We investigated possible causes of spurious associations in the PCLO region (chr7:82,032,093-82,436,848). First, these findings were not due to plate effects as inspection of plate-specific association data for these SNPs did not show any marked outliers or systematic biases. Second, review of allelic intensity cluster plots on which genotype calls were based revealed adequate performance of the Perlegen genotype calling algorithm. Third, inspection of additional quality control metrics did not suggest systematic problems with SNPs in this region. Fourth, inspection of LD matrices excluded very high LD as the sole explanation for the results (Supplemental Figure 10), and none of the genotyped SNPs had strong LD (r2 ≥ 0.8) with rs2715148 (the SNP with the smallest p-value in the PCLO region). Fifth, population stratification can cause false positive findings but this did not appear to explain the PCLO association: (a) the same 11 SNPs had p-values among the top 200 associations in unadjusted analyses as well as with adjustment via principal components and stratified analyses; and (b) for the 57 SNPs in the PCLO region, the p-values across these three
