GWAS Analysis of Chromosome 10 - Purdue University...1 76066 85987554 36003093 69233817 90492330...
Transcript of GWAS Analysis of Chromosome 10 - Purdue University...1 76066 85987554 36003093 69233817 90492330...
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GWAS Analysis of Chromosome 10
(Continuous Variable)Group 5
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Hepatic Steatosis: accumulation of triglycerides in hepatocyte lipid droplets
J C Cohen et al. Science 2011;332:1519-1523
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LiverTriglycerides
• LiverTGsaremaintainedthrough:• Acquisitionthroughuptakeoflipoproteinparticlesorfreefattyacids(secretedfromwhiteadipose)
• Denovosynthesisfromacetyl-CoAprecursors• Removalviaβ-oxidation,orsecretionofTG-richVLDLparticles
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Why Chromosome 10? Significantly differentially expressed gene H2YAF2, from the binary DEG analysis, is located on chromosome 10
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Original data = 27658 SNPs
Filtered data = 27339 SNPs
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Did NOT filter based on relatedness
Would result in filtering out 15% of SNPs
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ZERO genes met the p<10-8 criteriaMost significant gene: p<10-5
TheAlleleFREquency Database(ALFRED)
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SNP11010552isinaSNPcluster:Theyareallintergenicb/wLOC439954andPBEF2,allunknownfunctions(frombothUCSCGenomebrowser,GTEx,andALFRED)withsamefrequency
rs7092191(AtoC,r2=.9)rs10827617(AtoC,r2=.632)rs7067812(AtoC,r2=.632)
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Next most significant genes: p<10-4
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GG AAAG
From:GTEX
*Involvedinfattyacidoxidation(Reactome)eQTL
PHYHexpressionisdiminishedinthepresenceofrs7916990
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LiverMuscle
(GTEx)
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UCSCGenomeBrowser
rs7916990(neartranscriptionfactorbindingsites)
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GTEX(showingeQTL’s forPHYH)
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(SNAP)
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Thank you!