertight, leakproof pack- to prevent breakage). In all cases, fectious substances affecting ani- aging to enclose and protect the desiccants should be used for sam- mals only”. primary receptacle. Several pri- ples that are sensitive to humidity. Category B comprises any infec- mary receptacles may be placed tious substance that does not meet in one secondary packaging, but 3.9.3 Labelling of parcels the above-mentioned criteria. Most sufficient additional absorbent ma- human specimens, such as blood terial should be used to absorb all All outer packages must bear a Unit- samples, tissues, saliva, exfoliated fluid in case of breakage. ed Nations packaging specification cells, or urine not contaminated by • The outer packaging is the ship- highly pathogenic viruses, will fall ping packaging, made of a suitable into Category B. The proper ship- cushioning material, to protect the Fig. 28. Dry ice (−78.5 °C). ping name for such substances is contents from outside influences 3 SECTION UN 3373: “Biological Substance, while the package is in transit. An Category B”. itemized list of contents must be Biospecimens or derived prod- enclosed between the secondary ucts that have been specifically treat- packaging and the outer packaging. ed to neutralize infectious agents, or Appropriate insulation should for which there is a minimal likeli- be used. For example, for 8 °C to hood that pathogens are present, −20 °C, use gel packs; for −78.5 °C, are not subject to these regulations. use dry ice (Fig. 28); and if samples The proper shipping name for such need to be kept at −150 °C, trans- substances is “Exempt Human (or port them in a dry shipper containing

Animal) Specimens”. LN2. Ensure that enough refrigerant is included to allow for a 24-hour de- 3.9.2 Packaging lay in shipping. In-transit temperature monitor- The basic triple packaging system ing solutions that feature alarms as applies to all substances. It consists well as reporting are commercially of three layers, as follows (Fig. 27). available.

Section 3. Recommendations for biobanks 53 marking, according to the category to confirm with the recipient before specimens, from the study design in which the specimens fall. For Cat- the shipment that someone will be to final laboratory analyses. This egory A, Packing Instruction P620 available to receive the samples. scheme underlines the central role applies. For Category B, Packing When shipping biospecimens of biobanks as the transfer structure Instruction P650 applies. Detailed internationally, the sender must be between biospecimen collection instructions are described in the aware of the requirements and reg- and laboratory analysis. It also un- IATA Dangerous Goods Regulations ulations in the destination country derlines the fact that, in developing (IATA, 2015c). All packages must before initiating the shipment, and a study protocol, each step in this have shipper details and consignee must ensure that the consignment sequence of events must be clearly details (name of institute, address, adheres to these regulations. defined. The flow of information and contact name, email, and telephone It is important to select an ap- biospecimens, as defined by pro- number). propriate shipping company. Some tocols and procedures, will ensure companies offer more dedicated the formation of a collection that 3.9.4 Constraints services for biospecimens, such as contains traceable biospecimens refilling of dry ice, handling of cus- and yields interpretable results. The When preparing to transport biospec- toms paperwork, and step-by-step biobank is an essential source of imens, it is important to consider ship- monitoring and tracking. information and recommendations ping time, distance, climate, season, for the collection of biospecimens method of transportation, and regula- 3.10 Biobank workflow and for their annotation, storage, tions, as well as the type and num- processing, and flow from the par- ber of biospecimens to be sent and Fig. 29 shows the sequence and the ticipant to the laboratory where they their intended use. It is also important flow of information, data, and bio- will be analysed.

Fig. 29. Biobank workflow.

NSIS ST ESIN

Shiin nfore consent

liotin ollection sale rotocol rearation

ollection ION annotation C Retrieal Sale rocessin

ata recors abellin

IE section 4. Selected protocols

4.1 Processing of blood DBS can be used for molecular biol- • Whatman Protein Saver Card (e.g. specimens ogy techniques and other diagnostic Whatman, 903; 10534612); assays. The cost and difficulty of cold • gas-impermeable storage bag (e.g. If serum and plasma samples are chain shipping of plasma samples are Fisher Scientific, NC9307519); being collected, the blood should greatly reduced by the use of DBS, • desiccant pack (e.g. Whatman, be centrifuged as soon as possible which can be shipped as non-dan- 10548234); after blood collection and separated gerous goods. • humidity indicator cards (e.g. Multi- immediately after centrifuging so that Always wear gloves when han- sorb Des Manufacture, MS200032); the samples can be frozen as soon as dling filter papers, and hold them • card drying rack (e.g. VWR, 89015- possible. This is critical for time-sen- only by the upper corner, marked 592) (optional; cards can be placed sitive samples for protein studies, for out for labelling. Do not allow the on a dry worktop if a drying rack is example. For the processing of blood card to come into contact with any not available); specimens, the following protocols unclean surface (e.g. bench, base of • gloves, preferably powder-free; and are recommended. hood). • sample label. The procedure should be per- 4.1.1 Filter paper dried blood formed in accordance with the relevant 4.1.1.1 Collection of DBS from spot collection, processing, health and safety practices specific finger prick storage, and shipment to specimen handling and waste disposal. A minimum level of training is i. Disinfect the selected site and Dried blood spot (DBS) is an easy required to perform the procedure. prick it using a lancet/needle. and inexpensive means of collection Reagents and materials required: ii. Uniformly saturate the entire circle and storage of peripheral blood spec- • finger prick device (e.g. Unistik 2 by quickly and gently touching, imens in settings where collection device; Fisher Scientific, 22-0227); not pressing, the puncture site to 4 SECTION and storage of plasma is not optimal. • alcohol swab; the filter paper.

Section 4. Selected protocols 55 iii. Note: Do not touch the Whatman 4.1.1.2 Preparation of DBS from DMSO is needed to keep them alive card at any stage of collection. EDTA, ACD, or heparin tubes while freezing. iv. After the collection of five blood i. Dispense 50 μL of DMSO into two spots, clean the site and leave it DBS can also be prepared from 1 mL sterile cryovials. unbandaged. EDTA, ACD, and heparin blood tubes. ii. Invert the EDTA tube twice, and v. Allow the blood spots to air-dry, i. Before starting, mix vacutainers then add 450 μL of blood to each without the flap covering the containing anticoagulated blood cryovial. spots, in a clean dry place that is by inversion. iii. Invert the cryovial to mix the protected from rodents or insects ii. Wipe the top of the vacutainer whole blood with the DMSO. and direct sunlight, for at least with 70% ethanol before opening Note: DMSO is cytotoxic at room 4 hours (overnight drying may the lid. temperature; therefore, as soon be needed in areas with higher iii. Using a micropipette, apply 40 µL as it is mixed with blood, it should humidity). of blood onto the circle on the be placed in a controlled-rate vi. Do not heat or stack DBS cards DBS card. freezer. or allow them to touch other iv. Air-dry the filter paper thoroughly iv. Transfer to −80 °C after at least surfaces during the drying pro- by following step v above (Sec- 4 hours. cess. tion 4.1.1.1), and continue with the vii. Tuck in the flap of the card as rest of the protocol as described 4.1.3 Plasma indicated on the card. above. viii. Clearly label the card with the pa- Plasma collected in EDTA or ACD tient identifier and date, or label it 4.1.1.3 Shipping of DBS cards tubes can be used for bioassays, with a prepared barcode label. plasma DNA isolation, proteomic ix. Be sure the DBS card is com- DBS are classified as “Exempt Bi- analysis, and biomarker discovery. pletely dry before packing. ological Specimens” according to i. Spin the vacutainer (about 9 mL) x. Insert the DBS card into a gas-im- the ICAO and IATA shipping regula- at 815g for 10 minutes at 4 °C to permeable plastic bag containing tions. DBS bags should be shipped separate plasma from blood cells. a desiccant pack and a humidity in courier envelopes or boxes under ii. After wiping each tube with indicator. Do not store more than ambient conditions according to 70% alcohol, remove about 3 mL one card per bag. the triple packaging system (see of plasma. (The tube can be xi. Ensure that the patient identifier Section 3.9.2). retained for white blood cell and date (or the prepared bar- i. Provide a shipping manifest for extraction.) code label) are on the outside of all boxes. The shipping manifests iii. Transfer to a labelled 15 mL tube, the bag as well as on the DBS must exactly match the label in- and centrifuge at 2500g for 10 card. formation and the order in the as- minutes at 4 °C. xii. Seal the plastic bag. sociated shipment, including the iv. Aliquot plasma into 1 mL labelled xiii. Place the sealed bag containing global specimen IDs. cryovials (three or four aliquots).

the DBS card in a clean, dry area ii. Provide a box map for all boxes. v. Place in LN2 dewar to snap- of the laboratory with no exposure The box maps must exactly match freeze.

to direct sunlight, free of insects the label information and the order vi. Store at −80 °C or in LN2. or rodents, and where ambient in the associated shipment, includ- The purpose of double-spinning temperatures will not exceed ing the global specimen IDs. the plasma is to remove all cellular 30 °C. iii. Record the courier service and contaminants so that the plasma is xiv. The room should be temperature- the courier air bill number on the suitable for plasma DNA analysis. and humidity-controlled (temper- specimen shipment notice. Therefore, it is extremely important ature of 20–22 °C and humidity of iv. Advance notification of shipment not to disturb the buffy coat after the not more than 22%). must be made to the recipient. first spin and any pellet after the sec- xv. Check the desiccant pack before ond spin. shipment of the DBS card and 4.1.2 Whole blood replace it if the colour of the hu- 4.1.4 Platelet-poor plasma midity indicator has changed from Whole blood is to be prepared from blue to pink or colourless. EDTA tubes. The anticoagulated Platelet-poor plasma can be used for xvi. Ship the DBS cards at ambient blood can be snap-frozen as it is. the isolation of plasma DNA (from temperature. If the blood cells are needed intact, EDTA tubes).

56 i. Spin blood at 3200g for 12 min- v. If division of the sample is nec- vii. Spin at 450g for 10 minutes. utes at room temperature. essary, at this point pour 25 mL viii. Pour off the supernatant into a ii. Pipette off plasma using a plas- of the sample into another centri- waste container containing chlo- tic Pasteur pipette. Transfer into fuge tube. rine bleach. Add 3 mL of cold a tube. vi. Spin both tubes at 1200g for 10 freezing mix (10% DMSO, 20% iii. Spin plasma at 2000g for 10 min- minutes. fetal calf serum [FCS], RPMI utes at 4 °C. vii. Repeat the washing if red blood 1640) and resuspend. iv. Aliquot into 1 mL aliquots in la- cells persist. ix. Dispense the white blood cells belled cryovials. viii. Carefully pour off the supernatant. into three 1 mL labelled cryovials v. Store at −80 °C. ix. Using a swirling motion, remove that have been sitting on ice. the pellet with a pipette and trans- x. Place on ice. Place vials in a 4.1.5 Buffy coat cells fer it to a labelled cryovial. controlled-rate freezer so as to

x. Store at −80 °C or in LN2 until cryopreserve cells under condi- The buffy coat is a thin, greyish-white further use. tions that maintain cell viability. layer of white blood cells (leukocytes As an alternative, red blood cells This should be done as soon as and lymphocytes) and platelets cov- can be lysed by using an ammoni- possible, because DMSO is toxic ering the top of the packed red blood um-containing lysis buffer. at room temperature. cells after centrifugation at 450g xi. Transfer on a weekly basis to LN2 (from EDTA- or ACD-containing 4.1.7 White blood cells tanks. blood tubes). Instead of a separation based on i. After having spun the blood, White blood cells collected in EDTA Ficoll, a Percoll separation can be take the buffy coat off with about or ACD tubes can be used for DNA used. 100 μL of plasma using a dispos- extraction and the creation of cell able sterile Pasteur pipette; be lines. 4.1.8 Serum careful not to lift red blood cells. i. Transfer the remaining blood ii. Lyse the remaining red blood cells from the plasma spin to a labelled The blood is collected into tubes by addition of red blood cell lysis 50 mL tube containing 10 mL of without addition of anticoagulants. buffer at room temperature. RPMI 1640. Then, two phases are distinguish- iii. Spin the tube at 450g for 10 min- ii. After swabbing the lid of this tube able: a solid phase containing fibrin utes at room temperature. with alcohol, aliquot 3 mL of Ficoll and cells, and a fluid phase contain- iv. Resuspend the pellet. into each of two clearly labelled ing the serum. v. Aliquot as appropriate into la- 15 mL tubes. This process should be complet- belled cryovials. iii. Carefully layer 9 mL of diluted ed after 30 minutes at room temper- vi. Place in LN2 to snap-freeze. blood onto each tube of Ficoll. ature, after which the process de- vii. Store in LN2. Treat gently, and do not mix, but scribed below should start. spin as soon as possible. i. Spin blood at 1500g for 10 min- 4.1.6 Blood pellets (white iv. Spin at 450g for 30 minutes. Note: utes at room temperature. blood cells) When centrifuging, do not use the ii. Aliquot 1 mL portions of the su- brake. pernatant into labelled cryovials.

