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Meeting Report Meeting Report National Initiatives: Opportunities for Knowledge Exchange & Collaboration Wednesday, May 24th, 2017 – Wellcome Trust (London, UK) Co-hosted by Genomics England and Australian Genomics Table of Contents National Initiatives, International Opportunities 3 ​ Presentations from National Initiatives 4 ​ Current UK Plans 5 ​ Data Breakout Workshop Report 6 ​ Regulatory Breakout Workshop Report 7 ​ Clinical & Education Breakout Workshop Report 9 ​ Data-sharing: Opportunities and Challenges 11 ​ Summary & Next Steps 13 ​ Appendix I: Meeting Agenda 14 ​ Appendix II: Meeting Attendees 15 ​ National Initiatives, International Opportunities Three years after the launch of the Global Alliance for Genomics and Health (GA4GH) and six months after the first GA4GH-hosted convention of national genomics initiatives, Kathryn North (Australian ​ Genomics) and Mark Caulfield (Genomics England) convened representatives from 13 National ​ Initiatives in genomic data collection to discuss areas of potential collaboration. North provided an overview of recent GA4GH strategic planning efforts, which aim to identify best standards for implementing genomics in clinical practice. “An important part of GA4GH is how the tools and standards that are being developed get used,” she said, pointing out the important role of National Initiatives in helping define those tools. An important outcome of that work, North said, was a renewed focus on engaging partners—including big genomic sequencing initiatives as well as National Initiatives like those in the room—in order to avoid duplication of efforts across multiple countries or the collection of clinical genomic data that are not shareable or interoperable. The goal of the meeting was to identify potential areas of collaboration and resource/expertise sharing, as well as common needs across National Initiatives that GA4GH can incorporate into its “toolbox” of data sharing standards and tools. North also promoted the concept of a “TripAdvisor for Genomics,” wherein National Initiatives will be able to learn from one another about positive and negative experiences, suggest best practices to others, and work to iteratively improve the tools they develop and use. For instance, she noted that developing an informed consent that adequately takes into account the needs of indigenous populations and cultural sensitivities is relevant across all National Initiatives. She also noted that diagnostic evidence can be transferable across nations, and need only be customized according to local healthcare costs to be immediately locally relevant. Going forward, North said that efforts to convene National Initiatives, such as the present meeting and a recent meeting of the Global Genomic Medicine Collaborative (G2MC), will be better aligned and result in at least one annual conference to continue the conversation and work toward aligning National Initiatives to ensure interoperable, shareable clinical and genomic data. 2 Presentations from National Initiatives For more details on each of the following, see the Program Booklet released prior to the meeting. ​ ​ Australia | Slides ​ Kathryn North (Australian Genomics) Brazil | Slides ​ Benilton Carvalho (UNICAMP – BIPMed) Canada | Slides ​ Marc LePage (Genome Canada) Finland | Slides ​ Markus Perola (National Institute for Health and Welfare, Finland) GenomeAsia 100K | Slides ​ Lakshmi Santhosh (GenomeAsia 100k) Global Gene Corp (India) | Slides ​ Paul Jones (Global Gene Corp) Netherlands | Slides | Video ​ ​ ​ Gerrit Meijer (Netherlands Cancer Institute) Qatar | Slides ​ Said Ismail (Qatar Genome Programme) South Africa | Slides ​ Nicola Mulder (University of Cape Town) Switzerland | Slides ​ Torsten Schwede (SIB Swiss Institute of Bioinformatics) ​ Turkey | Slides ​ Osman Ugur Sezerman (Acibadem University) United States of America | Slides ​ David Glazer (Verily), Teri Manolio (NHGRI/NIH), and Heidi Rehm (Harvard Medical School; The Broad Institute) United Kingdom | Slides ​ Mark Caulfield (Genomics England; Queen Mary, University of London) 3 Current UK Plans Sir John Chisholm, executive chair of the Genomics England Board, spoke on his vision for genomic ​ ​ research. “We are all engaged in the most significant program of the human race in the 21st century,” he said. “If we’re successful, we’ll change the human experience from what it had been throughout history and evolution—that health is something which gets done to you by some force outside of you—to something you have control over.” This change is possible because we will soon be able to understand the genome, and to use it to predict outcomes. “It’s a fantastic vision, but it’s very hard and it will take most of rest of the century to get there,” said Chisholm. He cited two challenges