Mutagenesys
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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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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

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!


Why mutagenesys

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


Scope of mutagenesys

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)... “


Mutagenesys

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


Coverage of mutagenesys

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


Availability

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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