To identify loci associated with lymphocyte counts, we conducted a GWAS using lymphocyte counts from 462 Hutterite subjects as the phenotypes, and genome-wide genotypes (using the Affymetrix 500k array platform; see Materials and Methods; 24,26,27). After filtering SNPs based on quality control measures (Materials and Methods), 279 749 autosomal SNPs remained. We tested for genetic association with lymphocyte counts using a general two-allele model (GTAM) test (24), which accounts for the known relatedness between individuals in our sample. A quantile–quantile plot did not indicate any remaining population structure or global departures from the null expectation (Supplementary Material, Fig. S1), and accordingly, the genomic inflation factor was calculated to be only 1.03.
