Post on 27-Jul-2020
GWAS Analysis of Chromosome 10
(Continuous Variable)Group 5
Hepatic Steatosis: accumulation of triglycerides in hepatocyte lipid droplets
J C Cohen et al. Science 2011;332:1519-1523
LiverTriglycerides
• LiverTGsaremaintainedthrough:• Acquisitionthroughuptakeoflipoproteinparticlesorfreefattyacids(secretedfromwhiteadipose)
• Denovosynthesisfromacetyl-CoAprecursors• Removalviaβ-oxidation,orsecretionofTG-richVLDLparticles
Why Chromosome 10? Significantly differentially expressed gene H2YAF2, from the binary DEG analysis, is located on chromosome 10
Original data = 27658 SNPs
Filtered data = 27339 SNPs
Did NOT filter based on relatedness
Would result in filtering out 15% of SNPs
ZERO genes met the p<10-8 criteriaMost significant gene: p<10-5
TheAlleleFREquency Database(ALFRED)
SNP11010552isinaSNPcluster:Theyareallintergenicb/wLOC439954andPBEF2,allunknownfunctions(frombothUCSCGenomebrowser,GTEx,andALFRED)withsamefrequency
rs7092191(AtoC,r2=.9)rs10827617(AtoC,r2=.632)rs7067812(AtoC,r2=.632)
Next most significant genes: p<10-4
GG AAAG
From:GTEX
*Involvedinfattyacidoxidation(Reactome)eQTL
PHYHexpressionisdiminishedinthepresenceofrs7916990
LiverMuscle
(GTEx)
UCSCGenomeBrowser
rs7916990(neartranscriptionfactorbindingsites)
GTEX(showingeQTL’s forPHYH)
(SNAP)
Thank you!