Blood pellets can be used for the v. Remove most of the top layer iii. Place into LN2 dewar or dry ice to isolation of DNA (from EDTA or ACD (RPMI 1640) using a 1 mL Ep- snap-freeze. tubes). pendorf tip, and discard about iv. Transfer to −80 °C freezer or LN2. i. Transfer blood from the original 3–4 mL into a waste container tube to a labelled 50 mL tube. containing chlorine bleach. 4.2 Processing of solid tissue ii. Fill the tube with Tris-EDTA buff- vi. Collect white blood cells with the er (formula) and mix vigorously. same Eppendorf tip using a swirl- Careful and well-documented pro- Place on ice for 5–10 minutes. ing motion to “vacuum up” white cessing of tissue specimens is cru- iii. Spin at 1200g for 10 minutes. blood cells. Do not take too much cial to the overall usefulness of the iv. Carefully pour off the supernatant Ficoll (third layer), because it is biobank as a resource for scientific into a waste container containing toxic to the cells. Place the white research. Detailed records of the chlorine bleach. Briefly vortex blood cells into a labelled 15 mL first steps in the process of sample the pellet and add 50 mL of Tris- tube containing 10 mL of RPMI handling include the times of an- 4 SECTION EDTA buffer. Shake vigorously. 1640. aesthesia administration, ligation of

Section 4. Selected protocols 57 vessels, and specimen removal from freezing. All the different pre-analyt- 4.2.1.5 Role of the pathologist the patient. ical conditions and durations should These factors are important to be documented. i. Macroscopically describe the assess tissue quality, because they specimen as usual. affect the quality of the resulting bio- 4.2.1.1 Safety ii. Using clean instruments and on a molecules. The most commonly de- clean surface (sterile foil or clean scribed factor that has an impact on All procedures should be carried out dissection board), dissect the tis- tissue quality is the warm ischaemia in accordance with the local codes of sue specimen. Clean or change time, which is the period from when practice. Working with LN2 and iso- instruments between dissecting the blood supply is ligated until the pentane is hazardous; all procedures normal tissue and tumour tissue. specimen is placed in fixative in the must comply with local safety rules iii. Take representative parts of tis- pathology laboratory. Studies have specific to these chemicals. All tissue sue for routine diagnosis (for fixa- demonstrated that changes in both must be handled as if it is potentially tion and embedding) as a priority, RNA and protein occur during this infectious. and decide whether there is suf- time (Dash et al., 2002). ficient material available for the These protocols for collecting 4.2.1.2 Hospital ward tissue bank. and freezing tissue samples were a. Supply the research technician developed within the European Hu- Consent must be obtained from the with a tissue sample or sam- man Frozen Tumour Tissue Bank patient before surgery (if applicable, ples for biobanking representa- (TuBaFrost) project (Riegman et al., according to the law and procedures tive parts of the lesion, normal 2006b) and the Standardisation and in the country where the samples are tissue, and pre-malignant con- Improvement of Generic Pre-ana- being collected). ditions. lytical Tools and Procedures for In b. Perform QC of frozen tissue Vitro Diagnostics (SPIDIA) project 4.2.1.3 Operating theatre and annotation. (Malentacchi et al., 2015). These recommended protocols i. Deliver the notification of tissue 4.2.1.6 Role of the technician contain choices and recommen- collection (and the consent form, dations for preserving solid tissue, if needed) to the surgeon, or high- i. Prepare the tissue sample for and describe the roles of key peo- light on the operating list. snap-freezing on a clean sur- ple involved in the process. Consult ii. The surgeon should: face and using clean instruments; the CEN norms for more detailed a. complete the pathology form (if change instruments between pre- information on the processing of possible, in advance); paring normal tissue and tumour snap-frozen tissue and FFPE sam- b. perform the operative proce- tissue. The minimum volume of ples for protein DNA and RNA isola- dure and record the time of ar- tissue for snap-freezing is ap- tion (CEN/TS 16826-1–2 and CEN/ terial clamping and of excision proximately 0.5 cm3, although the TS 16827-1–3). of the specimen; and amount of tissue available will dif- c. place the specimen in a la- fer depending on the sample site. 4.2.1 Snap-freezing belled sterile pot or bag and Smaller fragments should still be put it on ice. snap-frozen and stored in the tis- Snap-freezing is the process by iii. The operating theatre staff should sue bank; if there is sufficient ma- which samples are lowered to tem- send the fresh tissue specimen terial, freeze duplicate samples. peratures below −70 °C very rapidly to the pathology department ii. Pre-cool the freezing medium using dry ice or LN2. This method immediately. isopentane (2-methylbutane) until can provide excellent sample integ- opaque drops begin to appear in rity and a wide array of options for 4.2.1.4 Histopathology the isopentane and the solution tissue analysis, including extraction department becomes misty; this will bring the of proteins, RNA, and DNA for use isopentane towards its freezing in research diagnosis. Before tissues i. Notify the pathologist and the tis- point (−160 °C), the optimal freez- are stabilized by freezing, the protein, sue bank research technician (if ing point for the tissue. Options:

RNA, and DNA profiles can change, not already present). a. LN2: suspend a vessel of iso- and these changes depend on the ii. Check the paperwork and allo- pentane in LN2. duration of warm and cold ischaemia cate a pathology number to the b. Dry ice: add dry ice (cardice) to and the ambient temperature before specimen as routine. the isopentane until a slush is

58 formed, or suspend a vessel of b. Orientate the tissue on a 4.2.3 Storage of FFPE blocks isopentane in dry ice. piece of cork and an equally and slides iii. Label cryovials, cryomoulds, or sized piece of Whatman paper cryostraws with a barcode and/ soaked in physiological salt i. FFPE blocks and sections mount- or sequential code (depending on solution. ed on slides can be stored at room local laboratory practice). Use a c. If the cryostraw system is used temperature. Prevent exposure of waterproof pen with ink that is to introduce a carrot of tissue blocks to sun or extreme temper- able to withstand long-term stor- into the straw, thermally seal ature variation or humidity. age at low temperatures. The each extremity and place in ii. Store blocks in moisture-resistant

sequential code is the local in- LN2. cardboard boxes or plastic stor- ventory code and must not relate age boxes. to the pathology number or other 4.2.2 Storage of tissue iii. Transfer details to the computer- identifiers. If a barcode is used, ized database system. readable recognition must also Storage of tissue can be done ac- iv. Update the database when sam- be included to make the sample cording to different protocols accord- ples are moved or depleted. identifier readable at institutions ing to the equipment available in the where there are no barcode facility. Options for storage: 4.2.4 Formalin fixation readers. i. Transfer the snap-frozen sam- iv. Record the local sequential code, ple from the isopentane to a Formalin fixation is standard practice the pathology number, the date, pre-chilled storage container for in most routine histopathology labo- the lag time from arterial clamp- transfer to either a locked −80 °C ratories. The following guidelines

ing and excision to freezing, freezer or a LN2 storage facility address specific issues related to and the type of tissue (the site, in the liquid or vapour phase. For preservation of formalin-fixed spec- and also whether the sample is storage for longer than 5 years, imens in biobanks. Table 6 provides

tumour, normal, and/or pre-ma- LN2 in the liquid or vapour phase information on the composition of lignant) in the inventory book. If is recommended. neutral buffered formalin. a barcode system is in use, the ii. Place cryostraws in a designat- i. Tissue specimens should not be barcode can be scanned into the ed visotube within a goblet (re- bigger than 3 cm × 2 cm × 0.5 cm.

LIMS and the above-mentioned movable LN2 storage elements) ii. Specimens should be fixed in

data recorded. and place in the locked LN2 fresh 10% neutral buffered for- v. Freeze directly in isopentane. Do repository. malin for a minimum of 4 hours not remove the tissue from the a. Store duplicate samples in a and a maximum of 48 hours, after isopentane until freezing is com- different storage facility if this which they should be embedded plete (5 seconds or less, depend- is available. in paraffin in accordance with ing on size), but ensure that the b. Check the backup system for conventional techniques. sample does not crack. Remove the storage repository – either iii. All reagents should be DNase- the sample from the isopentane a backup freezer running con- and RNase-free (e.g. prepared us- and enclose it in the labelled cryo- stantly or adequate supplies ing diethylpyrocarbonate [DEPC]

vial. It is good practice to strive of LN2. water). to snap-freeze all tissue within c. Record the storage details iv. Fixation media, such as Bouin’s 30 minutes of excision from the in the inventory system, and solution, that contain picric acid patient. Tissue subject to a delay check earlier data that were should be avoided, because this of up to 2 hours should still be col- entered. At a minimum, the compound interferes with subse- lected and the delay noted with- information recorded will in- quent PCR analysis of extracted in the local inventory database. clude the inventory number nucleic acids. Options for freezing: (local sequential code), the v. Alcohol fixation may be used as a. Embed the tissue samples in location, the pathology num- an alternative to formalin fixation. OCT compound and freeze in ber, the type of tissue (the site, For this, tissue is placed into 70% isopentane, or freeze directly and also whether the sample alcohol (diluted with DEPC water) in isopentane. The isopen- is tumour, unaffected/normal, for a minimum of 4 hours. tane used is cooled either by and/or pre-malignant), the lag Because of the chemical hazards SECTION 4 SECTION suspension in LN2 or through time between excision and of formalin, it can be desirable to use addition of dry ice. freezing, and the date. alternatives to formalin as a routine

Section 4. Selected protocols 59 Table 6. Composition of neutral buffered formalin and 70% ethanol

Composition Total volume

10% neutral buffered formalin (in 40% formaldehyde) 100 mL

100% formaldehyde 37–40 mL

Na2HPO4 (anhydrous) 6.5 g

NaH2PO4 4.0 g

Distilled water 900 mL

70% ethanol

100% absolute alcohol 70 mL of absolute alcohol + 30 mL of water 100 mL

96% ethanol 73 mL of 96% ethanol + 27 mL of water 100 mL

fixative. However, the effect of long- tion, simply remove the tissue from protocol, problems, or issues re- term storage with these alternative RNAlater and process. lated to the collection and storage. fixatives on the desired macromole- cules is not always known and should 4.2.6 Shipment of tissues and 4.3 Processing of urine and be established empirically. slides buccal cells

4.2.5 RNAlater FFPE tissues and slides are shipped The following protocols for process- at ambient temperature in accor- ing of urine and buccal cells contain This substance protects RNA in fresh dance with the established shipment recommended procedures. specimens. It eliminates the need guidelines and protocols of the send- to immediately process or freeze ing and recipient institutions. Please 4.3.1 Urine samples. refer to Section 3.9 for more details. i. Plastic or glass containers for 4.2.5.1 Tissue 4.2.7 Quality control for tissue collection of urine should be samples clean and dry, should have a 50– Cut the tissue to be smaller than 3000 mL capacity, a wide mouth, 0.5 cm in at least one dimension, i. Ensure that the reagents have and a leakproof cap, and should and then submerge the tissue in 5 vol- not expired and are of the correct be clearly labelled. umes of RNAlater (e.g. a 0.5 g sample composition and volumes. ii. When in transit, urine collections requires about 2.5 mL of RNAlater). ii. Keep high-quality records on all should be maintained on ice or variables related to specimens, refrigerated. 4.2.5.2 Cells FFPE tissues, and slides, includ- iii. Urine should be aliquoted according the time of tissue collection, ing to the volume needed for anal- Resuspend the pelleted cells in a the processing time, and the pe- ysis or storage. small volume of phosphate-buffered riod of storage before shipment iv. Depending on the analyte to be saline (PBS) before adding 5–10 and/or use. measured, a preservative may be volumes of RNAlater. added during collection or before 4.2.8 Data to be recorded aliquoting.

