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Carlos Alvarez BCMM/CMHG/CGT Joint Meeting September 15 th , 2011

Multidimensional genomics in mammalian cohorts. Carlos Alvarez BCMM/CMHG/CGT Joint Meeting September 15 th , 2011. L ab background. PhD, mol. genetics of vision ( Drosophila ) Postdoc, mol. neurosci . & genomics (rodents) Lab Head, Novartis (hum., rodent)

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Carlos Alvarez BCMM/CMHG/CGT Joint Meeting September 15 th , 2011

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  1. Multidimensional genomics in mammalian cohorts Carlos Alvarez BCMM/CMHG/CGT Joint Meeting September 15th, 2011

  2. Lab background • PhD, mol. genetics of vision (Drosophila) • Postdoc, mol. neurosci. & genomics (rodents) • Lab Head, Novartis (hum., rodent) • Themes – evolution, bioinformatics, genomics

  3. Why study CNV in dogs? Genetics Variation (morphological, physiological & behavioral) ≥ 15,000 YA 150-200 YA 400 breeds • 450 inherited diseases • Dog genome similar to human • 5-7X shorter lifespan v. humans • 75M dogs in USA • Low intra-breed variation; high inter ▪ 65X difference sm/largest breeds (wt.) ▪ ~250X smallest/largest individuals

  4. Ongoing genetic studies in dogs • a. DNA copy number variation (CNV; custom 1M feature) • b. Genome wide association in complex genetics (12x175k SNP) Genome Res. 2008

  5. Integrating CNV and SNP haplotypes Rowell et al. TMM 2011

  6. Coat color: Dominant Black locus Kerns et al. (2007) Genetics 176:1679. KBlack > kbrindle > kyellow In humans, pigmentarymosaicism(not mutation, but effect of two genetic cell types)

  7. CNV explains brindle Dominant black gene Identified CNV associated with brindle and developed first genetic test

  8. Complex genetics of osteosarcoma Approach (for germ line): High OSA risk pop. w/ 100X reduced variation 2a. Allele-wise GWA analysis 2b. Dimensional reduction of allele ratios

  9. Multidimensional genomics in longitudinal cohorts

  10. Conclusion Longitudinal cohorts will enable determination of genetic alterations (SNPs, CNV) contributing to disease initiation, progression and promotion … and of the relative contributions of genetics and environment

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