From the same liver samples received from the Liver Tissue Resource, DNA was obtained from 240 samples for genotyping. Genotyping was performed on the Illumina human 610 quad beadchip platform (GPL8887) at the Northwestern University Center for Genetic Medicine Genomics Core Facility according to the manufacturer's instructions. One sample was removed because it had a no call rate >10%. The initial marker set comprised 620,901 markers. 8,300 markers were removed because they showed significant deviation from Hardy-Weinberg equilibrium (HWE, Fischer's exact test, p<0.001). 29,705 SNPs were removed from the analysis because they had a no call rate in more than >10% of the samples. Hence, our final marker set is comprised of 583,073 SNPs. Identity by descent analysis, performed in Plink, revealed 14 pairs of duplicated samples. Erroneous, redundant sample collection was later confirmed by the tissue bank. Genotype and expression data for these samples were merged for all downstream analyses. The final sample set therefore consisted of 225 unique samples.
