Recommendations for Biobanks

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

Essential Strongly recommended Optional

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 par- ing 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-contact- ing 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 sig- nificantly 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 sta- bility 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 ly- ophilized 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

Sharing/access T Sample collection Analysis Annotation Data output T ESI TININ TECNIC EETISE IT E T Sample storage E S Freeze–thaw C Sample processing Safety Access

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-threat- ening 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

Shipping Informed consent

Aliquoting/ Collection sample protocol preparation

Collection/ ION annotation C Retrieval Sample processing

Data records Labelling