4.2.5.3 Storage v. Store urine at −80 °C or below in LN2. i. Date and time of tissue collection. RNAlater-treated tissue and cell sam- ii. Number of unprocessed samples, 4.3.2 Buccal cells ples can be stored at 4 °C for 1 month, FFPE blocks, and slides prepared. at 25 °C for 1 week, or at −20 °C for iii. Date and time of shipping. i. A collection kit (containing mouth- an indefinite period. For RNA isola- iv. Any variations or deviations from the wash, a 50 mL plastic tube, a

60 plastic biohazard bottle, and saliva proteome. The protocol for col- should be swabbed with a moist- courier packaging) is mailed or lection and processing of saliva is de- ened cotton applicator onto the given to the participant, along rived from the consortium’s Salivary lateral dorsum of the tongue to with an instruction sheet. The par- Proteome Handbook Procedures and stimulate the secretion. Aim to ticipant is to brush their teeth as Protocols (Hu et al., 2007). collect at least 200 μL of subman- usual, rinse their mouth out well i. Saliva collection should be done dibular saliva. with water twice, and then wait 2 in the morning (aim for 10:00– v. For the collection of sublingual hours. The participant should not 11:00 am if possible). Ask the saliva, the protocol is similar to eat or drink anything other than subject to refrain from eating, that described above for collec- water during this time. drinking, or oral hygiene proce- tion of submandibular saliva. The ii. After 2 hours, 10 mL of commer- dures for at least 1 hour before only difference is that the duc- cial mouthwash should be poured the collection. tal orifices of the submandibular into the tube, and then 10 mL of ii. The subject should be given gland are blocked off. Aim to col- tap water should be added. This drinking water (bottled) and asked lect > 100 μL of sublingual saliva diluted mouthwash should be to rinse their mouth out well (with- every time. placed into the mouth (without out drinking the water). vi. For the collection of parotid saliva, swallowing) and swished around iii. Five minutes after this oral rinse, use a parotid cup to collect the sa- vigorously for 30 seconds. the subject should be asked to liva. Parotid cups may be placed iii. The mouthwash should then be spit whole saliva into a 50 mL ster- bilaterally if the clinical investiga- spat back into the plastic tube, and ile centrifuge tube. The subject tor so chooses. This will enable the tube should be sealed tightly. should refrain from talking. It is the simultaneous collection from iv. The sample should be sent back better for the subject to drop their each parotid gland. The citric acid to the biobank immediately for head down and let the saliva run stimulation should be performed processing, or stored at 4 °C un- naturally to the front of the mouth, as described above. Aim to col- til it is sent, but it should be sent hold this position for a while, and lect > 1 mL of parotid saliva. The within 24 hours. spit into the tube provided. The first 0.1 mL of parotid saliva col- v. When the sample arrives at the subject will spit into the collection lected should be discarded, to laboratory, transfer the mouth- tube about once a minute for up ensure that fresh parotid saliva wash to 15 mL conical test tubes. to 10 minutes. The goal for each is obtained. vi. Add 35 mL of Tris-EDTA to the whole saliva donation should be Note: The collected samples mouthwash sample and spin at about 5 mL. Require that the tube should be kept on ice at all times 450g for 5 minutes. be placed on ice while collecting before processing. vii. Decant the supernatant and dis- whole saliva. Remind the subject vii. For sample processing using pro- card. not to cough up mucus, so that teinase inhibitors, to each 100 μL viii. Wash the cells twice, each time saliva is collected, not phlegm. of saliva: with 45 mL of Tris-EDTA. iv. For the collection of subman- a. Add 0.2 μL of proteinase inhibi- ix. Resuspend the cell pellet in 50 μL dibular saliva, use 2 × 2-inch cot- tor cocktail from standard stock of Tris-EDTA and transfer to 2 mL ton gauze to block the opening solution (Sigma, P8340), and labelled cryovials. of each parotid duct. Dry up the invert gently. x. Store the sample at −80 °C or in floor of the mouth, and block the b. Add 0.3 μL of sodium ortho-

LN2. openings of the sublingual gland vanadate (Na3VO4) (Sigma, Note: Buccal cells can also be (both sides), and have the sub- S6508) from standard stock of collected with other means, such as ject raise their tongue slightly to 400 mM, and invert gently. brushes. elevate the opening to the sub- viii. Centrifuge the specimens at mandibular gland. Begin to collect 2600g for 15 minutes at 4 °C (if 4.4 Collection and processing submandibular saliva by using a you note that incomplete separa- of saliva sterilized Wolf device. A sterilized tion has occurred, increase the and disposable yellow tip (for pi- spin time to 20 minutes). Then: A research consortium at the Univer- pette P200) should be connect- a. Remove the supernatants from sity of California, Los Angeles was ed into the device and changed the samples and label them funded by the United States National after every collection. During the with the term “super”, which Institute of Dental and Craniofacial collection, at 2-minute intervals, stands for the supernatant 4 SECTION Research to investigate the human a few grains of citric acid powder phase of the saliva.

Section 4. Selected protocols 61 b. Taking care not to disturb the sampled, take a separate speci- the head from the centre of one pellet and keeping the pellet as men and smear it onto another ear to the centre of the other, is in the original tubes, label the slide. gather a lock of hair at least the original tubes as “pellet”. ii. Immediately fix each slide. Either thickness of a pencil, and tie it ix. Freeze the samples at −80 °C. use spray fixative, at a right an- together near the root end (near gle to, and at a distance of 20 cm the scalp) using a small string or 4.5 Processing of cervical from, the slide, or immerse the a rubber band. cells slide in a container of 95% eth- ii. Cut the hair as close to the scalp anol for at least 5 minutes. If the as possible without cutting the In a Pap smear test, a sample of slide is not fixed immediately, the scalp. cells is taken from the uterine cervix cells will dry and become mis- iii. Maintain the horizontal position of using a wooden spatula or a brush, shapen; it will then not be possi- the hairs in the bundle by wrap- smeared onto a slide, and examined ble to read the slide accurately ping the cut section in aluminium under a microscope for abnormal in the laboratory. foil or plastic wrap. cells (precancer or cancer). This iii. Gently close and remove the iv. Indicate the root end and the tip protocol is a selected protocol from speculum. end by marking the foil or plastic diverse collection procedures. iv. Place all used instruments in wrap with a permanent marker or Note the following: decontamination solution. with a paper label. Do not use i. It is best not to take a smear from tape on the hair itself. a woman who is actively men- 4.5.3 After taking the smear v. Place the specimen in a clean, struating or has symptoms of an dry, labelled paper envelope for acute infection. Slight bleeding is i. Label the frosted edge of each shipment to the laboratory. Note acceptable. slide carefully. whether bleaches, hair dye, or ii. Pregnancy is not an ideal time for ii. On the patient record, note and medications (e.g. selenium or a Pap smear, because it can give illustrate any features you have minoxidil) were used. misleading results. noted: visibility of the transforma- Please note that hair from oth- tion zone, inflammation, ulcers or er sources (pubic, axillary, beard, 4.5.1 Taking the sample of other lesions, or abnormal dis- moustache, chest, etc.) may also cells charge. Note whether other sam- be analysed if head hair is not ples were taken, for example Pap available. Insert the long tip of the spatula into smears of other areas, and if the the cervical os, and rotate the spatula woman has been referred else- 4.6.2 Nails through a full circle (360°). If the cer- where, note to whom and when. vical broom brush is used, place the A clean pair of nail clippers should tip of the brush into the cervical os, 4.6 Processing of hair and be used. To clean nail clippers thor- and rotate the brush gently through nails oughly, they should be rubbed with three 360° circles. alcohol swabs. Nails should be clean These protocols are recommended of all polish, dirt, and debris. Nail clip- 4.5.2 Taking the Pap smear for collecting hair or nail specimens. pings from each finger or toe should be collected and packaged sepa- i. Smear both sides of the spatu- 4.6.1 Hair rately in plastic bottles. Each bottle la (or the contents of the brush) should be labelled with the mass of onto the glass slide with one or Head hair may be collected as follows. the nail collected and its source (e.g. two careful swipes. If any abnor- i. Along an imaginary line drawn right index finger) (NMS Labs and malities are seen outside the area across the middle of the back of ExperTox).

62 References

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68 annex 1. IARC policy on access to human biological materials

A1.1 Definitions

1.1 The IARC Biobank (IBB): the IBB is a centralized biological resource storage facility for samples collected from studies conducted worldwide by IARC in collaboration with international partners (http://ibb.iarc.fr/). 1.2 The Laboratory Services and Biobank Group (LSB): LSB is responsible for the management of the IBB. The Group also provides services in pre-analytical sample processing and shipment. 1.3 Biological resources: include human tissues, cells, biological fluids/derived products, and associated sample quality data. 1.4 Sample collections: include biological resources based on common characteristics (e.g. sera from individuals from a population-based study; a clinical collection of breast cancer tissues). 1.5 Associated data: include anonymized data associated with biological samples, sample annotations, and data on sample quality. 1.6 Steering committee for multicentre studies: the steering committee has a coordinating role for a particular study, with responsibilities for coordinating research activities, including with regard to use of the study’s biological resources. 1.7 IARC Principal Investigator (PI): the PI is the IARC scientist who is responsible for the sample collection at IARC. 1.8 IARC Custodian (CU): the CU is the IARC scientist to whom the responsibility for the sample collection was assigned after the departure of the original IARC PI. 1.9 Biobank Steering Committee (BSC): the BSC is the committee that oversees the biobanking activities at IARC. 1.10 Biobank Application sub-Committee (BAC): the BAC is the sub-Committee appointed by the BSC to assist in the handling of requests for human sample access. 1.11 IARC Ethics Committee (IEC): the role of the IEC is to provide ethical evaluation of all IARC projects within its competence (http://ethics.iarc.fr/).

Annex 1. IARC policy on access to human biological materials 69 1.12 Requestor: the requestor is a scientist affiliated with a public research institution or organization based in any country who is applying to access IARC sample collections for the purpose of research. 1.13 User: the user is a requestor who has received the necessary approvals to access IARC samples. 1.14 Material Transfer Agreement (MTA): the MTA is an agreement developed and signed between IARC and the host institute of the requestor, which governs the terms and conditions under which the parties will collaborate. 1.15 Study results: all laboratory results obtained from the use of IARC samples.

