DNA Testing: Living Longer Via Personal Genomics

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

Numerous useful applications of genomics
Ancestry
Pregnancy screening
Identity (paternity, forensics)
Health conditions
Pharmaceutical response
Athletic performance
Aging profile
October 10, 2010 DIYgenomics.org Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg

Example: what to do with your data
Check if you have the risk allele for the BDNF gene
Determine related SNP/rsID#, rs6265 (neuroplasticity)
Search genomic data for rs6265 genotype (e.g., CC)
Determine the risk allele (which letter?) (e.g.; G 1 )
Opportunity: genomic database with three minimal fields: gene, rsid# and risk allele
Current genomics search resources
PharmGKB, dbSNP, GWAS catalog, SNPedia
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.

Finding your BDNF data, variant rs6265 October 10, 2010 DIYgenomics.org
Consumer genomic services genotype 600,000-1m variants but only map a few up to the annotation browser

Conflicting consumer genomic test results October 10, 2010 DIYgenomics.org Source: http://dnasnips.com/dnaSnips/Heart.html

DIYgenomics: genomic service comparison October 10, 2010 DIYgenomics.org
Companies use
Different genes/variants
Different population averages
Different quantitative scoring methodologies
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/

DIYgenomics app - Android
Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions
October 10, 2010 DIYgenomics.org Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan

DIYgenomics app - iPhone October 10, 2010 DIYgenomics.org
Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions
Application developed by: Ted Odet, Greg Smith (ManyFriends.com)

Drug response October 10, 2010 DIYgenomics.org

Athletic performance
Power/endurance (sprinter or marathoner)
ACTN3 rs1815739 CC (power), TT (endurance); ACE rs1799752 DD (power), II (endurance)
Ligament injury
Favorable genotype: COL5A1 rs12722 CC and GDF5 rs143383 GG
Head injury
Two copies of ApoE ε4 (rs429358, rs7412) suggest slower recovery from head injuries
Strength
Favorable genotype: H1F1A rs11549465 TT, HFE rs1799945 GG, and HFE rs1800562 AA
Increased HDL in response to exercise
Favorable genotype: IL-6 rs1800795 GG
October 10, 2010 DIYgenomics.org http://www.genome.duke.edu/education/seminars/journal-club/documents/Assael_2009.pdf More information: DIYgenomics.org Athletic Performance

DIYgenomics study #1: MTHFR
Do common mutations in the MTHFR gene prevent vitamin B from working correctly?
Test whether 2 variations in the MTHFR gene (methylenetetrahydrofolate reductase) keep vitamin B9 (folic acid) from being metabolized into its active form (folate)
rs1801133/C677T
rs1801131/A1298C
Without this form of vitamin B, homocysteine may accumulate
Risk: nutritional deficiencies and symptoms associated with diabetes complications, including vascular damage and nerve damage
50% or more of the population may have some form of MTHFR polymorphism
October 10, 2010 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR

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)

DIYgenomics MTHFR study protocol October 10, 2010 DIYgenomics.org
Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes
Protocol confirmed with two separate experts in the field
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
(2 week periods)
B-complex
L-methylfolate
B-complex + L-methylfolate

MTHFR pilot study results October 10, 2010 DIYgenomics.org
Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants
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

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

DIYgenomics aging study
Genomics + physical biomarkers + intervention
Top twenty genomic mechanisms of aging
Aging-specific genetics
Diabetes and metabolic disease
Catabolism (waste removal) and other
Heart disease and blood operations
Cancer
Top twenty phenotypic biomarkers of aging
Interventions
Traditional
Novel
October 10, 2010 DIYgenomics.org More information: http://diygenomics.pbworks.com/Aging Image credit: http://www-nmr.cabm.rutgers.edu

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

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

Genomics comparison scorecard October 10, 2010 DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website
Which service to buy?
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

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?

DNA Testing: Living Longer Via Personal Genomics

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