After exclusion of 41 SNPs, individual call rates were calculated using the entire multi-ethnic sample (n = 548) and after stratifying by DNA type, i.e. genomic (gDNA) and whole genome amplified (wgaDNA) DNA. Individuals with a call rate <90% were removed from the analysis (n = 14) for a total of 500 individuals with gDNA and 34 individuals with wgaDNA. While there was a substantial difference between the call rate distributions for the gDNA samples (99.6% of individuals with a call rate ≥95%) in comparison with the wgaDNA samples (85.3% of individuals with a call rate ≥95%), inspection of Illumina data for SNPs with drastically discordant SNP call rates between the two DNA types revealed reliable genotyping calls for SNPs with a SNP call rate calculated using only wgaDNA samples of ≥80%. Thus, for 51 SNPs in which the SNP call rate was ≤80% for wgaDNA samples, we only report analyses using the individuals with gDNA samples.
