Genome-wide genotypes for individuals included in the GWAS (n = 462) were obtained using the Affymetrix GeneChip® Mapping 500K Array Set [Affy 500k; Affymetrix, Santa Clara, CA, USA; genotype data previously reported in (65,66)]. Genotypes were called using BRLMM (http://media.affymetrix.com/support/technical/whitepapers/brlmm_whitepaper.pdf). Only SNPs with minor allele frequencies ≥ 5%, call rates ≥ 95%, Hardy–Weinberg equilibrium P-values ≥ 0.001 and fewer than five Mendelian errors across all subjects genotyped on the Affy 500k set (regardless of whether lymphocyte counts were available; n = 695) were included. SNP coordinates were re-annotated to the human genome (hg18, March 2006) according to the dbSNP130 records obtained using UCSC (http://genome.ucsc.edu/; 67) and Galaxy (http://main.g2.bx.psu.edu/; 68,69). After quality control and remapping, 279 749 SNPs were included in the GWAS.
