Genotyping data from the Affymetrix 500K panel. SNP genotyping was performed with the commercial release of the Affymetrix 500K genotyping array. The genotyping was carried out at the Perlegen genotyping facility in Mountain View, California. Genotyping was attempted on 548 samples. 18 samples were unable to be genotyped because of poor DNA quality, and an additional 13 samples were removed after genotyping because their overall call rate did not exceed the 90% cutoff we required. We then applied SNP-wise quality checks on the 517 samples that were successfully genotyped. The Affymetrix 500K array consisted of 500,568 SNPs in total, 429,545 SNPs provided quality data from the genotyping assay, and we rejected those SNPs with a call rate < 75%, resulting in a final panel of 393,494 SNPs. We further filtered out SNPs with minor allele frequencies < 4% (81,646 SNPs) or SNPs that deviated from Hardy-Weinberg equilibrium (p < 10−4; 1,104 SNPs). The resulting set of 310,744 SNPs were used to carry out tests for association to the liver gene expression traits in the HLC.
