Microtask crowdsourcing for annotating diseases in PubMed abstracts (ASHG 2014)
The Empowered Genome Community (ASHG 2013)
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Transcript of The Empowered Genome Community (ASHG 2013)
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Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
���a���
THE EMPOWERED���GENOME COMMUNITY���
a ���
SHAREABLE JOINT INTERPRETATION OF ���HUMAN WHOLE GENOMES FOR RESEARCH ���
a���
NATHAN PEARSON, PRINCIPAL GENOME SCIENTIST, QIAGEN
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Living M
oonwalkers
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
PGP UYG
Rise of the Genonauts
Time
AWARE S
EQUENCEES
(~)
source: xkcd.com/893
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moonwalkers
~300 aware whole-genome sequencees
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
PGP UYG
Rise of the Genonauts
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Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
One genome: Much ado about…something? Today, a typical healthy sequencee gets back
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One genome: Much ado about…something?
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
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)
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Making a genome reliably informative
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
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.
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Making a genome reliably informative
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
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.
Why one genome says so little (yet)
• Health is complex • Rare variants abound • Data are scarce
![Page 8: The Empowered Genome Community (ASHG 2013)](https://reader034.fdocuments.net/reader034/viewer/2022051412/5495d095b479596a4d8b4dfd/html5/thumbnails/8.jpg)
Making a genome reliably informative
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
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.
![Page 9: The Empowered Genome Community (ASHG 2013)](https://reader034.fdocuments.net/reader034/viewer/2022051412/5495d095b479596a4d8b4dfd/html5/thumbnails/9.jpg)
Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
• 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.
The Empowered Genome Community ���ow.ly/pZCXB
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Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
• 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
Ingenuity Variant Analysis in a nutshell
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Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
• 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.
Proof of principle: Open, collaborative myopia analysis���variants.ingenuity.com/community-myopia
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Using Variant Analysis: Call confidence & credibility
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Using Variant Analysis: General functional intrigue
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Using Variant Analysis: Rarity
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Using Variant Analysis: Rare variant association
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Using Variant Analysis: Rare variant association
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Using Variant Analysis: Rare variant association
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Using Variant Analysis: Myopia-relevance
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Using Variant Analysis: Myopia-relevance
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Using Variant Analysis: Myopia-relevance
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Using Variant Analysis: Myopia-relevance
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Using Variant Analysis: Saving your filters
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Talk 102 Empowered Genome Community [email protected] data at ow.ly/pYNSC
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.
Joining the Empowered Genome Community ���ow.ly/q56u4
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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 [email protected] data at ow.ly/pYNSC