Each SNP had approximately 15 PAF estimates per array. For each pool, a small number of SNPs had fewer than 20 PAF estimates available and these SNPs were dropped. After normalization, SNPs were removed from the analysis if they had a -log10(p) value > 6 for the quality control score described in Macgregor et al. (2008). SNPs from the sex chromosomes were also dropped. Overall, on the deCODE run 1M v3 arrays, ~918000 SNPs passed quality control (the vast majority of omitted SNPs were dropped due to their having <1% frequency in the CEU HapMap samples). For the QIMR run 1M v1 arrays, ~375k SNPs from the “bottom” strand were included in the analysis with the deCODE generated data (i.e. ~40% of SNPs had data from 6 arrays per pool, with the remainder typed on 3 arrays per pool).