A1.2 Sample access: principles and policies

A1.2.1 Introduction

The IARC Biobank (IBB) comprises one of the largest and most varied collections of cancer-related samples in the world. The IBB is publicly funded by IARC Participating States and research grants and hosts more than 50 different studies, led or coordinated by IARC scientists.

Over the years, IARC has developed or coordinated a considerable number of large molecular epidemiological studies involving specimen collections. These studies are extremely diverse in their size, design, and governance and in the type of biomarker analyses involved. Study designs include case series, prevalence studies, case–control studies, and cohort studies. Most of the samples in the IBB are body fluids, including plasma, serum, and urine as well as extracted DNA samples.

A table of biospecimens stored at IARC is available on the IBB website (http://ibb.iarc.fr/docs/collection_table.pdf). The table provides details of sample origin, primary study design, key words describing the collection, and the name of the IARC PI/CU to contact for further information by potential requestors.

The IBB includes, as part of its governance structure, the Biobank Steering Committee (BSC) and the IARC Ethics Committee (IEC). The BSC oversees the IBB and provides advice to the Director in terms of the strategic development of IARC biobank activities. The IEC provides ethical guidance and evaluates all IARC projects within its competence.

A1.2.2 Guiding principles

The mission of IARC includes promoting cancer research internationally. As a publicly funded international organization with a mandate for collaborative research, IARC wishes to ensure that biospecimens stored within the Agency are being put to the best possible use. Within this context, the samples stored at IARC are available for research projects consistent with IARC’s scientific goals and the IARC/WHO legal and ethical standard practices.

The principle of access means that samples and data entrusted to the Agency should be put to best possible scientific use taking into account the best interest of the participants and for public benefit. In particular, IARC PIs and CUs are encouraged to identify new potential uses and users of the resources and to make cancer researchers worldwide aware of these progressions in scientific research.

Access to and use of IBB biological samples are governed by the following principles: • As an overarching principle, the biological samples stored under the Agency’s custodianship in the IBB remain the property of the national collaborating centre as the original source, unless otherwise specified under a separate agreement. Consequently, access to IBB biological samples for third parties will only be granted by IARC after consultation and agreement with the relevant national centre and the IARC PI/CU as applicable. • Applications by requestors for access to IARC’s biological samples will be required to follow the sample request procedure described below. • The confidentiality and data protection principles of IARC also apply to the IBB by maintaining participants’ confidentiality and anonymity; the rights, privacy, and consent of participants must be protected and respected at all times.

70 • IBB biological samples will be made available for use in a timely and responsible manner taking into account the need to ensure data validity and sample integrity. • IBB biological samples can only be used for research and non-profit purposes. • All extensions to the use of human biological material beyond the aims and objectives for which samples were initially collected and provided, subject to the above-mentioned overarching principle, must also be approved by the IEC and be in line with the medium- and long-term objectives of IARC. • To ensure ongoing enrichment of the IARC biological sample collections, users will be required to provide IARC with the results arising from specific analyses (including biological sample analysis, derived variables, etc.) carried out using the data and/or samples provided by the IBB, unless otherwise specified in a previous agreement. • Management for access purposes will be cost-neutral to the IBB; requestors will contribute to the cost of sample retrieval, pre-analytical processing, and shipment according to standard costs published by the IBB. • IARC reserves the right to refuse any request without a necessity to provide justification for decisions made, although appropriate feedback will normally be provided regarding a refusal for access.

A1.3 Limits on the use of IBB biological samples

IBB biological samples can only be used for research and non-profit purposes by investigators affiliated with public sector research organizations. Access may be denied for certain specific reasons, for example: • The available sample volume is insufficient for delivery of samples without compromising the future scientific value of the collection. • The project overlaps with ongoing or planned projects or analyses, leading to unnecessary duplication of work and a waste of materials and other resources. • The scientific quality of the project is considered inadequate. Scientific quality and ability to administer the project will be more specifically considered by the IARC PI/CU and the IEC. The applicant will have to show evidence of expertise, resources, and financing for the successful completion of the project. • There are ethical or legal issues with the proposal, including, for example, when the proposed use is not consistent with the specified purpose of the specimen collection in the original informed consent. • The proposed project is in contradiction with IARC’s mission and goals towards public health or against the above- mentioned guiding principles.

A1.4 Procedure for accessing IARC biological resources and monitoring

A1.4.1 Sample request procedure

Access to IARC biological samples is a six-step procedure, summarized in Fig. A1.1.

Step 1: Requests for accessing IARC biospecimens should be initially directed to the IARC Biobank ([email protected]). The requestor will be required to complete a Project Application Form (CIRC 66 11/2013) and a Partner Profile Form (CIRC 67 11/2013) to provide information on project, requestor, and requesting institute.

Step 2: After review of the Project Application Form and Partner Profile Form, the IARC Biobank submits the request to the IARC PI/CU, to assist in the handling of the request.

Step 3: The IARC PI/CU will carry out an initial review of the request for recommendation to the BSC/BAC. • In the case of multicentre studies with already defined procedures, the IARC PI/CU will contact the steering committee of the study, when there is one in place (e.g. the steering committee for the European Prospective Investigation into Cancer and Nutrition [EPIC] study). The relevant steering committee will review the request according to its established protocol and provide feedback through the IARC PI/CU.

Step 4: Once the request has been approved by the BSC/BAC, or the relevant steering committee when applicable, the requestor is informed. The IARC Ethics Questionnaire must then be submitted to the IEC for ethical approval.

Annex 1. IARC policy on access to human biological materials 71 Fig. A1.1. Sample request procedure. BAC, Biobank Application sub-Committee; BSC, Biobank Steering Commit- tee; CU, IARC custodian; IEC, IARC Ethics Committee; PI, IARC principal investigator.

72 Step 5: Subject to ethical approval by the IEC, a Biobank Request Form (CIRC 68 11/2013) must be completed by the requestor and sent to the IARC Biobank, together with all required supporting documents; these will enable the IARC Biobank to prepare the requested samples and the related MTA (using form CIRC 41 04/2013).

Step 6: Upon receipt of the signed MTA and payment of relevant sample access charges, the IARC Biobank will proceed with shipment of the samples for the project.

A1.4.2 Monitoring and follow-up

In order for the IARC Biobank to monitor use of IARC biological resources, the requestor will be required to submit a Project Progress Report (using form CIRC 69 11/2013) on a 6-monthly basis after samples have been sent.

A1.5 Responsibilities of the requestor/requesting institution

In submitting requests to access IARC biological resources, requestors have the following responsibilities.

A1.5.1 Requesting and receiving

Requestors should: • be affiliated to a recognized academic or other public research organization; • follow the sample request procedure described above, and accept the provisions and general principles contained in the present policy; • pay all sample access charges as invoiced by the IARC Biobank; and • comply with any request to discard sample(s) if notified by IARC that subject(s) have withdrawn permission for the use of donated sample(s).

A1.5.2 During the study

Requestors should: • accept and undertake research in the context of the ownership of samples and data as stipulated in the IARC MTA (CIRC 41 04/2013); • provide plans for publication of the study results in peer-reviewed journals within 1 year of reception of the samples (or provide clear justification for the requirement of a longer period); • report on progress made within the project (using form CIRC 69 11/2013), every 6 months until the study has been completed and remaining samples, if any, have been destroyed or returned to IARC (as is stipulated in the MTA); and • ensure compliance with the terms and conditions of the MTA; users found to be in breach of the MTA will be denied future access to the IARC biological resources.

A1.5.3 At the end of the study

Requestors should: • report on the outcome of the study upon completion, including publications (using form CIRC 69 11/2013); • return any unused samples to IARC, unless otherwise stated in the MTA (CIRC 41 04/2013); and • provide IARC with a copy of the results generated within the project through use of the IARC biological resources (raw data or other relevant format agreed upon with IARC) within 6 months of publication.

A1.6 Acknowledgement in publications

Full acknowledgement of the sources of all biological resources must be included in any publications that arise from access to and use of the IBB resources. All publications must include at a minimum the following acknowledgement: “The research was made possible using the data/samples provided by the IARC Biobank.” In addition, where applicable, the acknowledgements must refer to the original sample source centre as well as the source of funding. Specific authorship rules may apply in some instances; these will be agreed upon on a case-by-case basis.

Annex 1. IARC policy on access to human biological materials 73 A1.7 Reference documents

7.1 IARC Policy on Access to Human Biological Materials (IARC/Access Policy/Group-BSC/EN/11/2013): http://ibb.iarc.fr/docs/iarc-policy-access.pdf 7.2 Project Application Form (CIRC 66 11/2013): http://ibb.iarc.fr/docs/IBB_ProjectForm.dot 7.3 Partner Profile Form (CIRC 67 11/2013): http://ibb.iarc.fr/docs/IBB_PartnerForm.dot 7.4 IARC Ethics Questionnaire: http://ethics.iarc.fr/Submission/index.php 7.5 Biobank Request Form (CIRC 68 11/2013): http://ibb.iarc.fr/docs/IBB_RequestForm.dot 7.6 MTA Form (CIRC 41 04/2013): http://ibb.iarc.fr/access/index.php 7.7 Project Progress Report Form (CIRC 69 11/2013): http://ibb.iarc.fr/docs/IBB_ReportForm.dot

74 annex 2. Guidelines for informed consent

These guidelines are made up of the following three sections: design decisions; guidance for broad consent participant information sheets and consent forms; and links to biobank-specific templates for participant information sheets and consent forms.

A2.1 Design decisions

This section contains useful points to consider when designing participant information sheets and consent forms for biobanks.

A2.1.1 Where do I start?

The templates for participant information sheets and consent forms listed in Section A2.3 are a good place to start to get an idea of the general contents of participant information sheets and consent forms.

A2.1.2 Will I provide the participant information sheet and the consent form as separate documents?

It is common practice to provide these documents separately, and this may be the most practical solution for biobanks in terms of the storage and distribution of these documents. However, in clinical trials that involve biobanking, the two documents are often combined, which ensures that the participant information sheet and the consent form used are stored together.

A2.1.3 Will I require that the participants initial or tick the boxes on the consent form?

It is recommended that biobanks follow best practice in clinical trials, which requires that participants initial the boxes on the consent form. It is worth making this requirement clear on the consent form itself.

Annex 2. Guidelines for informed consent 75 A2.1.4 Will I provide opt-in/opt-out statements on the consent form?

The most critical thing to consider before providing opt-in/opt-out statements is whether the biobank can support this. For example, allowing the participant to opt out of research that involves animals but not being able to enforce this when distributing samples will cause problems for the biobank. The most common problem is that the biobank database does not record the participant’s decisions, resulting in a time-consuming search for the consent form each time a sample is distributed. If opt-in/opt-out statements are provided, add two boxes, marked with “yes” and “no”, to the consent form so that it is clear that these statements are optional. See the information on dynamic consent in Table A2.2 for examples of possible opt-in/opt-out statements.

A2.1.5 Should I consider what might happen to the samples in the future?

It is very important that when the participant information sheets and consent forms are being developed, the biobank should carefully consider the possible future use of the samples and data, so that the biobank can inform the participant at the outset and will not need to re-contact them for further permissions. Some examples of areas to consider are: issues that are potentially ethically or legally challenging, such as transfer of samples or data across national borders or use of samples and data by commercial researchers (see the recommendations in Section 3.1.2.3); return of results and incidental findings (see Section 3.1.4); access to and sharing of samples and data (see Section 3.1.5); when participants might need to be re-contacted; and whether the participants need to receive information or give consent via an interpreter. If an interpreter is needed, lines may need to be added to the consent form to allow the interpreter to sign the form.

