My Personal Odyssey with Big Data - Brad Popovich
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My Personal Odyssey with Big Data
Brad Popovich
Chief Scien2fic Officer December 5, 2013
The early days of exploring my personal genome
• 1976: My first whole genome analysis (46 XY) • 1980-‐2000: I looked at almost every gene I could
in my personal genome for CFTR, FMR1, DMD, DM, HD, SCA, SMA, MELAS, MERRF, etc.
• LiUle concern personally • ExcepWon: APOE
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My early concern: Demen<a
• PosiWve family history: • Increase life Wme risk (20-‐25% vs. 10%)
• APOE • e4/e4: further increase in risk
• Good news: • APP (2012) protecWve mutaWon (A673T)
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2013-‐2014: My personal Whole Genome Sequence (WGS)
Logical next step • It’s my personal “blue print”
• Provides potenWal for informed decision making • It’s accessible • Learn the difference between talking about
genomics vs. being a consumer
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Consumer driven genomics
WGS 2007: First offered by Knome ($350k)
2009: Illumina ($45k) 2013: TesWng now offered by several labs/companies for approximately $5k
Genotyping tesWng available from several labs/companies (e.g. 23andMe @ $99)
• FDA (November 2013)
• Class acWon suit (December 2013) 6
Obtaining my personal WGS
Presently several opWons for WGS Illumina: Understand Your Genome (UYG)
• Physician referral required • Reason for my referral: General medical knowledge -‐
not for any specific medical quesWon
• DNA sequence generated in CAP/CLIA accredited lab • UYG Course in March 2014
• Sokware tool provided: MyGenome App • App allows future genomic interrogaWon
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FDA Approval: November 19, 2013 • For the first Wme, the U.S. Food and Drug AdministraWon has cleared a next-‐
generaWon sequencer for use in clinical laboratories, advancing the use of genomic medicine in rouWne medical care.
• Francis Collins (NEJM): "The markeWng authorizaWon for the first next-‐generaWon genome sequencer represents a significant step forward in the ability to generate genomic informaWon that will ulWmately improve paWent care. The availability of high-‐throughput DNA sequencers will enable physicians to take a comprehensive look at a paWent's geneWc blueprint, or genome, to search for a wide range of variaWons or changes that increase risk of disease, drive the disease process, and/or affect response to medicaWons and other treatments. Such informaWon has the potenWal to benefit paWents in many ways. This acWon reflects our naWon's commitment to a future in which health-‐care professionals will be able to use each person's unique genome”
• FDA also approved the first test system based on two devices -‐ the Illumina MiSeqDx instrument and the reagents in the Illumina Universal Kit -‐ to allow laboratories to develop and validate sequencing of any part of the paWent's genome.
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Whole Genome Sequence (WGS) • Few technical barriers • ApplicaWons
• Primarily a research tool • Clinically: cancer, infecWous diseases, and difficult to diagnosis diseases
• Difference between WGS, exome and targeted gene panel approaches
• Size of corresponding data sets for human
• WGS 3x109 bp (file size Gb – Mb)
• Exome = 3x107 bp (approx 1% of WGS)
• BoUleneck…interpreWng the data
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Interpre<ng Whole Genome Sequence Necessary to know
• What’s normal vs. a variant across the enWre genome
• Phenotypic consequences of normal vs. variant genotype Current barriers
• Size of human cohorts available for comparison
• Lack of staWsWcal power to validate research findings • Quality of phenotypic data
• Lack of adequate EMR, data standards, QA, and QC Ideal clinical applicaWons
• Allow normal vs. abnormal comparison in the same paWent (e.g. cancer) 10
What do I expect to learn from my WGS?
• What being a consumer of genomic informaWon feels like • Some detected variants will cause concern
• Will the HC system accommodate medically acWonable follow-‐up?
• Most variants will lack the necessary data to have clinical uWlity
• How can we move from variants of unknown significance to significant?
• What’s the impact of waiWng?
• Can apps ease the burden on the system? 11
What do I expect to learn from my WGS? (Con<nued)
• Family maUers • Modified risk for demenWa
• CommunicaWons with family members • Impacts on my insurability
• Life • Disability
• What professional support will be required?
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Genome BC and WGS
• Many of the projects funded by Genome BC are already performing WGS on research subjects
• I anWcipate that in the near future most projects on humans will be using WGS or WES
• ObservaWon: ASHG and AMP 2013
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Genome Bri<sh Columbia and WGS
What is the role of Genome BC in making WGS clinically useful and cost effecWve? • Stop geneWc / genomic excepWonalism • Coordinate the large-‐scale collecWon of genomic data in
a manner that addresses privacy and confidenWality
• Develop strong baseline protecWons for parWcipants in clinical and/or research applicaWons of WGS
• Promote data access and sharing • Develop standards for the integraWon of genomic
informaWon into health records • Facilitate access to genomic informaWon so all BriWsh
Columbians benefit 14
What’s missing?
A plan! • R&D
• ComputaWonal infrastructure • Privacy policy/law • Access policy • Pla{orms • Data repository
• Clinical implementaWon • Medical evidence and health economic data
• Linkage of genomic data into HC records • Improved receptor capacity
• Physicians, geneWc counselors, apps, etc.
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Applica<ons
Human • Cancer • InfecWous diseases • Difficult to diagnose
diseases
• Pharmacogenomics • Forensics • Public health • Newborn screening
Non-‐human • Forestry • Fisheries • Environmental monitoring • Agri-‐Food Industry • Mining
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Conclusions
• I am about to conclude an important chapter in my genomic odyssey
• I plan to use my experience to inform the work that Genome BC is doing to make this technology accessible, useful, and economically viable to the ciWzens of BC, Canada, and beyond
• We need to end geneWc excepWonalism
• We need leadership and a plan!
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