There is remarkable agreement for SNP genotypes called with the Illumina and Affymetrix platforms. The concordance is estimated to be 99.85%. However, there is a substantially higher no-call rate with the Affymetrix platform and the no-call rate appears to be genotype- and SNP-specific. This differential no-call rate gave rise to 4 (13%) significant departures from HWE in 32 SNPs that showed one or more discrepancy between the two platforms. The SNP that showed the largest number of discrepancies (rs958883 in the Illumina dataset and tsc0260848 in the Affymetrix dataset) was analyzed to determine if the presence of double recombinants could help resolve the differences. Analysis of recombination in 12 White families gave persuasive evidence of increased recombination using the Affymetrix genotypes but no increase using the Illumina genotypes. Analysis of a single family that contained 3 offspring with the disputed genotype identified 3 double recombinants using the Affymetrix genotypes but none with the Illumina genotypes.
