Whole genome sequencing enables all genetic variants present in a sample set to be tested directly for association with a given disease or trait. To quantify the benefit of having more complete ascertainment of genetic variation beyond that achievable with genotyping arrays, we carried out expression quantitative trait loci (eQTL) association tests on the 142 low coverage samples for which expression data are available in the cell lines27. When association analysis (Spearman rank correlation, FDR < 5%, eQTLs within 50 kb of probe) was performed using all sites discovered in the low coverage project, a larger number of significant eQTLs (increase of ~20% to 50%) was observed as compared to association analysis restricted to sites present on the Illumina 1M chip (Supplementary Table 6). The increase was lower in the CHB+JPT and CEU samples, where greater LD exists between previously examined and newly discovered variants, and higher in the YRI samples, where there are more novel variants and less LD. These results indicate that, while modern genotyping arrays capture most of the common variation, there remain substantial additional contributions to phenotypic variation from the variants not well captured by the arrays.
