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Where are we now? Where do we want to go?

Where are we now? Where do we want to go?. 9:05-9:25 AM 17-Nov-2008 NAS: Collecting, storing, protecting & accessing biological data collected in social surveys. Thanks to:. Human Systems Biology. Integrate diverse data types -- holistic not just inherited genome sequence

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Where are we now? Where do we want to go?

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  1. Where are we now? Where do we want to go? 9:05-9:25 AM 17-Nov-2008 NAS: Collecting, storing, protecting & accessing biological data collected in social surveys Thanks to:

  2. Human Systems Biology Integrate diverse data types -- holistic not just inherited genome sequence Limited traits (dual use technologies: research & clinical) One TRAIT per cohort Deidentified GENOME

  3. PersonalGenomes.orgInherited + Environmental Genomics One in a life-time genome + yearly ( to daily) tests Public Health Bio-weather map : Allergens, Microbes, Viruses VDJ-ome Personal stem-cells epigenome (RNA,mC) TRAITS (Phenome) PERSONAL GENOME 3M alleles Microbiome

  4. DNA Explorer, $80 (Ages 10 and up) www.discovery.com DIY DNA Genographic Project $99 23andme $399 Time Magazine Nov 2008 invention of the year

  5. Genetic Exceptionalism? Standard of care (non-genetic): Sedentary? Statins? Vegan? Aspirin? Wine? Cell-phones? Cars? Very small odds-ratios, aimed at public health rather than individuals Conventional clinical genetics: PKU, BRCA1 .. 1361 genes (+5/week) > 4M babies/yr in USA Highly predictable & huge impact. Why shouldn’t genetics deal with small (uncertain) risk factors like the rest of medicine?

  6. 6 of the first 8 full diploid genomes are non-anonymous • JCV Celera/JCVI • JDW Roche/Baylor • MK LUMC • DS Knome • RP Knome • YH BGI

  7. Trends toward openness HR 2764“SEC. 218. all investigators funded by the NIH submit .. an electronic version of their final, peer-reviewed manuscripts .., to be made publicly available” (make science paid for by tax-payers accessible to the tax-payers, not just the experts) PatientsLikeMe.com: MS, Parkinson’s, ALS, Depression, Anxiety, Bipolar, OCD, HIV/AIDS“sharing your healthcare experiences and outcomes is good.” (Full names & photos)

  8. Control 22q11DS Noonan Smith-Magenis William’s Imaging Diagnostics Hammond et al, Am J Med Genet 2004, Am J Hum Genet 2005

  9. Is promising anonymity realistic? Are we in denial? Trends in laws to make data public (not just at elite institutions):e.g.H.R. 2764, SEC. 218. 26Dec07 open-access for all NIH-funded research. SEC, GINA, etc (12) Identify individual case/control status from pooled SNP data Homer et al PLoS Genetics 2008 (11) Re-identification after “de-identification” using public data. Group Insurance list of birth date, gender, zip code sufficient to re-identify medical records of Governor Weld & family via voter-registration records (1998) Self identification trend (genome-altruists) (10) Unapproved self-identification. e.g. Celera IRB. (Kennedy Science. 2002) (9) Obtaining data about oneself via FOIA or sympathetic researchers. (8) DNA data CODIS data in the public domain. even if acquitted index

  10. Is promising anonymity realistic? Are we in denial? Accessing “Secure data” (7) Laptop loss. 26 million Veterans' medical records, SSN & disabilities stolen Jun 2006. (6) Hacking. A hacker gained access to confidential medical info at the U. Washington Medical Center -- 4000 files (names, conditions, etc, 2000) (5) Combination of surnames from genotype with geographical info An anonymous sperm donor traced on the internet 2005 by his 15 year old son who used his own Y chromosome data. (4) Identification by phenotype. If CT or MR imaging data is part of a study, one could reconstruct a person’s appearance . Even blood chemistry can be identifying in some cases. (3) Inferring phenotype from genotypeMarkers for eye, skin, and hair color, height, weight, geographical features, dysmorphologies, etc. are known & the list is growing. (2) “Abandoned DNA bearing samples (e.g. hair, dandruff, hand-prints, etc.) (1) Government subpoena. False positive IDs and/or family coercion index

  11. 8 Next Generation Sequencing Platforms

  12. Sequencing tracked Moore’s law (2X / 2 yr) until 2004-8 (10X / yr) $/bp 40X 98% genome $5K in Q2-2009 ($50 for 1%?)

  13. Plummeting costs & diversity of options Genographic sequencing DNAdirect Navigenics $2500 chips 0.02% 23andme $400 Knome CGI 98% 1% PersonalGenome.org sequencing

  14. Over 600 alleles of BRCA1 (Myriad/DNAdirect* sequencing not chips)

  15. (non-anonymous action in response to “non-actionable” tests) What if there is no current cure? DougMelton’s son, Sam, has diabetes Huntington's Chorea NancyWexler’s family Adrenoleukodystrophy AugustoOdone’s son ALS Heywood family PatientsLikeMe.com Cancer, substance abuse BettyFord Parkinson’s Michael J. Fox Hugh Rienhoff MyDaughtersDNA.org

  16. PersonalGenomes.org : gene/environment/trait data 1660 0431 1846 1070 1730 1677 1687 1731 1833 1781 1) Avoid over-promising on de-identification 2) 100% onExam to assure informed consent 3) Open access (very low barrier to researchers) 4) Low cost coding sequence + regulatory data 5) Multi-traits: imaging, iPS stem cell RNA, microbes 6) Cells available for personal functional genomics 7) IRB approval for 100,000 diverse volunteers Lunshof JE, Chadwick R, Vorhaus DB, Church GM. From genetic privacy to open consent. Nat Rev Genet. 2008 Lunshof JE, Chadwick R, Church GM (2008) Hippocrates revisited? Old ideals and new realities. Genomic Med. 2(1-2):1-3.

  17. PGP Microbiome-Resistome: 18 Antibiotics Dantas, Sommer, Church unpublished

  18. Antibody (& TCR) VDJ regions VH*DH*NH*JH*Vkl*Jkl 46*23*N * 6 * 67* 5 = > 2M combinations , 750 bp, >1E10 cells Roth DB et al Mol Cell Biol. 1989 9:3049 N (1-13): 14 22 13 15 10 4 5 4 2 2 3 2 1 Lefranc, The Immunoglobulin FactsBook; Janeway, Immunobiology 2001

  19. N-region lengths in circulating B-cells 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Length (aa)

  20. PersonalGenomes.orgInherited + Environmental Genomics One in a life-time genome + yearly ( to daily) tests Public Health Bio-weather map : Allergens, Microbes, Viruses VDJ-ome Personal stem-cells epigenome (RNA,mC) TRAITS (Phenome) PERSONAL GENOME 3M alleles Microbiome

  21. Personal Genomics Scope (& Issues) • Ancestry (paternity) • Forensics (abandoned DNA) • Research (anonymity issues) • Science education/curiosity (more) • Microbes, immune, RNA, cancer (more research) • Investment preview (early adopters: cf. fax, PC, www) • Medically actionable given new research or personal data • Medically actionable immediately (setting data thresholds) • (1361 clinical diseases in genetests.org 16-Nov-2008)

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