Large-scale data integration for systems- level understanding of complex diseases How do GWAS, NexGen sequencing, microRNAs and ‘-OMICs’ relate? Sergio E. Baranzini, PhD Associate Professor, Department of Neurology University of California, San Francisco B2PM Vancouver, BC March 8-9, 2011
Physiological/pathological Process (health/disease) neurodegenerative metabolic autoimmunity cancer infectious Cell cycle apoptosis Cellular process Cell differentiation pathways proteins expression genomic
The complex disease paradox • >80 susceptibility variants found to date • <25% heritability explained
CD4 + T Lymphocytes Twins 041896 Twins 230178 Twins 041907 Affected Unaffected Affected Unaffected Affected Unaffected Reads (x10 9 ) >1 >1 n.d. n.d. n.d. n.d. Coverage (X) 21.7 22.5 n.d. n.d. n.d. n.d. Coverage of Reference (%) 99.6 99.5 n.d. n.d. n.d. n.d. Number of SNPs (x10 6 ) 3.55 3.66 n.d. n.d. n.d. n.d. SNP differences / total 3,241 / 1,089,550 n.d. n.d. n.d. n.d. DNA Confirmed by Sanger Seq. 0 / 15 Number of indels (x10 6 ) 0.22 0.20 n.d. n.d. n.d. n.d. Indel differences / total 213 / 27,121 n.d. n.d. n.d. n.d. SNP differences / total 126 / 736,908 153 / 783,342 120 / 796,990 CNV differences / total 0 / 143 0 / 13 0 / 58 Number of CpG sites 2,146,620 2,033,078 1,636,285 1,917,131 1,779,140 1,642,200 CpG differences 2 10 176 mRNA reads (x10 6 ) 50/63 51/62 63 68 65 57 Number of differentially 13,714 / 28,443 8,595 / 28,443 14,163 / 28,443 expressed genes / total cSNP differences / total 322 / 51,523 1,017 / 40,833 380 / 18,503 RNA Differential allelic expression 115 n.d. n.d. Number of differentially 1,721 / 22,877 n.d. n.d. expressed genes / total
Coverage GS1641 GS1679 GS1685 GS1687 GS1748 GS1768 GS1843 GS1881 GS1883 GS1884 GS1901 GS1922 GS2023 10X 0.963 0.960 0.966 0.960 0.963 0.966 0.963 0.967 0.965 0.961 0.966 0.968 0.963 20X 0.938 0.927 0.940 0.928 0.937 0.943 0.936 0.947 0.938 0.931 0.946 0.947 0.930 30X 0.897 0.872 0.898 0.874 0.896 0.905 0.892 0.918 0.892 0.884 0.915 0.916 0.870 40X 0.836 0.790 0.830 0.794 0.836 0.845 0.827 0.875 0.818 0.816 0.868 0.867 0.772 50X 0.756 0.685 0.737 0.693 0.756 0.760 0.742 0.817 0.716 0.730 0.805 0.800 0.640 60X 0.659 0.565 0.623 0.577 0.660 0.653 0.641 0.746 0.593 0.632 0.728 0.716 0.491 100X 0.242 0.145 0.184 0.165 0.252 0.213 0.233 0.395 0.157 0.247 0.355 0.318 0.085
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