DNA Testing: Living Longer Via Personal Genomics

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Current status, cost, and applications of personal genome sequencing

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DNA Testing: Living Longer Via Personal Genomics

  1. 1. DNA Testing: Living Longer Via Personal Genomics Melanie Swan +1-650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] October 10, 2010 Slides: http://slideshare.net/LaBlogga
  2. 2. Numerous useful applications of genomics <ul><li>Ancestry </li></ul><ul><li>Pregnancy screening </li></ul><ul><li>Identity (paternity, forensics) </li></ul><ul><li>Health conditions </li></ul><ul><li>Pharmaceutical response </li></ul><ul><li>Athletic performance </li></ul><ul><li>Aging profile </li></ul>October 10, 2010 DIYgenomics.org Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg
  3. 3. Example: what to do with your data <ul><li>Check if you have the risk allele for the BDNF gene </li></ul><ul><li>Determine related SNP/rsID#, rs6265 (neuroplasticity) </li></ul><ul><li>Search genomic data for rs6265 genotype (e.g., CC) </li></ul><ul><li>Determine the risk allele (which letter?) (e.g.; G 1 ) </li></ul><ul><li>Opportunity: genomic database with three minimal fields: gene, rsid# and risk allele </li></ul><ul><li>Current genomics search resources </li></ul><ul><ul><li>PharmGKB, dbSNP, GWAS catalog, SNPedia </li></ul></ul>October 10, 2010 DIYgenomics.org Source: http://www.wired.com/wiredscience/2009/10/genetically-bad-driving 1 Ribeiro, L. et. Al., The brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism and depression in Mexican-Americans. Cellular, Molecular and Developmental Neuroscience. May 8, 2007.
  4. 4. Finding your BDNF data, variant rs6265 October 10, 2010 DIYgenomics.org <ul><li>Consumer genomic services genotype 600,000-1m variants but only map a few up to the annotation browser </li></ul>
  5. 5. Conflicting consumer genomic test results October 10, 2010 DIYgenomics.org Source: http://dnasnips.com/dnaSnips/Heart.html
  6. 6. DIYgenomics: genomic service comparison October 10, 2010 DIYgenomics.org <ul><li>Companies use </li></ul><ul><ul><li>Different genes/variants </li></ul></ul><ul><ul><li>Different population averages </li></ul></ul><ul><ul><li>Different quantitative scoring methodologies </li></ul></ul>Risk for top 20 Health Conditions Response to 250 Drugs Source: Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010 , May;12(5):279-8 . http://www.diygenomics.org/webapp/gen_data.php Private data upload: Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/
  7. 7. DIYgenomics app - Android <ul><li>Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions </li></ul>October 10, 2010 DIYgenomics.org Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan
  8. 8. DIYgenomics app - iPhone October 10, 2010 DIYgenomics.org <ul><li>Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions </li></ul>Application developed by: Ted Odet, Greg Smith (ManyFriends.com)
  9. 9. Drug response October 10, 2010 DIYgenomics.org
  10. 10. Athletic performance <ul><li>Power/endurance (sprinter or marathoner) </li></ul><ul><ul><li>ACTN3 rs1815739 CC (power), TT (endurance); ACE rs1799752 DD (power), II (endurance) </li></ul></ul><ul><li>Ligament injury </li></ul><ul><ul><li>Favorable genotype: COL5A1 rs12722 CC and GDF5 rs143383 GG </li></ul></ul><ul><li>Head injury </li></ul><ul><ul><li>Two copies of ApoE ε4 (rs429358, rs7412) suggest slower recovery from head injuries </li></ul></ul><ul><li>Strength </li></ul><ul><ul><li>Favorable genotype: H1F1A rs11549465 TT, HFE rs1799945 GG, and HFE rs1800562 AA </li></ul></ul><ul><li>Increased HDL in response to exercise </li></ul><ul><ul><li>Favorable genotype: IL-6 rs1800795 GG </li></ul></ul>October 10, 2010 DIYgenomics.org http://www.genome.duke.edu/education/seminars/journal-club/documents/Assael_2009.pdf More information: DIYgenomics.org Athletic Performance