A2.2 Guidance for broad consent participant information sheets and consent forms

Table A2.1 provides information on the headings that would be expected on a biobank participant information sheet aiming for a broad consent approach. The optional sections apply only to specific types of biobanks or specific types of research being conducted.

Table A2.1. Sections for inclusion on a biobank participant information sheet, indicating whether these are optional or mandatory; the initial statements or questions can be used as titles in the participant information sheet

Section Mandatory or optional?

Why are human tissues and body fluids vital for research? Mandatory

What is the purpose of the biobank? Mandatory Answering questions such as: • What is the aim of the biobank? • Is the biobank disease-specific? • Is unspecified future research (secondary use) planned?

Who has approved the research? Mandatory

Why am I being invited? Mandatory

What will happen if I agree to participate? Mandatory Answering questions such as: • Is access to medical or other health-related records planned?

Will my samples be used in genetic research? Mandatory

What are the benefits and risks of taking part? Mandatory

Who will have access to my samples and data? Mandatory Answering questions such as: • Can the samples and/or data be transferred to/used by/shared with other researchers/biobanks/institutions? – Is this individual-level/aggregated/genetic data? – Will the samples be shared? • Can the samples and/or data be transferred to/used by/shared with researchers in other countries? • Will the data be included in a public database? • Can the samples be accessed by commercial organizations?

76 Table A2.1. Sections for inclusion on a biobank participant information sheet, indicating whether these are optional or mandatory; the initial statements or questions can be used as titles in the participant information sheet (continued)

Section Mandatory or optional?

How will my samples and data be stored? Mandatory Answering questions such as: • What are the privacy/data protection mechanisms?

How long will my samples and data be stored? Mandatory

Will I find out results of the research? Mandatory Answering questions such as: • Will any results (general or individual) be returned to the participant? • How will any return of results take place? • What options does the participant have?

What if I change my mind? Mandatory Answering questions such as: • What withdrawal options are there? • What happens to samples and/or data after withdrawal?

Contact details for the biobank Mandatory

Will my cells or tissue be used for research involving animals? Optional

Will my cells or tissue be used to create cell lines? Optional

Will my cells or tissue be used for research linked to reproduction? Optional

Can I donate cells or tissues after death? Optional

Will I receive any compensation for being involved? Optional

Detailed explanations about tissue, cells, and DNA: Optional Human cells and tissues DNA and genes How cells and tissue are collected Use of human tissue and fluids for medical education and audit Details for specific types of tissues or donors (e.g. stem cells, healthy donors)

Detailed information about biobank governance Optional Answering questions such as: • What type of committee reviews applications for access to biobank samples and/or data, and who serves on this committee? • What type of contracts must those accessing the biobank samples and/or data complete (e.g. Material Transfer Agreements)? • How is the biobank governed?

Detailed information for postmortem donors Optional

Information about whether samples and/or data are collected from vulnerable persons or populations and how Optional that works Answering questions such as: • Can samples and/or data be used after children participating in the study become adults?

Preferences for re-contact (see Table A2.2) Optional

Table A2.2 provides information on the consent statements that might be expected on a biobank consent form aiming for a broad consent approach. Some of these consent options may be required by the legal system in a particular country, for example the need to gain specific consent to access medical records. In addition, legal requirements may mean that consent is needed to transfer samples or data across national borders if this may occur in the biobank. Opt-in/opt-out statements should be included only when these are recordable, actionable by the biobank, and practicable.

Annex 2. Guidelines for informed consent 77 Table A2.2. Items for consideration on a biobank consent form, including options that may be provided as consent statements and possible opt-in/opt-out statements

Example of statement on consent form (italic means that text Area must be adapted)

The participant confirms that they have read and understood I have read and understood the information pamphlet [version/date]. a particular participant information sheet I have had the opportunity to consider the information it contains and to ask all the questions I had. I have obtained satisfactory answers to my questions.

The participant confirms that they have had the risks and benefits of The risks and benefits of my participation have been explained to me. participation explained to them

The participant understands that participation in the research is I understand that my participation is voluntary. I am free to withdraw voluntary at any time, without giving any reason.

Use of samples and data by commercial researchers I understand that some of these research projects may be carried out by commercial organizations and that I will not benefit financially if this research leads to new treatments or medical tests.

Use of samples for genetic research These samples may be used for genetic research.

Access to medical records I give permission for information about me, provided by me or found in my medical and other health-related records, to be supplied to and stored by [name of biobank] for research purposes. or I give permission for access to my medical and other health- related records, and for long-term storage and use of this and other information about me, for health-related research purposes (even after my incapacity or death).

Contacting general practitioner for information My general practitioner can be contacted for information relevant to my condition and current treatment.

Possible opt-in/opt-out statements (to be used when these are recordable, actionable by the biobank, and practicable)

Re-contacting participants to ask for further information or about We may like to re-contact you in the future to ask for further samples participation in new studies or information that may be of use to researchers, or for further permissions relating to the use of the samples and information you have already donated. I agree that [name of biobank] may re-contact me in the future to ask me to provide additional samples or information related to [name of biobank] or to invite me to participate in a new study. I understand that this does not oblige me to provide the samples or to participate in further research.

Re-contacting participant with information arising from the study These are the areas where permission may be requested, if relevant: The text included here in the consent form will depend on the A. Agreement or opt-in/opt-out to receiving general research project biobank’s policy in relation to return of study results results, for example in the form of a newsletter or email. B. Agreement or opt-in/opt-out to receiving the results of any physical examination conducted as part of the sample or data collection, in which case also briefly explain the circumstances under which this may take place and the mechanisms by which it would be achieved. C. Agreement or opt-in/opt-out to receiving the results of any tests for infectious diseases conducted on the samples. Briefly explain the related circumstances and mechanisms, as in B. D. Agreement or opt-in/opt-out to receiving individual-level research results or other incidental findings arising from the research. Briefly explain the related circumstances and mechanisms, as in B.

Transfer of samples or data across national borders Do you give permission for samples to be sent to centres outside [name of country]?

Experiments involving animals Do you give permission for your samples to be used in experiments using [animal type, e.g. rodents (rats or mice)]?

Creation of cell lines from the tissue These samples may be used to create cell lines.

78 A2.3 Links to biobank-specific templates for participant information sheets and consent forms

The documents and links listed below can be used as reference materials to produce biobank participant information sheets and consent forms.

1. World Health Organization (WHO): • WHO Informed Consent Form Templates: http://www.who.int/rpc/research_ethics/informed_consent/en/ • WHO Informed Consent Form Template for Consent for Storage and Future Use of Unused Samples: http://www.who.int/entity/rpc/research_ethics/Informed%20consent%20for%20sample%20storage.doc?ua=1

2. Public Population Project in Genomics and Society (P3G): • P3G-IPAC Generic Clauses/Agreements Database, to assist researchers in building documents: http://www. p3g.org/resources/ipac • P3G Generic Information Pamphlet and Consent Form (2014): http://www.p3g.org/system/files/biobank_toolkit_ documents/P3G%20Generic%20Info%20Pamphlet%20and%20Consent%20Form%20for%20Biobanks_0.pdf

3. Global Alliance for Genomics and Health (GA4GH): • Consent tools in relation to international data sharing: http://www.p3g.org/sites/default/files/site/default/files/ GA4GH-Consent%20Tools-FINAL%20%281%29.pdf

4. Human Heredity and Health in Africa (H3Africa): • H3Africa Guidelines for Informed Consent (2013), guidance for designing consent materials for genomic research in African contexts: http://h3africa.org/images/FinalPoliciesDocuments/H3A%20WG%20Guidelines%20 Informed%20Consent_FINAL_01082013.pdf

5. Beskow LM, Friedman JY, Hardy NC, Lin L, Weinfurt KP (2010). Developing a simplified consent form for biobanking. PLoS One. 5(10):e13302. http://dx.doi.org/10.1371/journal.pone.0013302

6. Strategic Tissue Repository Alliances Through Unified Methods (STRATUM) project: • Consent Models Work Package tools, including a two-page combined participant information sheet and consent form template and an in-depth biobank participant information sheet template: http://stratumbiobanking.org/ consent.html

7. UK Biobank: • Consent form: http://www.ukbiobank.ac.uk/wp-content/uploads/2011/06/Consent_form.pdf • Participant information sheet: http://www.ukbiobank.ac.uk/wp-content/uploads/2011/06/Participant_information_ leaflet.pdf?phpMyAdmin=trmKQlYdjjnQIgJ%2CfAzikMhEnx6

8. Children’s Cancer and Leukaemia Group (CCLG): • Information sheets for involving children in biobank research: http://www.cclg.org.uk/tissue-bank/information- for-patients

Annex 2. Guidelines for informed consent 79 annex 3. Template consent form for biobanking

This template is based on Public Population Project in Genomics and Society (P3G) database resources.

General considerations

• The information brochure and consent form should be clear, in plain language, easy to read, and written in large fonts (size may vary according to the target population). The date of the version of the form should be identified in the footer, and pages should be numbered “Page x of y”. In the information pamphlet, the term “you” should be used to refer to potential participants. In the consent form, the term “I” should be used. • Researchers should follow a culturally sensitive process of providing information to obtain participants’ consent. In particular, in some communities, obtaining the agreement of local community leadership for the proposed research is mandatory and this agreement should be sought before the preparation of consent forms and before obtaining the consent of any participant from that community. In addition, the degree of autonomy that individuals have may vary between cultures. In preparing for the consent process, the researcher must therefore consider applicable norms and traditions. • Other considerations may be specific to certain populations (e.g. research involving children, vulnerable populations), and additional requirements may apply to the consent process. Researchers should ensure that all such specific requirements are taken into account when preparing consent materials.

The following text presents generic template language in the preparation of biobanking consent forms for adult participants (italic means that text must be adapted).

80 [Insert logo and letterhead of biobank]

INFORMATION PAMPHLET AND CONSENT FORM FOR PARTICIPANTS [Name of biobank/Title of study]

[Name of Principal Investigator] [Name of organization] [Names of funders and sponsors] [Contact information]

Preamble

We are inviting you to take part in the creation of a resource for research called [identify biobank/title of study]. Your participation is voluntary. Before you decide whether or not to participate and sign the consent form, please take your time to read this information pamphlet. This document may contain information or words that you do not understand. Please ask us if there is something you do not understand, or if you would like more information. It is important that you fully comprehend what participation in this project entails.

1. Nature and objectives of the study

[Describe the study purpose, in addition to the current and future scope of research.]

The [identify biobank/title of study] is a resource that contains biological materials, such as DNA samples, in addition to health/lifestyle information and personal information (data) on a large number of people over time. It has been set up so that it can be used in the future as a resource for researchers undertaking a wide range of medical research.

Optional clauses - If applicable, provide specific information as to “large number of people involved”; - If applicable, specify types of future “medical research” (e.g. specific disease/research area).

This [biobank/study] has two main aims. The first aim is to gain a better understanding of the interactions between genes, the environment, and our lifestyle that influence our health or cause diseases. The second aim is to use this understanding to develop new drugs, genetic tests, and treatments, and to create public health strategies that will benefit everyone.

Your participation in this project involves you giving broad consent. This means that you allow your personal information and samples to be used for a variety of future medical research approved by an ethics committee, but which cannot be specified at the present time.

