Finding and accessing human genome data with Repositive
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The slides of the workshop I gave on May 29th 2017 at the European society for Human Genetics in Copenhagen, Denmark. Here I present the Repositive platform, a tool that helps scientist find and access human genome data.
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Finding and accessing human genome data with Repositive
- 1. We are always looking for data Finding & Accessing Human Genome Data 28 May 2017 @manuelcorpas @repositive
- 2. "Scientists identify 40 genes that she new light on biology of intelligence" 22 May 2017
- 6. 13 cohorts
- 7. No access to online methods
- 8. No links to datasets
- 10. Where is the data?!?!
- 17. 11 155 2 2 4 4 7 780 0 5 10 15 20 25 30 35 40 45 GB FI NL FR DE CH EE BE DK ES SI IE SE 0 5 10 15 20 25 30 35 CA MD MA WA NY TX AZ DC NJ NC PA UT TN CO IN FL LA VA IL ME OH MO MI SC OR 1 1 1 1 1 1 Data sources across the globe GEO location of 278 data sources analysed. Found by tracking IP address of the source. These include: Public Repositories Universities Companies BioBanks Research consortiums
- 19. 2001: 1 human genome 2005: Personal Genome Project Human Genome Diversity Project HapMap 2016: 2M AstraZeneca - HLI 2008: 1000 Genomes (1092 genomes, since increased to ~2500) Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) 2011: H3Africa 2012: International Cancer Genome Consortium International Initiatives
- 20. The Population-Scale National Genome Project Race
- 21. National Genome Project Race
- 22. 2003 National Genome Project Race
- 23. deCODE 2003 National Genome Project Race
- 24. UK10K 2008 National Genome Project Race
- 27. Precision Medicine Estonian Biobank SardiNIA Denmark Saudi Kadoorie Biobank Indigenous Genomics Japan Netherlands 2015 National Genome Project Race
- 29. 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Large amounts of data, but not accessible ≈ .5PB Open Access 80+PB Sequenced Genome data available in public repos Exponential growth rate Under-utilised data has huge potential for medical research
- 31. • Required by funders • Cannot publish unless accession number given • Specialised • ENA • EGA • dbGaP • dbSNP… • Generalist • Dryad • figshare Public Repositories
- 32. Open vs Managed Access Open Access 75,000,000 per month Managed Access 150 per month 500,000 fold difference Stephan Beck
- 33. Data source content Assay Types Dedicated to…
- 34. Hundreds of data sources …but they aren’t easy to find! http://tinyurl.com/plos-biology-repositiveFirst 30 data sources listed here: 10 25 33 35 102 174 239 0 50 100 150 200 250 300 Jan-15 Mar-15 Jun-15 Sep-15 Dec-15 Mar-16 Jun-16
- 35. Case studies Raquel, PhD Student, London, UK. Researching genes associated with rare eye disorders. Problems: - Doesn’t know where to look for data. - Doesn't know if data even exists. “I gave up on finding the data - it was very time consuming and not proving fruitful – so I started focusing more on generating my own data.”
- 36. Access to Managed Data Benefits: • Strict governance • Individuals are protected • Review of consent • Applicant signs for full responsibility for governance Disadvantages: • No control of data once access is given • High barrier for access – too high?
- 37. NIH / eRA Commons login No Yes Organisation registered with eRA Organisation has DUNS number No No Write research proposal Yes + 2-3 days + 1-2 weeks + 1 week Yes Submit proposal + 1-2 days Access granted Find/Download/Decrypt data + 1-4 weeks Science… + 1-2 days PRO Tip: If you use human genomic data, apply for the GRU datasets in dbGaP, one application – access to all the GRU datasets. dbGaP application process Blog Post: http://blog.repositive.io/how-to-successfully-apply-for-access-to-dbgap/
- 38. Sanger eDAM Account No Write research proposal + 1 hour Yes Submit proposal + 1-2 days Access granted Find/Download/Decrypt data + 2-7 days Science… + 1-2 days EGA application process Blog Post: http://blog.repositive.io/how-to-successfully-apply-for-access-to-ega/
- 40. What is our mission? 1. Finding 2. Accessing 3. Sharing
- 41. #DATAEUREKA
- 43. The meaning of #dataeureka 1. We have actively helped a user F/A/S genomic data 2. An employee recognises a feature that makes a difference in F/A/S 3. Product-market fit that justifies Repositive existence
- 44. May 22nd • Twitter • 7 May 8th • Twitter • 26
- 49. 1-click to human genomic data access to make finding data as easy as finding a book on Amazon, book a hotel on Expedia!
- 50. Simpler workflow for data access Discover and access Search, see related results Find colleagues & their data interests Co-annotate data & community feedback
- 54. Repositive 23andMe Datasets Breakdown
- 55. 1000 Genomes samples used Population Subpopulation Description Number African (207) YRI Yoruba in Ibadan, Nigeria 108 LWK Luhya in Webuye, Kenya 99 Asian (300) CHB Han Chinese in Beijing, China 103 JPT Japanese in Tokyo, Japan 104 CHS Southern Hand Chinese 93 European (336) TSI Toscani in Italia 107 GBR British in England and Scotland 87 FIN Finnish in Finland 96 IBS Iberian Population in Spain 46
- 56. PCA of 23andMe & G1k (African, Asian, European)
- 57. Open Access Datasets Even More European-Biased Than Scientific Literature?
- 58. 2,402 23andMe African cluster 50 samps 43 OpenSNP Of which 11 reported ethnicity: 10 African/Black 1 Many inc African Asian cluster 58 samps 46 OpenSNP Of which 5 reported ethnicity: 4 East Asian 1 Korean Surnames suggestive in 13 other cases European (2098) ancestry cluster? (by default)
- 60. Come & Talk to Us! BOOTH 732
Editor's Notes
- March 2016 239 total sources
- Because interpretation requires LOTS of data And although data exists around the world, it is siloed, and even if available, it is not accessible This is Jenn, a genetic researcher –our target customer- seeking to interpret data from genetic diseases and cancer She needs data from other patients to compare and interpret Mabels DNA She also has data available in her own lab, but she cannot share because of concerns how to deal with secure access to sensitive data and data governance, e.g. vetting of users
- Population scale genome sequencing projects have been launched all over the world More than 80PB of human genomic data is being sequenced Every year BUT To date only around .5PB of data available in public repositories
- Every data source Mixed data dedicated to anything Sources dedicated to specific March 2016 239 total sources
- June 2016
- Examples of researchers looking for genomics data. All have problems, even though in different parts of the world, in different industries and with different research questions.
- Because interpretation requires LOTS of data And although data exists around the world, it is siloed, and even if available, it is not accessible This is Jenn, a genetic researcher –our target customer- seeking to interpret data from genetic diseases and cancer She needs data from other patients to compare and interpret Mabels DNA She also has data available in her own lab, but she cannot share because of concerns on how to deal with secure access to sensitive data and data governance, e.g. vetting of users
- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data
- Our vision is to make genomic data access as easy as finding a book on Amazon or book a hotel on Expedia
- KEY POINTS: Repositive builds tools for genomics data search & access. We’re really good at it. We have the expertise in-house. It’s what we do. Aside from building a highly functional tool, we’ve taken the time to prioritise User Experience, streamlining of user workflows & presentation. Within a month of our formal platform launch we have over 600 registered users. 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
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- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data