We performed a HWE assessment of the 34 autosomal SNPs that showed one or more discrepancies between the two platforms. This assessment was performed on a panel of 245 unrelated Whites drawn from the COGA families. None of the 34 SNPs from the Illumina platform was significantly out of equilibrium. Four of the 34 SNPs from the Affymetrix platform were found not to be in HWE (tsc0546488, p < 0.0001; tsc1018661, p = 0.014; tsc0039689, p = 0.023; tsc0280570, p = 0.022). None of these departures from HWE proportions is due to discrepancies in allele calling, however, because the number of discrepancies for tsc0546488, tsc1018661, tsc0039689, and tsc0280570 are only 1, 1, 3, and 1, respectively. Rather, the departures from HWE are due to differential no-calls in the Affymetrix platform. Compared to their Illumina counterparts (where genotypes are reported for all 245 unrelated individuals for each SNP), the number of no-calls for tsc0546488, tsc1018661, tsc0039689, and tsc0280570 are 51, 25, 18, and 28. For the first 3 SNPs all of the no-calls were for genotypes called heterozygous in the Illumina