Optional clauses - If applicable, specify types of medical research that will use the biobank (e.g. specific disease/ research area). If other types of research are indicated, add: “Some future types of research may require your specific consent.” - If data linkage is planned, add: “Your personal data will have to be regularly updated by being linked to your medical record and other sources of administrative health information. If, after reading this information pamphlet, you do not agree to any of these aspects, you should not take part.”

Annex 3. Template consent form for biobanking 81 2. Prospective participants

[Outline the total number of expected participants, and explain why the individual was selected to participate.]

The [biobank/study] involves the participation of [number] people between [age] and [age] years of age from [region].

You have been chosen from [identify database, registry, etc.] to be invited to participate.

Optional clauses - If applicable, specify targeted disease or specific illness. - If applicable, add: “You are being asked to participate because you are a patient at [name of hospital/ institution]” or “You have been identified by your personal doctor as someone who is in the correct age bracket and meets the relevant criteria to participate.”

However, please note that you should not participate if [enumerate exclusion criteria].

3. Researchers and institutions conducting the study

[This section should also disclose any conflicts of interest.]

The [biobank/study] is a research effort led by [identify institution(s)]. This institution is responsible for the practical aspects, such as data collection and secure storage of samples and data. It will be the point of contact for you, and for the researchers who use the biobank. The person who has overall responsibility for the management of the biobank is [name of executive director]. If you need to contact the biobank for any reason, please telephone [name] at [telephone number], email [email address], or write to [mailing address].

The [biobank/study] is supported by [identify institution(s)] and is funded by [name(s) of sponsor(s)/government agency]. The [name of study] has received approval from [name of research ethics committee].

4. What does participation involve?

[Outline study procedures; what participants are expected to do throughout the course of the study; include types of information being gathered (samples and data); amount of information being gathered; tests to be performed (manner of acquiring samples); questionnaires; length of time; location, etc.]

If you choose to participate, you will be asked to:

(1) Undergo a physical assessment, which involves you: • attending an appointment at [insert location], which will last approximately [insert duration of appointment]; • providing a [insert sample type (e.g. blood, urine, saliva)] sample of [insert amount/measures of samples taken], which the biobank will store; • answering a questionnaire on [insert topics (e.g. your health and lifestyle, family, and medical history)] that will take approximately [insert length of time]; and • allowing our staff members to perform basic measurements, including [insert measurement types (e.g. measuring your weight, height, and blood pressure)].

The physical assessment will be conducted by [qualified health professionals (e.g. nurses, physicians)]. In total, it should take approximately [insert duration of entire assessment].

(2) Allow your samples and data to be stored and used in coded form by researchers for many years [if applicable, specify length of time].

82 Optional clauses - If applicable, add: “Allow your personal information contained in your administrative health records to be accessed now and in the future.” - If applicable, add: “We may continue to access these records even if you become unable to make decisions for yourself or after your death.”

5. Study risks

[List possible disadvantages or risks (e.g. discomfort, malaise, stress, transportation costs, time).]

Your participation entails few risks. The physical assessment involves little risk. The taking of a blood sample for DNA analysis may cause some bleeding, bruising, dizziness, and/or discomfort. You should be aware that certain physical measurements that will be taken [e.g. your weight] and/or some of the questions you will be asked in the questionnaire may be personal in nature. The storage of your samples and the extraction of DNA involve minimal risk, because rigorous security measures are in place (as described below) and all samples will be kept in a high-security facility.

Unless required by law or a court order, access to this information will not be offered to third parties such as employers, insurance companies, or family members. Only authorized staff members will have access to your information. For requests for access by researchers, they will not be given any information that would allow them to identify you. The utmost care will be taken to ensure the confidentiality of all data.

6. Potential study benefits

You will not directly benefit by taking part in this study, because the most important health benefits will be realized many years from now. Rather, your participation will contribute to the advancement of scientific knowledge and help future generations, because your participation is expected to improve our understanding of genetic and non-genetic factors that affect the health of the population.

However, any immediate, life-threatening condition will be reported to you immediately so that you can obtain emergency care.

7. Privacy and confidentiality

[Specify who will have access to the participants’ personal information and the types of information.]

The information in your file could include your past and present medical history, in addition to information about your life and test results from examinations and procedures done during this study. Your file could also contain information such as your name, sex, date of birth, and ethnic origin.

All information collected about you will remain confidential. No one will have access to your directly identifying information, that is information that identifies you through specific identifiers such as your name, your social insurance number, and your personal health number.

To protect your privacy, your information will be coded. “Coded” means that your information has been stripped of any direct or indirect identifiers, which are replaced by a numerical code. A list that links the coded information with your identity will be kept secure, to allow for your re-identification in certain circumstances. Your unique code will enable us to link the information from different data sets to you, but at the same time, will enable us to keep your identity confidential when we give your data to other researchers to use.

While study information could be printed in journals or shared with other people at scientific meetings or for teaching purposes, it will not be possible to identify you. Your identity will be kept confidential. All data will be presented as group data, rather than individual data.

Annex 3. Template consent form for biobanking 83 Also, specific rules regulate access to your data and samples by researchers. Researchers will not have access to any of your personal information.

8. Access to your data and samples

Only approved research studies can gain access to your coded data and samples, in order to protect your privacy. An approved researcher can be from [outline the approved users as per access policy (e.g. academia, a charitable organization, a private company, or a public institution)]. All projects must be approved by the [identify the access committee], who will essentially review whether the proposed study has received prior scientific and ethical approval by the relevant committees, and that the study fits within the purpose of the biobank and meets other general requirements.

Researchers have to sign agreements that control their access to data and samples, and they are not permitted to disclose or transfer data or samples to anyone else or to use them for purposes other than those agreed to. Researchers must also agree that they will not attempt to re-identify you from your data and samples and should immediately report any re-identification of participants to the biobank.

We also expect to receive access requests from overseas researchers and international collaborators. These researchers must follow the same procedures as all other researchers. All access is subject to the strictest scientific and ethical scrutiny, as described above.

When transferred samples are no longer needed for the purpose for which they were given to researchers, researchers must [return them to the biobank or destroy them]. Researchers must also return their research results to the biobank, so that those results are available for other researchers to use in the future. This facilitates future research and enriches the database of the [name of biobank].

9. Storage of your data and samples

[Specify where the data and samples will be stored (location) and how long they will be stored.]

Your data and samples will be stored in a database at [name of institution/hospital and location]. This is a secure facility, meeting international security and safety standards for laboratories. Also, in order to keep your information confidential, numerous safeguards are in place. In particular, we will: • remove personal identifiers such as your name or date of birth from your samples and records; • assign codes to your samples and records; • keep your personal details separate from your data and samples; • use stringent security measures to prevent unauthorized use, including strict access controls, computer security and data encryption techniques, confidentiality agreements, and staff training; • hold information in secure databases, which can be accessed only by the authorized staff members and by approved researchers, who will only have access to coded information; and • have a decoding step that will allow us to re-link your personal details with your samples and information, should you want to withdraw from the study or in order to make sure that the database records are correct.

Your samples and data will be kept for a period of [identify period of conservation (e.g. number of years)]. After this period, your samples and data will be [destroyed or transferred], unless an ethics committee decides otherwise.

Optional clause If samples and data are transferred at the end of the period of conservation, specify where the data and samples will be transferred [name of biobank].

84 10. Withdrawing from the study

[Indicate treatment (planned use and storage procedures) of already collected data/samples.]

You may choose whether or not you wish to take part in this study. If you choose to take part now, you can change your mind later and withdraw, meaning stop participating at any time and for any reason.

You can withdraw by [indicate ways for participant to signal their withdrawal (e.g. by telephone, by email, by mail, and whom to contact)]. You will receive a letter confirming your withdrawal.

If you withdraw, your identifiable samples and the data derived from your samples and other personal information will be destroyed if possible. Data that are already being used for research cannot be destroyed or removed.

The code that enables us to re-link your samples and personal information will be deleted so that no further information about you will be collected. Only your signed consent form and a copy of the letter confirming your withdrawal will be kept as a record of your wishes. Such a withdrawal will prevent information about you from contributing to further research and analyses.

11. Return of research results

[Outline the biobank’s policy as to returning results, including the results from the laboratory assessment and physical assessment, general research results, individual research results, and incidental findings. If the biobank’s policy is to return individual results, indicate who has the obligation of returning these results and for how long.]

(a) Results from laboratory assessment and initial physical assessment

You can choose to immediately receive the results of your physical assessment, such as [specify results that can be returned], from your [type of assessment (e.g. BMI, ECG, blood pressure)]. These results will be provided with the appropriate explanations (e.g. your measurements alongside “standard measures”). You can decide whether you want these measurements sent to you or not.* If, during the physical assessment, we find something that we feel should be explored further, we will advise you to see your personal doctor, because the assessment is not a clinical check-up.

Optional clause * If applicable, add: “You can ask that they be sent to your personal doctor.”

(b) General research results

General research results, meaning aggregate results derived from the analysis of the data and samples of research participants, will also be made available to participants, researchers, and any other people who might be interested through [state format (e.g. website, newsletter)]. This is done to make data more readily available to researchers and encourage medical advances. Such data will not have any identifiers that will enable anyone to link the data to you. You can access these results through the biobank [specify how/where participants can find these results].

Individual research results are results discovered during the course of research that concern you and have potential health or reproductive consequences.

Incidental findings are unforeseen findings about you that have potential health or reproductive consequences. Although they were discovered during the course of research, they are outside of the study objectives.

Annex 3. Template consent form for biobanking 85 Alternative clauses Alternative clause 1: “We will not return any individual research results or incidental findings to you”; or Alternative clause 2: “With your consent, we will return individual research results or incidental findings to you when they are scientifically valid, they are clinically significant, and there is a recognized therapeutic or preventive measure or way of changing the clinical course of the disease or condition. These results will be returned to you by [e.g. the Principal Investigator, a qualified health professional] for a period of [number of years]. After this period, the biobank will no longer return individual research results to you.”

12. Re-contact

With your permission, we may re-contact you to invite you to update your questionnaire or to provide additional samples or to be involved in new research projects by other researchers that could require additional physical assessments, tests, and questions.

13. Compensation

[Include travel expenses and the procedure for reimbursement.]

Alternative clauses - If compensation is not offered, add: “Your participation is on a voluntary basis. You will not be compensated for your participation.” - If compensation is offered, add: “Your participation is on a voluntary basis. However, as compensation you will receive [specific amount] for [type of visit (e.g. a visit to the clinic or a home visit], travel expenses, and other inconveniences related to your participation.”

14. Possible commercialization

[Explain the potential uses of data and samples, including the development of intellectual property and commercial uses.]

[Identify biobank or specific committee] has been set up as the [guardian/owner/custodian] of the database and sample collection. The use of your data and samples might someday lead to the commercialization of a medical or genetic test or product. This may be done by a university or hospital, a commercial company, or both working in partnership. This means that researchers, including, potentially, commercial companies, may benefit financially. You will not derive any personal financial advantage from this commercialization.

15. Closure of the biobank

[Explain what will happen upon the closure of the biobank, whether the closure is scheduled or unplanned.]

If the [name of biobank] were to close for whatever reason, [see Alternative clauses].

Alternative clauses Alternative clause 1: “all of the research results and information will be put into an archive that will be overseen by the [identify committee]”; Alternative clause 2: “all of the samples and data will be destroyed”; or Alternative clause 3: “all of the samples and data will be transferred to [identify existing biobank]”.

86 16. Your questions or concerns

If you have any questions or concerns, please contact [insert name of person] free of charge at [insert telephone number] or by mail/email at [insert mailing address and/or email address].

If you wish to make a complaint about any aspect of this study at any time, please contact [insert name of person] free of charge at [insert telephone number] or by mail/email at [insert mailing address and/or email address]. We take all comments seriously and will get back to you as soon as possible.

