The Empowered Genome Community (ASHG 2013)
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An overview of the Empowered Genome Community, an initiative to help people who have had their whole genomes sequenced, through efforts such as the Personal Genome Project (PGP) and Understand Your Genome program (UYG), make their genomes more scientifically useful, by exploring and sharing them with each other and with researchers, through a secure online genome interpretation application, Ingenuity Variant Analysis. Learn more, including how to join the community yourself, at http://ow.ly/pZCXB. The slides here also walk through preliminary findings from an openly crowd-refinable proof-of-principle analysis of myopia (nearsightedness) in 111 people's whole genomes. Anyone can dig into the myopia analysis, and help refine it with an eye to jointly publishing robust findings, at http://variants.ingenuity.com/community-myopia.
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The Empowered Genome Community (ASHG 2013)
- 1. a THE EMPOWERED GENOME COMMUNITY a SHAREABLE JOINT INTERPRETATION OF HUMAN WHOLE GENOMES FOR RESEARCH a NATHAN PEARSON, PRINCIPAL GENOME SCIENTIST, QIAGEN Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 2. Rise of the Genonauts UYG PGP Living Moonwalkers AWARE SEQUENCEES (~) source: xkcd.com/893 Time Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 3. Rise of the Genonauts moonwalkers PGP UYG ~300 aware whole-genome sequencees Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 4. One genome: Much ado about…something? Today, a typical healthy sequencee gets back Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 5. One genome: Much ado about…something? Today, a typical healthy sequencee gets back • Vast raw(ish) data in tricky formats • A prognostic-minded single-genome report (frozen waffles) • An app(?) for browsing fenced-in parts of one genome and, if intrepid, may learn • A fair bit about ancestry • Less about drugs and mirrors • A smidgen about family health • What’s missing (meta-lesson) Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 6. Making a genome reliably informative Why one genome says so little (yet) • Health is complex • Rare variants abound • Data are scarce 3 challenges loom • Sequencees can’t easily mine much from their genomes. • Deep insight entails first comparing many well-phenotyped genomes. • Researchers need more such genomes. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 7. Making a genome reliably informative Why one genome says so little (yet) • Health is complex • Rare variants abound • Data are scarce 3 challenges loom • Sequencees can’t easily mine much from their genomes. • Deep insight entails first comparing many well-phenotyped genomes. • Researchers need more such genomes. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 8. Making a genome reliably informative 3 challenges loom • Sequencees can’t easily mine much from their genomes. • Deep insight entails first comparing many well-phenotyped genomes. • Researchers need more such genomes. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 9. The Empowered Genome Community ow.ly/pZCXB • Give sequencees access to a secure platform for exploring genomes, singly and jointly, with other citizen-scientists full-time researchers. • Help healthy adults make their genomes directly useful, to ask What can my our genomes do for me humanity? • Leverage deep functional knowledge sensible comparison methods (e.g., rare variant association tests) to give current data silos (PGP/hard drives) a working bakery for collaborative insight, via Ingenuity Variant Analysis. • Let sequencees own and control their private data. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 10. Ingenuity Variant Analysis in a nutshell • Secure web platform for interpreting called human genomes • Simple interface to flexibly annotate compare genomes, to shortlist candidate variants, genes, gene sets • Leverages deep functional knowledge base, with rigorously curated published findings, well structured ontology, smart interaction modeling • Statistically robust methods for interpreting (multi-)proband/kindred, matched tumor, and big case/control cohort studies • Shareable, to spark collaborative discovery • Hear Tracy Brandt (Mt. Sinai) Phil Tsao (Stanford) present work using Variant Analysis today at 12:30 in room 051 Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 11. Proof of principle: Open, collaborative myopia analysis variants.ingenuity.com/community-myopia • Pool well-phenotyped genomes to unravel common, complex disease, highlighting utility of community model • 111 phenotype-surveyed PGP genomes (66 cases, 55 controls) • Openly crowd-refinable, with an eye to publishing robust findings • First-pass findings highlight 12 plausibly myopia-relevant genes enriched with rare, functionally suspect variants in cases v. controls • Refine findings with your insights on myopia etiology epidemiology, sample structure, validation. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 12. Using Variant Analysis Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 13. Using Variant Analysis: Call confidence credibility Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 14. Using Variant Analysis: General functional intrigue Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 15. Using Variant Analysis: Rarity Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 16. Using Variant Analysis: Rare variant association Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 17. Using Variant Analysis: Rare variant association Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 18. Using Variant Analysis: Rare variant association Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 19. Using Variant Analysis: Myopia-relevance Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 20. Using Variant Analysis: Myopia-relevance Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 21. Using Variant Analysis: Myopia-relevance Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 22. Using Variant Analysis: Myopia-relevance Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 23. Using Variant Analysis: Saving your filters Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 24. Joining the Empowered Genome Community ow.ly/q56u4 Bring your genome, to interpret it – and, if desired, pool with others. • If a PGP sequencee, request your genome. • If a UYG/other sequencee, upload your genome as .vcf. • Explore it, and share with others if you wish. Bring your mind, to help interpret Community genomes. • Refine the myopia analysis, export your filter settings, and write me! • Collaborate on other forthcoming studies. Bring your wishlist, to find needed cases/controls. • Write me, to coordinate outreach. Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
- 25. Thanks. PGP and UYG sequencees Jason Bobe, Michael Chou, George Church, Madeleine Price-Ball John Mayfield, CarriLyn Mead, Erica Ramos Kevin Davies, Yaniv Erlich, Robert Green, Razib Khan, Gholson Lyon, Chris Mason, David Mittelman, Ayanna Monteverdi, Elin Silveous, Dale Yuzuki David Bachinsky, Steven Berley, Massimo Delledonne, David Delorenzo, Joel Dudley, William Faucett, Patrick Frosk, Terry Gaasterland, Konrad Karczewski, Joanne Mason, Steve Pinker, Jeannie Schaller, Randeep Singh, Elia Stupka, Eric Topol, Elizabeth Varga, Ron Zimmern Brent Applegate, Dione Bailey, Doug Bassett, Sarah Betadam, Carla Bullitt, Helen Cao, David Dailey, Julie Deschenes, Aysel Heckel, Andreas Krämer, Laurent Martin, Antonio Montano, Bryant Macy, Anand Muthiah, Jake Leschly, Curt Palm, Dan Richards, Colin Sanford, Thomas Theuringer Talk 102 Empowered Genome Community npearson@ingenuity.com data at ow.ly/pYNSC
Editor's Notes
- One adult genome says much about ancestry, and a bit about drug response, but otherwise little about health. As such, getting your genome today is like tuning into a station from aliens…then realizing it’s mostly spam ads. Need to filter. Challenges include causal complexity, abundance of rare variants, and paucity of dataTo move from diagnostic to prognostic genomic healthcare, must first compare many genomes, in context of phenotypeBut genomes still costly, so researchers struggle to gather enough to informatively compare1 genome sound and fury signifying…something?.