in particular: 1) Genomic medicine involves “colossal” amounts—millions, tens of millions, or even 100s of millions—of data points. This scale is necessary because of the low probability of making connections between the genome and human health. Additionally, because very few associations are monogenic, combinatorial problems make unpacking the genome a very difficult and complex pursuit. In the past, scientific programs have built individual research cohorts for each study. This will not work with clinical genomic research, because no organization has enough money to fund research cohorts at this scale. The only way to achieve cohorts of the size needed is by aligning fully consented patient data from the healthcare system with genomic data. No one country will be able to do this alone so national programs must collaborate. 2) Given that no one country can do it alone, nations must agree on rigorous standards and protocols, as artifacts of non-harmonized data collection processes will make it impossible to understand outcomes across a combined data set. Implementing standards and protocols in routine healthcare will be difficult, Chisholm said, “but it’s something where the prize is so great, it’s worth doing.” In the four years since it was launched, Genomics England has spent considerable effort and made progress on the development of standards and protocols for data collection and getting them implemented across the UK’s National Health System. Now, he said, that needs to be taken to the international stage. He invited meeting attendees to “form a club” to work together to agree on standards and protocols for clinical genomic data sharing. This will allow for federated data sharing that is protective of participant confidentiality and privacy and enables “this transformation of the human experience in the 21st century.” 4 Data Breakout Workshop Report Discussion Aim 1: Establish a comprehensive set of use cases/scenarios for a genome-phenome database ​ ● Genome/phenome association databases should allow hypothesis free discovery. Need to map across disparate data models to enable interoperability. ● Other types of databases: ○ Gene/variant databases (e.g., ClinGen, CIViC) that store relationships with particular disorders and various levels of evidence from existing databases. ○ Databases of findings (e.g., DECIPHER, NSIGHT). These vary from a simple spreadsheet to sophisticated softwares. Harmonization would have immediate clinical impact. ■ GA4GH can help scope areas in need of new standards, (i.e., database of findings). National Initiatives can be a user group to guide development of and test standards through implementation. ■ National Initiatives need to come together to form a “club” to discuss many things, one of which is standards. GA4GH and G2MC are obvious partners in that part of the discussion. There needs to be a structure for coming to consensus and then accessing the agreements that have been made. Aim 2: Establish a list of all large-scale population genomics projects internationally ​ ● How many genomes are accessible? Few relative to the number of genomes sequenced. ​ ​ Aim 3: Survey activity of genome/phenome data sharing and map impediments to sharing ​ ● Philosophical reasons academics and clinicians don’t share, but also technical challenges. E.g., majority of genomes sequenced aren’t in a database at all. Also, no standards for sharing, so people don’t feel empowered to do so responsibly. ● What types of data are we missing in the conversation? ○ Clinical, panels, arrays, and exome data are also relevant for patient. ○ Data that don’t exist in a shareable format (e.g, genomes in hard drive; non-digitized data in clinical records). ● Need to incentivize clinicians to share, possibly by returning details about discoveries as a result. Need epidemiologists to help identify gaps in data that are collected. ● Academic reward system does not incentivize sharing in biomedical disciplines. Demonstrations of clinical impact to reinforce a virtuous cycle will naturally alleviate the problem in time. ● Key insights will come from healthcare and large-cohort research studies. Actions ● Web-based catalogue of real world genome/phenome database use cases, including underlying technology set and how the databases are used. Goal: to track whether technologies being ​ ​ developed are fit for purpose. Use HQL query for analytics. ● Catalogue of National Initiatives’ challenges, strategies, technologies, and data sharing status. ● Measure regular constructive access to and use of data being produced and shared. 5 Regulatory Breakout Workshop Report Discussion ● Data sharing motivated by benefit to human health; no country has enough data. ● GWAS data sharing was generally helpful if imperfect. Must make new
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