Biosb2017_Repositive
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Slides about Finding & Accessing human genomic data for research, presented by Charlotte at BioSB 2017 in the
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Biosb2017_Repositive
- 1. We are always looking for data Finding & Accessing Human Genomic Data for research BioSB 2017 Tweets welcome #dataeureka @repositiveio
- 2. Genomic data is important for research Pre-clinical drug discovery Diagnostics and treatments of genetic diseases
- 3. “Consensus among researchers, clinicians, politicians & the public that genomics will transform biomedical research, healthcare and lifestyle choices” Stephan Beck, UCL OPPORTUNITY
- 4. Genome Technology Evolution 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
- 5. 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 Large amounts of data, but not accessible ≈ .5PB Sequence available 80+PB Sequenced every year WGS data available in public repos Exponential growth rate Under-utilised data has huge potential for medical research
- 6. How many data sources? How many sources of human genomic data do you know about?
- 7. 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 35 102 174 239 314 506 582 0 100 200 300 400 500 600 700 Jan-15 Mar-15 Jun-15 Sep-15 Dec-15 Mar-16 Jun-16 Sep-16 Dec-16 Mar-17 Data Sources Identified
- 8. The researchers’ pain points FRAGMENTED
- 9. 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
- 10. The researchers’ pain points CONFUSING
- 11. • Required by funders • Cannot publish unless accession number given • Specialised for genomics • ArrayExpress • EGA • dbGaP • GEO… • Generalist • Dryad • Figshare… See http://discover.repositive.io for more Public Repositories
- 12. The researchers’ pain points FRAGMENTED No holistic approach to discover new data HIDDEN
- 13. The researchers’ pain points FRAGMENTED No holistic approach to discover new data ADMIN BURDEN
- 14. Open Access • Eg. PGP, CC0 • Bermuda Accord Managed (Restricted or Controlled Access) • Data Access Committee • No effective agreement (policy vacuum) GOVERNANCE Models
- 15. Data accessibility Can download the data straight away or after logging in. Need to apply for access to the data. Has both Open and Restricted access data within one repository.
- 16. Access to Restricted 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?
- 17. Often a long process Bottlenecks: • Finding relevant and usable data • Getting authorisation to access data • Formatting data • Storing and moving data We studied the problem with qualitative interviews followed by a survey of researchers in human genetics T. A. van Schaik et al The need to redefine genomic data sharing: a focus on data accessibility, Applied & Translational Genomics, 2014 http://tinyurl.com/schaik-dnadigest
- 18. 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/
- 19. 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/
- 20. Where Repositive came from… Fiona Nielsen FOUNDER & CEO
- 21. @repositiveio
- 22. We are enabling best practices MAKE DATA DISCOVERABLE SIMPLIFY WORKFLOWS CONTRIBUTE TO COMMUNITY A platform to make human genomic data accessible for research
- 23. 1-click to human genomic data access to make finding data as easy as finding a book on Amazon, book a hotel on Expedia! Repositive
- 24. Simpler workflow for data access Our expertise is data search platforms Discover and access Search, see related results Find colleagues & their data interests Co-annotate data & community feedback
- 25. Connecting the world of genomic data
Editor's Notes
- Genomics data is needed for research and drug discovery It enables researchers to develop diagnostics and treatments for genetic diseases
- 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
- Data is fragmented in unconnected silos – makes it very difficult to discover data
- There are many public repositories, but It can be hugely confusing to know where to look for the right kind of data
- Data privacy Is a concern and controlled access is a requirement for many clinical datasets
- Accessing data is a time-consuming and bureaucratic exercise
- 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
- Just like Liz, and researcher struggling to get hold of the genomics data she needed for her researcher. So… she quite her job at illumina and decided to try and do something about that problem.
- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data
- FAIR data: https://www.force11.org/group/fairgroup/fairprinciples
- 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
- DNA.land OpenSNP PersonalGenomesProject Direct to consumer genetic tests & microbiome
- Our mission is to speed up research and diagnostics for genetic diseases by enabling efficient and ethical access to genomic research data
- 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 vetting of users