Thank you for considering taking part in this study!

Annex 3. Template consent form for biobanking 87 [Insert logo and letterhead of biobank]

PARTICIPANT CONSENT FORM [Name of biobank/Title of study]

Name of biobank: [insert name of biobank] Investigator(s): [insert name(s) of investigator(s)] Sponsor(s): [insert name(s) of sponsor(s)]

The goal of the [biobank/study] is [provide a brief summary of goal].

BY SIGNING THIS CONSENT FORM, I AGREE TO PARTICIPATE IN THE [BIOBANK/STUDY] AND DECLARE THAT:

 I have read and understood the information pamphlet [version/date]. I have had the opportunity to consider the information it contains and to ask all the questions I had. I have obtained satisfactory answers to my questions.

 The risks and benefits of my participation have been explained to me.

 I understand that my participation is voluntary. I am free to withdraw at any time, without giving any reason. This can be done by contacting [insert name] at [insert telephone number, email address, and/or mailing address]. I will receive a letter confirming my withdrawal.

 I understand that I will not receive any personal financial benefit from any possible commercialization of a test or product developed by using my data and samples.

 I understand that my participation does not entail any direct personal benefit. However, any immediate, life- threatening condition will be reported to me immediately so that I can obtain emergency care.

 I understand that upon closure of the biobank, my data and samples will be [specify policy for closure: archived, destroyed, or transferred to another biobank].

 I understand that unless access is required by law, only approved researchers will have access to my coded data and samples. Access is subject to ethics approval and oversight.

 I understand that general research results, meaning aggregate results, will be made available to participants, researchers, and other people who might be interested through [specify format (e.g. website, newsletter)] in order to make data more readily available and encourage medical advances.

I AGREE TO:

 Undergo a physical assessment, including: • attending an appointment at [insert location], which will last approximately [insert duration of appointment]; • providing a [insert sample type (e.g. blood, urine, saliva)] sample of [insert amount/measures of samples taken], which the biobank will store; • answering a questionnaire about [insert topics (e.g. my health and lifestyle, family, and medical history)]; and • allowing staff members to perform basic clinical measurements, including [insert measurement types (e.g. measuring my weight, height, and blood pressure)].

 Allow my coded data and samples of [insert sample type (e.g. blood, cells, DNA, urine, saliva)] to be used for various research purposes approved by the relevant research ethics committee.

88 Optional clause If specific disease/research area: “Allow my coded data and samples of [insert sample type (e.g. blood, cells, DNA, urine, saliva)] to be used for [specify disease/research area] approved by the relevant ethics committee. My approval will be required for other types of research.”

 Have my data and samples stored at [specify storage location] for [specify period of conservation]. All data and samples will be kept in a secure facility overseen by [insert name of individual or committee].

 Allow my data contained in administrative health records to be examined now and in the future. My records and samples will continue to be accessed even if I become unable to make decisions for myself or if I die.

Alternative clause If applicable: “Allow my data contained in administrative health records to be examined now and in the future. If I die, my records and samples will no longer be used.”

RETURN OF RESULTS

(a) Results from laboratory assessment and initial physical assessment

Optional clauses  I wish to receive the measurements or other results taken during the physical assessment and laboratory tests. YES £ NO £ [OR]  I wish to have the measurements or other results taken during the physical assessment and laboratory tests sent to my doctor. YES £ NO £

(b) Individual research results and incidental findings

Alternative clauses Alternative 1:  I understand that I will not receive any individual research results or incidental findings. Alternative 2:  I agree to have individual research results and incidental findings returned to me when these results are scientifically valid, have clinical significance, and are actionable (there is a recognized therapeutic or preventive measure or way of changing the clinical course of the disease or condition). YES £ NO £

RE-CONTACT

 I agree to be re-contacted by [identify biobank/study] to update my data (questionnaires or physical measures) or to provide additional data/samples. .YES £ NO £

 I agree to be re-contacted by [identify biobank/study] to participate in new research projects conducted by other researchers that could require additional physical assessments, tests, questions, or samples. .YES £ NO £

Annex 3. Template consent form for biobanking 89 CONFIRMATION BY INVESTIGATOR OR HIS/HER DESIGNEE

I described the [identify biobank/study], including the conditions of participation, to the participant. I explained the contents of the information pamphlet and consent form to the participant. Any questions were answered. I explained that participation was voluntary.

Investigator/Designee name...... Signed ...... Date......

Optional clause TRANSLATOR INFORMATION (if applicable) I was present during the meeting between [name of investigator/designee] and the participant. I translated, for the participant, the consent form and all information presented regarding the research project.

Translator name...... Signed ...... Date......

PARTICIPANT INFORMATION

I AGREE TO PARTICIPATE IN [BIOBANK/STUDY] AND WILL RECEIVE A COPY OF THIS CONSENT FORM AFTER I SIGN IT.

Name......

Signed...... Date......

THANK YOU FOR PARTICIPATING! FOR MORE INFORMATION, PLEASE CONTACT: [insert website, name of person to contact, telephone number, email address].

To file a complaint regarding your participation, please contact: [insert name of person to contact, telephone number, email address, and mailing address].

90 annex 4. Template Material/Data Transfer Agreement (MTA /DTA)

This template is based on the IARC MTA template. The text presents generic template language (italic means that text must be adapted).

[Insert logo of Providing Institute]

MATERIAL AND DATA TRANSFER AGREEMENT – MTA/DTA

MTA/DTA Reference Number: [to be provided by [insert name of Providing Institute]]

Subject to the terms and conditions of this Agreement, the [insert name of Providing Institute] hereby agrees to provide, and the Receiving Institute hereby agrees to accept, the Materials and Information specified below for such Purposes of Use and subject to such Restrictions on Use as specified below.

In this Agreement, the following expressions shall have the following meanings:

1. “Providing Institute”: [Insert name and full address of Providing Institute]

Contact: [insert name and contact details (including email address) of Providing Institute’s Principal Investigator]

2. “Receiving Institute”: [Insert name and full address of Receiving Institute]

Contact: [insert name and contact details (including email address) of Receiving Institute’s Principal Investigator]

Annex 4. Template Material/Data Transfer Agreement (MTA/DTA) 91 3. “Materials”: [Insert precise description of Materials], held by [insert name of Providing Institute], and made available to the Receiving Institute hereunder in a quantity of [insert quantity to be provided by Providing Institute].

4. “Information”: Any information, unpublished or otherwise, owned by [insert name of Providing Institute] and communicated to the Receiving Institute by [insert name of Providing Institute] during the term of this Agreement relating to the Materials, their production, properties, and/or experimental results observed using the Materials or any derivatives therefrom.

5. “Purposes of Use”: The Materials and Information are provided for the following purposes, as more fully described in Appendix 2 (the “Research Project”): [Insert a brief description of the purposes for which the Materials, and products incorporating or developed with the Materials, may be used.] [Add reference to a specific grant, etc. when appropriate.]

6. “Restrictions on Use”: The Materials and Information shall not be used for any purpose other than the Purposes of Use. In particular, the Materials and Information shall not be used for [insert any specific restrictions on use].

7. “Term of Agreement”: This Agreement shall remain in full force and effect as from the date of its signature by both parties for a duration of [specify duration/may be based on project duration].

8. “Materials Charges”:

PLEASE KEEP THE APPLICABLE CLAUSE (1) AND DELETE THE REST.

8.1 As per price list The cost of sample retrieval, processing – including DNA extraction – packaging, and shipment will be charged by [insert name of Providing Institute] to the Receiving Institute at the latest rate [indicate where rate will be made available for informational purposes]. or

8.1 As per agreed unit price The cost of sample retrieval, processing – including DNA extraction – packaging, and shipment will be charged by [insert name of Providing Institute] to the Receiving Institute at the following agreed rate: [list unit price]. or

8.1 Lump sum amount The cost of sample retrieval, processing – including DNA extraction – packaging, and shipment will be charged by [insert name of Providing Institute] to the Receiving Institute for the total lump sum amount of [amount and currency in words]. or

8.1 Free of charge The sample retrieval, processing – including DNA extraction – packaging, and shipment will be provided free of charge.

92 9. “General Conditions”: The General Conditions attached hereto under Appendix 1 form an integral part of this Agreement.

This Agreement is duly signed on behalf of the parties as follows:

Signed for and on behalf of [Providing Institute]:. Signed for and on behalf of Receiving Institute:

[Providing Institute] Responsible Scientist Receiving Institute Responsible Scientist

Name ...... Name ......

Title ...... Title ......

[Providing Institute] Authorized Official Receiving Institute Authorized Official

Name ...... Name ......

Title ...... Title ......

Date ...... Date ......

Annex 4. Template Material/Data Transfer Agreement (MTA/DTA) 93 APPENDIX 1 – GENERAL CONDITIONS

1. Use

1.1 The Materials and Information are supplied by [insert name of Providing Institute] to the Receiving Institute solely for the Purposes of Use and subject to the Restrictions on Use as set out herein.

1.2 The Materials and Information shall not be used in human subjects, in clinical trials, or for diagnostic purposes involving human subjects without the written consent of [insert name of Providing Institute].

1.3 Other than for and within the Purposes of Use, and as specifically described in Appendix 2, the Materials and Information shall not be transferred, offered for sale, or otherwise used without the prior written agreement of [insert name of Providing Institute].

1.4 The Receiving Institute shall allow only parties who have a need to know for the Purposes of Use and who are bound by similar obligations of confidentiality and Restrictions on Use as contained in this Agreement to have access to the Materials and Information.

1.5 The Receiving Institute shall require any party handling and/or using the Materials and Information to comply with all relevant laws, rules, and regulations applicable to the use of such Materials and Information.

2. Confidentiality

2.1 The Information may incorporate confidential information of [insert name of Providing Institute]. Accordingly, if and to the extent that any such Information is clearly marked as “confidential”, the Receiving Institute shall during the Term of this Agreement and for a period of [insert number of years] years following its termination treat such Information as confidential and only disclose it under like obligations of confidentiality and Restrictions on Use as those contained herein. The Receiving Institute shall be deemed to have fulfilled its obligations if it exercises at least the same degree of care in maintaining confidentiality as it would in protecting its own confidential information.

2.2 The above-mentioned obligations of confidentiality shall not apply to Information which: (i) can be shown to have been known to the Receiving Institute at the time of its acquisition from [insert name of Providing Institute]; or (ii) is acquired from a third party, not in breach of any confidentiality obligation to [insert name of Providing Institute]; or (iii) is independently devised or arrived at by, on behalf of, or for the Receiving Institute without access to the Information; or (iv) enters the public domain otherwise than by breach of the undertakings set out in this Agreement.

2.3 In some cases, the Information may also incorporate confidential information pertaining to research participants having provided the Materials. The Materials provided to the Receiving Institute have been [coded or anonymized (provide description of data treatment here)]. If the Receiving Institute inadvertently receives information that identifies individual research participants, the Receiving Institute will take all reasonable and appropriate steps to protect the privacy and confidentiality of such information. This may require immediate destruction of the information on request of [insert name of Providing Institute]. The Receiving Institute agrees to make no intentional attempt to re-identify research participants through linkage of data or otherwise. The Receiving Institute will immediately report any identification of research participants to [insert name of Providing Institute].

3. Rights

3.1 Except for the rights explicitly granted hereunder, nothing contained in this Agreement shall be construed as conveying any rights under any patents or other intellectual property which either party may have or may hereafter obtain.

