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MutaGeneSys

MutaGeneSys. estimating individual disease susceptibility based on genome-wide SNP array data. Julia Stoyanovich (Ross lab), Itsik Pe’er. Nature Genetics Question of the Year. http://www.nature.com/ng/qoty

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MutaGeneSys

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  1. MutaGeneSys estimating individual disease susceptibility based on genome-wide SNP array data Julia Stoyanovich (Ross lab), Itsik Pe’er

  2. Nature Genetics Question of the Year http://www.nature.com/ng/qoty • “The sequencing of the equivalent of an entire human genome for $1,000 has been announced as a goal for the genetics community, and new technologies suggest that reaching this goal is a matter of when, rather than if…” • “What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?” • personalized medicine!

  3. Why MutaGeneSys? Complete genotype data is expensive to collect, so • focus on the interesting parts • 23andMe.com “genetics just got personal”, Navigenics, DecodeMe • 23andMe: 600K SNPs (5% of the total variation) for $999 • fill in the blanks(Pe’er I et al, Nat.Gen. 2006) • 5% are predictive of 80% of the total variation! • use correlation among markers in the genome, e.g., In population CEU, if rs17611:C and rs942152:C then rs7036980:C, with probability 0.967. In population YRI, if rs7516560:C then rs380390:C, with probability .609

  4. Scope of MutaGeneSys • Disease susceptibility based on single nucleotide polymorphisms (SNPs) • Stand on the shoulders of two giants • HapMap - catalogue of genetic variation in 3 populations, based on full genotype sequences in 270 individuals • OMIM - repository of publications about human genes and genetic disorders “… Mace et al. (2005) found a significant association between a C-T SNP (rs908832) in exon 14 of the ABCA2 gene (600047) and Alzheimer disease in a large case-control study involving 440 AD patients. Additional analysis showed the strongest association between the SNP and early-onset AD (odds ratio of 3.82 for disease development in carriers of the T allele compared to controls)... “

  5. Demo • MutaGeneSys with 23andMe genotype as query • Available to the community • Runs in real time • XML and HTML output • Cross-links to OMIM and HapMap

  6. Coverage of MutaGeneSys • Limited by the information about causal SNPs, known / available in OMIM: small but growing! (Feb 2007 to April 2008) • OMIM articles: 18003 to 19424 (8%) • causal SNPs: 187 to 527 (182%) • Significant growth in info about common variants associated with disease phenotypes • Single marker associations: 905 to 2498 • Two-marker associations: 396 to 1488

  7. Availability MutaGeneSys project page http://magnet.c2b2.columbia.edu/mutagenesys/ Our findings are used in • HapMap GBrowse, OMIM disease associations track http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B36/ • James Watson’s Personal Genome browser http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/ Bioinformatics 24 (3): 440, 2007.

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