In order to map genetic loci associated with lymphocyte count, we used the GTAM association test previously described in reference (73; see Supplementary data, Fig. S1 for a quantile–quantile plot of the GWAS results). Association testing is a two-step process. In the first step, the heritability of lymphocyte count was calculated for the sample using a maximum likelihood-based variance component estimation method (74). The fit of different models of heritability [environmental only (E), additive genetic effects (A + E), dominance genetic effects (D + E) or a full model (A + D + E)] were compared using the Bayesian information criterion, and the best fitting model was chosen (in our case, a model with additive and environmental effects with no dominance effects). We estimated the heritability of lymphocyte count in our sample to be 0.41. In the second step, each SNP was tested for association with the quantitative trait using a linear mixed-effects model framework. The model, below, has previously been described in detail (73):
