Data dialogue - Human Genomic Data Discovery
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Presenting at The Data Dialogue. Time to Share: Navigating Boundaries & Benefits - Afternoon session: Sharing difficult data. July 28 - 2016 @ University of Cambridge http://www.ses.ac.uk/event/data-dialogue-time-share-navigating-boundaries-benefits/ In this talk I present an overview of human genomic data sources around the world, their funding, access policies and type of data they contain. Discussing why data sharing is hard, including issues of data privacy and a research culture that does not incentivise sharing of data and results. Presented by Fiona Nielsen, founder and CEO of Repositive http://repositive.io
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Data dialogue - Human Genomic Data Discovery
- 1. Human Genomic Data Discoverability Fiona Nielsen – Data Dialogue, Cambridge – July 28th 2016
- 2. The surge of genomics data • High throughput technologies – biology is moving from the lab to the computer 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Genomes Sequenced 80+PB Sequenced every year
- 3. Population sequencing projects • For example 100,000 Genomes project in the UK
- 4. Where is the data? • A researcher in human genomics knows on average 4-5 data sources The need to redefine data sharing: http://www.sciencedirect.com/science/article/pii/S2212066114000386
- 5. Hundreds of data sources • Content overview of 163 data sources Assay Types Dedicated to…
- 6. Hundreds of data sources • Sizes vary from tens to 100s of thousands of samples 1 10 100 1000 10000 100000 1000000 Sample#(Log10) Top 5: GEO (1.8M) PMI Cohort Program (1M) Auria Biopankki (1M) EGA (~0.6M) SRA (~0.5M)
- 7. Which populations are represented? Aboriginals African Americans Africans Australians Chinese Malays Indians Danish Dutch Estonian Russian European Ancestry Finnish Icelandic Japanese Korean Latin Americans Saudi Swedish
- 8. Where does the data come from? 947560 0 8 8 66 0 2 6 6 8 50 62 3 2 5 0 0 2 3 International Interesting site to look at: http://omicsmaps.com/stats
- 9. Why is some data not shared? • Challenges for international research community: How to work across borders and silos?
- 10. Why is some data not shared? • Additional challenges for biomedical: Data privacy, data governance, patient consent, medical legislation
- 11. Also consider: Community-led resources • patient groups, academia, the general public
- 12. What needs to change? • Increased data visibility and accessibility positively benefit both researchers and patients ?
- 13. Pain points FRAGMENTED Poor visibility of available genomic data ADMIN BURDEN Huge overhead to manage data access BAD CULTURE Lack of data sharing habits in research culture
- 14. Best practices MAKE DATA DISCOVERABLE SIMPLIFY WORKFLOWS CONTRIBUTE TO COMMUNITY DNAdigest and Repositive – Connecting the world of genomic data http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002418
- 15. Panel discussion • What are best practices for sharing difficult data? FAIR data: Findable, Accessible, Interoperable, Reuseable
- 16. Translating and Commercialising Genomic Research 7-9 December 2016| Wellcome Genome Campus, Hinxton, Cambridge UK Applications open soon! Scientific programme committee Emmanuelle Astoul Wellcome Trust Sanger Institute, UK Fiona Nielsen Repositive/DNAdigest, UK Abel Ureta-Vidal Eagle Genomics, UK Ross Rounsevell Wellcome Trust Sanger Institute, UK Full details at: www.wellcomegenomecampus.org/coursesandconferences Topics will include: • Commercial opportunities arising from data aggregation • Exploiting bioinformatics tools • Externalising bioinformatics pipelines • Translating biomarkers, genetic signatures or gene panels
- 17. CEO Fiona Nielsen, fiona@repositive.io Try our free platform for discovering human genomic data http://repositive.io Follow us on twitter @repositiveio
Editor's Notes
- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data
- Falling cost of sequencing and techological advances General intro to the subject – assume audience are novices but from technical background What’s hot, what’s not Major recent advances Key tactical challenges Strategic issues faced Relevance to Pistoia Alliance activity and strategy (if appropriate)
- General intro to the subject – assume audience are novices but from technical background What’s hot, what’s not Major recent advances Key tactical challenges Strategic issues faced Relevance to Pistoia Alliance activity and strategy (if appropriate)
- The need to redefine data sharing: http://www.sciencedirect.com/science/article/pii/S2212066114000386
- DNA.land OpenSNP PersonalGenomesProject Direct to consumer genetic tests & microbiome
- In the light of the increasing costs of drug development, this is an opportunity not to miss!
- The Repositive platform is an online community and marketplace connecting data consumers with data providers. On Repositive, Jenn has Easy, Interactive search Faster data access workflow Easy access to new data collaborators Benefiting from reading feedback on data from community, colleagues, to assess data quality and utility The Repositive platform and technology will remove barriers to data sharing and will incentivise users to explore, contribute and collaborate in alignment with best practices
- Data is fragmented in unconnected silos – makes it very difficult to discover data Tracking data and working with data access requests is a time-consuming and bureaucratic exercise Difficult to build a user community without best practices and tools/platforms where users can share their data experience / findings
- FAIR data: https://www.force11.org/group/fairgroup/fairprinciples
- General intro to the subject – assume audience are novices but from technical background What’s hot, what’s not Major recent advances Key tactical challenges Strategic issues faced Relevance to Pistoia Alliance activity and strategy (if appropriate)
- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data