  11. 11. DIYgenomics study #1: MTHFR <ul><li>Do common mutations in the MTHFR gene prevent vitamin B from working correctly? </li></ul><ul><li>Test whether 2 variations in the MTHFR gene (methylenetetrahydrofolate reductase) keep vitamin B9 (folic acid) from being metabolized into its active form (folate) </li></ul><ul><ul><li>rs1801133/C677T </li></ul></ul><ul><ul><li>rs1801131/A1298C </li></ul></ul><ul><li>Without this form of vitamin B, homocysteine may accumulate </li></ul><ul><ul><li>Risk: nutritional deficiencies and symptoms associated with diabetes complications, including vascular damage and nerve damage </li></ul></ul><ul><li>50% or more of the population may have some form of MTHFR polymorphism </li></ul>October 10, 2010 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR
  12. 12. MTHFR pathway diagram October 10, 2010 DIYgenomics.org Aaron Vollrath; http://bit.ly/cHRzS8 Legend: where interventions impact the pathway 1 = Regular B-vitamin 2 = Active form of B9 (folate)
  13. 13. DIYgenomics MTHFR study protocol October 10, 2010 DIYgenomics.org <ul><li>Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes </li></ul><ul><li>Protocol confirmed with two separate experts in the field </li></ul>Source: http://diygenomics.pbworks.com/MTHFR 1. Genotype MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) 2. Phenotype Blood tests: B-12 and Homocysteine 3. Intervention <ul><li>(2 week periods) </li></ul><ul><li>B-complex </li></ul><ul><li>L-methylfolate </li></ul><ul><li>B-complex + L-methylfolate </li></ul>
  14. 14. MTHFR pilot study results October 10, 2010 DIYgenomics.org <ul><li>Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants </li></ul>Blood Test # 2. Homocysteine levels DIYgenomics MTHFR citizen science study 1 1. Genotype profiles Baseline LMF Source: http://diygenomics.pbworks.com/MTHFR_Results 1 Results are not statistically significant and are intended as a pilot demonstration of citizen science as a model Baseline + LMF Centrum Homocysteine umol/l Centrum
  15. 15. Boston University: Genetic Signatures of Exceptional Longevity in Humans October 10, 2010 DIYgenomics.org Source: Sebastiani P et al. Genetic Signatures of Exceptional Longevity in Humans. Science. 2010 Jul 21. http://diygenomics.org/citizengenomics/bu_longevity.php
  16. 16. DIYgenomics aging study <ul><li>Genomics + physical biomarkers + intervention </li></ul><ul><li>Top twenty genomic mechanisms of aging </li></ul><ul><ul><li>Aging-specific genetics </li></ul></ul><ul><ul><li>Diabetes and metabolic disease </li></ul></ul><ul><ul><li>Catabolism (waste removal) and other </li></ul></ul><ul><ul><li>Heart disease and blood operations </li></ul></ul><ul><ul><li>Cancer </li></ul></ul><ul><li>Top twenty phenotypic biomarkers of aging </li></ul><ul><li>Interventions </li></ul><ul><ul><li>Traditional </li></ul></ul><ul><ul><li>Novel </li></ul></ul>October 10, 2010 DIYgenomics.org More information: http://diygenomics.pbworks.com/Aging Image credit: http://www-nmr.cabm.rutgers.edu
  17. 17. DNA sequencing: 10x/yr improvement October 10, 2010 DIYgenomics.org April 1, 2010 Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif Dec. 14, 2009
  18. 18. Direct-to-Consumer genomics landscape October 10, 2010 DIYgenomics.org Single/few condition Multiple condition Whole genome Cost 1 Medical condition $9,500 Service Breadth Public studies Matchmaking ScientificMatch $1,995 GenePartner $10-$99 Paternity Genelex $200-$475 Identigene $149-$399 Pregnancy Screening Counsyl $349 Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Coriell 15 conditions Scripps (Navigenics) 28 conditions Pers. Genome Proj. Conditions undisclosed Harvard Med. Sch. Genetic disorders, Predisposition DNA Direct $200-$3,500 Matrix Genomics $199-$799 Drug sensitivity, $ Exome 23andme 174 conditions Navigenics* 40 conditions deCODEme 49 conditions $1,000 $429 $299 Genomics 71 conditions Pathway* $2,500 $999 $2,000 $985 *Must be physician-ordered Knome EdgeBio $6,000 $19,500 Knome Illumina $48,000 $350,000 $99,500 $68,500 $20,000 1 $39,500
  19. 19. Genomics comparison scorecard October 10, 2010 DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website <ul><li>Which service to buy? </li></ul>Consumer genomic service # Cond-itions Cost Report Data access Visible research quality 1 Updates deCODEme 49 $2,000  +   +  + 23andme 174 $429     Navigenics 40 $999    Pathway Genomics 71 $299  Coriell 7-15 public study PGP (Personal Genome Project) n/a public study
  20. 20. Melanie Swan +1-650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] Slides: http://slideshare.net/LaBlogga Creative Commons 3.0 license Thank you! Questions?

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