94 3.2 [Insert name of Providing Institute] shall retain ownership of the Materials and Information and shall have the unrestricted right to use, assign, or distribute the Materials and Information to any third parties for any other purposes. The Receiving Institute acknowledges and agrees that nothing contained in this Agreement shall be deemed to grant to the Receiving Institute any intellectual property rights in any of the Materials or Information provided hereunder.

3.3 The Receiving Institute must not make intellectual property claims on Materials or Information derived directly from [insert name of Providing Institute]. However, the importance of downstream inventions made with [insert name of Providing Institute] Materials is recognized; patents on such inventions are permitted. In doing so, the Receiving Institute agrees to implement licensing policies that will not obstruct further research. The Receiving Institute will own all results, data, and inventions which arise under the Research Project described in Appendix 2.

OPTIONAL ADDITIONAL CLAUSE: The Receiving Institute does, however, grant to [insert name of Providing Institute] a perpetual, non-cancellable, royalty-free, worldwide license, with right to sublicense, to use study results for all purposes.

4. Return of Individual-Level Results

OPTIONAL CLAUSES:

4.1 No return of individual-level results: Individual Research Results and Incidental Findings will not be returned to [insert name of Providing Institute]. or

4.1 Return of individual-level results: Participants in [insert name of Providing Institute] have consented to the return of Individual Research Results and Incidental Findings that are clinically significant, analytically valid, and actionable (i.e. treatable or preventable). If in the course of their research the Receiving Institute comes across such findings, they must be returned to the [insert name of Providing Institute].

5. Publications

5.1 Upon completion of the Research Project, the Receiving Institute will send to [insert name of Providing Institute] [specify: reports, enriched data, etc.]. The Receiving Institute must endeavour to publish results in an academic journal or in an open access database. The Receiving Institute agrees to acknowledge [insert name of Providing Institute] in any publication or presentation on work derived in whole or in part from the Materials and to supply [insert name of Providing Institute] with a copy or web address of any publication.

6. Warranties and Liabilities

6.1 [ Insert name of Providing Institute] makes no warranty of the fitness of the Materials for any particular purpose or any other warranty, either express or implied. However, to the best of [insert name of Providing Institute]’s knowledge, the use of the Materials and/or Information within the Purposes of Use shall not infringe on the proprietary rights of any third party.

6.2 [ Insert name of Providing Institute] will not be liable for damages related to the provision of Materials to the Receiving Institute. This includes but is not limited to damages in relation to inaccuracies, lack of comprehensiveness, or use of the Information and Materials and/or Information, or any delay or break in supply by [insert name of Providing Institute]. The Receiving Institute acknowledges that [insert name of Providing Institute] makes no guarantee that the Materials and/or Information are free of contamination from viruses, latent viral genomes, or other infectious agents. The Receiving Institute agrees to treat the Materials as if they were not free from contamination, to ensure that appropriate biosafety training is provided to research personnel, and to implement appropriate biohazard containment measures.

Annex 4. Template Material/Data Transfer Agreement (MTA/DTA) 95 6.3 The Receiving Institute agrees that, except as may explicitly be provided in this Agreement, [insert name of Providing Institute] has no control over the use that is made of the Materials or the Information by the Receiving Institute in accordance with the terms of this Agreement. Consequently, the Receiving Institute agrees that [insert name of Providing Institute] shall not be liable for such use.

7. Amendment, Extension, and Termination

7.1 Any amendment to this Agreement, including extension of the Term of Agreement, shall be valid only by written amendment executed by the duly authorized officers of both parties.

7.2 Notwithstanding the conditions set forth in this Agreement, in particular the Purposes of Use, Restrictions on Use, and Confidentiality obligations, either party may terminate this Agreement with sixty (60) days prior written notice to the other party.

7.3 When the Research Project is completed or this Agreement is terminated, whichever comes first, any unused Materials will either be destroyed in compliance with all applicable statutes and regulations or will be returned to [insert name of Providing Institute] by the Receiving Institute upon [insert name of Providing Institute]’s request.

8. Miscellaneous

8.1 Nothing in this Agreement shall be interpreted as establishing a partnership between the parties or establishing one party as the agent of the other or conferring a right on one party to bind the other, except as may be specifically set out herein.

8.2 Any dispute relating to the interpretation or application of this Agreement shall, unless amicably settled, be subject to conciliation. In the event of failure of the latter, the dispute shall be settled by arbitration. The arbitration shall be conducted in accordance with the modalities to be agreed upon by the parties or, in the absence of agreement, with the rules of arbitration of the International Chamber of Commerce. The parties shall accept the arbitral award as final.

8.3 This Agreement sets forth the entire understanding between the parties and supersedes any prior agreements, written or verbal.

APPENDIX 2 – RESEARCH PROJECT

[Provide description of project/work to be performed using the Materials and/or Information.]

96 annex 5. Biobank, collection, study, and sample minimum data set and associated standards

Table A5.1 lists the minimum data set, which reduces the heterogeneity of sample-associated data and thus improves its quality. Such standardization enables biobanks to share samples in large studies and for research that requires samples from different sources.

Table A5.1. Minimum data set and associated standard available in BRISQ, SPREC, and MIABIS

Type of data set Data field Explanation of data field BRISQ Tier 1 SPREC MIABIS

Collection or study or biobank ID The unique ID or acronym of NA NA Text value the study

Study or biobank Acronym Short name NA NA Text

Collection or study or biobank Name Name of the study in English NA NA Text

Collection or study or biobank Description Description of the study aim; NA NA Text recommendation maximum, 2000 characters

Study Principal Name of the person responsible NA NA Text investigator for the study (e.g. the principal investigator) Collection or study Sex Sex of individuals can be one NA NA One or more values or more values Collection or study Age low Age of youngest donor NA NA Number

Collection or study Age high Age of oldest donor NA NA Number

Collection or study Age unit Unit of age NA NA Value can be in years, months, weeks, or days

Annex 5. Biobank, collection, study, and sample minimum data set and associated standards 97 Table A5.1. Minimum data set and associated standard available in BRISQ, SPREC, and MIABIS (continued)

Type of data set Data field Explanation of data field BRISQ Tier 1 SPREC MIABIS

Collection or study Data categories Type of data that is associated NA NA List of Yes/No with the collection or study values; also including whether biological samples are collected Collection or study Material type Can be several values defining NA NA List of fluid or solid type of specimen NCI definitions Collection Storage — NA NA List of value ranges temperature Collection Collection type The type of collection; can have NA NA List of collection several values types: case–control, cohort, longitudinal, etc. Collection Disease Main disease of interest; can NA NA Five subfields: be more than one ontology, ontology version, ontology code, ontology description, and free text Collection or study or biobank Contact Contact information for the NA NA Eight subfields for information contact person contact name and contact information (telephone, email, and address)

Study Study design Design of the study NA NA List of collection types: case–control, cohort, longitudinal, etc. Study Total number of Number of participants NA NA Number participants recruited Study Total number of Number of participants who NA NA Number sample donors provided samples Study Inclusion criteria Parameters to determine type NA NA List of values of donor Biobank Biobank URL Internet address of the biobank NA NA http address

Biobank Biobank juristic Person or entity legally NA NA Text value with name person responsible of juristic person Biobank Biobank country Country of the biobank NA NA ISO standard letter code Sample Sample ID Unique ID or acronym of the NA NA Text identifier or study barcode Sample Parent sample ID Specimen from which the NA NA Text identifier or sample was derived; only for barcode aliquots or derivatives Sample Type of sample Biological definition of the Called Value list; Called “material sample “biospecimen different list and type”; list of fluid or type”; solid codes for solid solid NCI definitions tissue, whole and liquid blood, serum, cells, etc.

Sample Type of primary How the specimen was Called “type of Value list; for NA container collected stabilization”; solids, the field for fluids, is called “type analogous to of collection” SPREC, but for and the values solids, SPREC are different calls this field “type of collection”

98 Table A5.1. Minimum data set and associated standard available in BRISQ, SPREC, and MIABIS (continued)

Type of data set Data field Explanation of data field BRISQ Tier 1 SPREC MIABIS

Sample Pre-centrifugation Time between collection and NA Value list NA delay processing in hours

Sample Centrifugation Centrifugation speed (in g) and NA Value list NA temperature

Sample Second Centrifugation speed (in g) and NA Value list NA centrifugation temperature

Sample Post-centrifugation Time between centrifugation NA Value list NA delay and storage in hours Sample Long-term Container and temperature NA Value list Called “storage storage temperature”; uses SPREC values and has additional value

LN2 Sample Type of collection Biopsy, surgical, FNA, etc. Called Value list NA “collection mechanism” Sample Warm ischaemia Ranges in minutes NA Value list NA time Sample Cold ischaemia Ranges in minutes NA Value list NA time Sample Fixation type OCT compound, RNAlater, etc. Called “consti- Value list; in NA tution and SPREC, only concentration refers to solid of preserva- samples tive”; indicates formulations to maintain a non- reactive state, but in BRISQ, also refers to fluid samples Sample Fixation time Value ranges mostly in hours NA Value list NA

Sample Long-term Type of preservation Can include Called “long- NA preservation formalin term storage”, fixation, combining freezing, and this value and indication of the values temperature of “storage temperature” in a single value list Sample Storage Temperature A temperature Called “long- NA temperature or range term storage”, combining this value and the values of “storage temperature” in a single value list Sample Sampled time Time of sampling NA NA The time when the sample was taken Sample Anatomical site The part of the body from which Organ of origin NA Five values: name, the sample was taken or site of blood version of ontology, draw anatomical code, description, and free text Sample Biospecimen For tissue, the pathological Normal, NA NA disease status status of the specific sample diseased, normal adjacent

Annex 5. Biobank, collection, study, and sample minimum data set and associated standards 99 Table A5.1. Minimum data set and associated standard available in BRISQ, SPREC, and MIABIS (continued)

Type of data set Data field Explanation of data field BRISQ Tier 1 SPREC MIABIS

Sample Clinical — Available NA NA characteristics medical information Sample Vital status — Alive or NA NA deceased Sample Clinical diagnosis Clinical information Clinical NA NA evaluation based on anamnesis and physical examination Sample Pathological Pathological information Macroscopic NA NA diagnosis and microscopic pathological evaluation Sample Collection How the sample was taken; FNA, pre- NA NA mechanism helps define also whether operative blood before or after treatment draw, etc. Sample Storage duration Field recording the length of Time between NA NA time that the sample has been acquisition and stored use Sample Shipping The temperature that Temperature NA NA temperature is maintained during maintained transportation during shipping Sample Composition Criteria used for use; this field Criteria used for NA NA assessment and is mainly only after use in a selection selection specific research study

BRISQ, Biospecimen Reporting for Improved Study Quality; FNA, fine-needle aspiration; ISO, International Organization for Standardization; LN2, liquid nitrogen; MIABIS, Minimum Information about Biobank Data Sharing; NA, not applicable; NCI, United States National Cancer Institute; OCT, optimal cutting temperature; SPREC, Sample PREanalytical Code.

100 Disclosures of interests

Dr Joakim Dillner reports that his unit at the Karolinska Institutet benefited from research funding from Sanofi Pasteur MSD and from Merck in 2014.

Dr Jan-Eric Litton reports holding intellectual property rights to the biobank lexicon Minimum Information about Biobank Data Sharing (MIABIS).

Dr Kurt Zatloukal reports having received personal consultancy fees from AstraZeneca and Daiichi Sankyo, support for travel from GlaxoSmithKline, and support from Daiichi Sankyo, Qiagen, and Siemens as an R&D partner. Dr Zatloukal is a European Committee for Standardization (CEN)/International Organization for Standardization (ISO) Technical Committee member.

Disclosures of interests 101 102