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Population-Scale Sequencing and the Future of Genomic Medicine Population-scale sequencing and the future of genomic medicine Learning from past and present efforts Talitha Dubow, Sonja Marjanovic For more information on this publication, visit www.rand.org/t/RR1520 Published by the RAND Corporation, Santa Monica, Calif., and Cambridge, UK R® is a registered trademark. © 2016 RAND Corporation RAND Europe is a not-for-profit organisation whose mission is to help improve policy and decisionmaking through research and analysis. RAND’s publications do not necessarily reflect the opinions of its research clients and sponsors. Limited Print and Electronic Distribution Rights This document and trademark(s) contained herein are protected by law. This representation of RAND intellectual property is provided for noncommercial use only. Unauthorized posting of this publication online is prohibited. Permission is given to duplicate this document for personal use only, as long as it is unaltered and complete. Permission is required from RAND to reproduce, or reuse in another form, any of its research documents for commercial use. For information on reprint and linking permissions, please visit www.rand.org/pubs/permissions.html. Support RAND Make a tax-deductible charitable contribution at www.rand.org/giving/contribute www.rand.org www.randeurope.org iii Preface Genomic medicine, as a field, has the potential RAND Europe is a not-for-profit organisation to change the way we prevent, manage and treat whose mission is to help improve policy and disease. However, the routine implementation decisionmaking through research and analysis. of genomic medicine in clinical care remains a RAND Europe’s clients include European future prospect. This paper provides a reflection governments, institutions, NGOs and firms with a on the variety of population-scale genome- need for rigorous, independent, multidisciplinary sequencing initiatives that have emerged over analysis. This document has been peer-reviewed the past two decades and examines their in accordance with RAND’s quality assurance social implications. We analyse the progress standards. For more information about this these initiatives have made, both in terms of document please contact: their scientific, technological and biomedical contributions, and in terms of their influence Dr Sonja Marjanovic on the institutions that govern science and RAND Europe innovation more widely. Based on our analysis, Westbrook Centre, Milton Road, we identify five areas of action for future Cambridge, CB4 1YG research and policy to consider. Tel. +44 (1223) 353 329 [email protected] v Table of contents Preface iii Table of contents v Tables vii Summary ix Context and objectives ix Methods ix Key findings ix Acknowledgements xv Abbreviations xvii Chapter One. Background and context 1 1.1. Introduction 1 1.2. Over two decades of scientific and technological progress have created new opportunities 2 1.3. Science has evolved faster than society’s readiness to harness it 3 Chapter Two. Methods 7 Chapter Three. Results 9 3.1. The diversity of aims and objectives across initiatives 9 3.2. Variety in scope and scale 11 3.3. Funding and partnerships 14 3.4. Data ownership, management and ethics 16 Chapter Four. In reflection 23 4.1. In reflection on achievements and evolving impacts 23 4.2. Looking forward to a future research, policy and service transformation agenda 26 References 31 Bibliography sorted by initiative: 31 Bibliography of other works cited: 43 Appendix 47 vii Tables Table 1. List of profiled initiatives xii Table 2. Aims and objectives across profiled initiatives 47 Table 3. Scope and scale of activities across profiled initiatives 50 Table 4. Funding and partnership arrangements 53 Table 5. Data ownership, management and ethics 56 Table 6. List of search terms 60 ix Summary Context and objectives and key wider literature on this topic (e.g. journal articles and reviews, websites of major initiatives, Genomic medicine, as a field, has the potential initiative reports, press releases and news to change the way we prevent, manage and articles). We complemented our search strategy treat disease. However, the implementation with a snowballing approach. We do not claim of genomic medicine in routine clinical care – to have profiled all population-scale sequencing through ‘personalised’, ‘precision’ or ‘stratified’ initiatives that exist; through the initiatives we have medicine – remains a future prospect due to reviewed, we have tried to represent the diversity a range of scientific and social challenges. that characterises the field. The 30 initiatives Frequently cited issues relate to test reliability profiled in this study are listed in Table 1. and validity, cost-effectiveness, health system and workforce readiness, and regulatory and Below we highlight key insights gained. More ethical concerns (McCarthy et al. 2013; Deloitte detailed information and examples of initiatives 2015; Milani et al. 2015; Manolio et al. 2015). associated with specific features and impacts are provided in the core report. Paving the way for a genomic medicine era is in part being facilitated by the evolution of population-scale sequencing initiatives. A diversity Key findings of such efforts has emerged in response to Diversity in form and purpose scientific and technological advances in genomics over the past 20 years. They have varied aims Population-based sequencing initiatives have and objectives, differ in scope and in scale of diverse goals, but we have witnessed a general activities, and in management and governance movement towards more clinically oriented arrangements. In this paper, we reflect on their efforts with time. Across the initiatives we variety and evolution, on the learning that they profiled, objectives spanned advancing the offer, and on implications for future research, knowledge base on genetic variation within and policy and practice. We draw insights from across populations; enriching disease specific, national initiatives and international collaborations, clinically relevant insights relating to diagnosis, both disease-centred and more general in risk prediction or treatment; the development their orientation, but all building on large-scale of new tools and methods for genetic studies; capacity-building (human resource capacity, population-sequencing data. We highlight the management and governance, infrastructure); social implications of scientific and technological catalysing translation and coordination across progress in this transformative field, and initiatives; and other aims (national security, particularly issues that influence how we might surveillance, commercial services). manage risk and reward in genomic medicine. The plethora of opportunities that have been Methods created by advances in genomic science are accompanied by a diversity of funders and We conducted a scoping review, searching partnerships, although the funding landscape Google and Google Scholar for evidence on is still dominated by public and third-sector diverse population-scale sequencing initiatives players. This is in some ways reflective of the x Population-scale sequencing and the future of genomic medicine state of the field and markets. The rationale for human resource capacity that will allow for public investment or public-private partnership is future research and innovation. partially based on the pre-competitive nature of • Some studies have advanced our collective the research conducted by many of the current knowledge on patterns of human migration, initiatives, as well as on government efforts to divergence and evolution, as well as estimated place their countries at the forefront of genomic rates of mutation in modern humans. research and to help catalyse genomics-based life-science industries. Most projects take But these initiatives have also had a lasting place within academic and research centres influence on the institutions that govern science and in partnerships between them (nationally more widely. Examples include: or internationally). Sequencing tasks are often • Transforming informed consent and research outsourced to specialist firms (with BGI and ethics practices and experimenting with new Illumina dominating the provider market). Aside models of feeding data back to research from this, only a small number of population- participants. Population-sequencing efforts, scale initiatives currently engage private-sector in particular those that are conducted as partners in the conduct of research. part of broader biobanking initiatives, have been at the centre of debates which have Progress, achievements and impact advanced group consent and community engagement processes in biomedical Over two decades of progress in this field have research, championed broad consent versus yielded numerous achievements and impacts – single-use consent principles, and introduced both direct and indirect. For example: novel models for feeding back research • Catalogues of population-specific genetic findings. Some initiatives have opted for variation have enabled further research – a full-feedback policy that would include namely, association studies that compare incidental findings; others provide feedback genetic and phenotypic traits in order to on findings directly related to the core advance knowledge of the genetic basis of research aim only; and some have opted out disease. of feedback provision (due to the absence of prospects for treatment, absence of informed • Biobank-based projects are providing consent on feedback provision issues, or comprehensive, longitudinal
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