Comparison of identical single nucleotide polymorphisms genotyped by the GeneChip Targeted Genotyping 25K, Affymetrix 500K and Illumina 550K platforms

Comparisons of targeted genotyping chips to ready-made chips are important because targeted chips are suitable for fine-scale association mapping with a reasonable cost. Genotypes produced by the Affymetrix Targeted Genotyping (TG) 25K, Affymetrix 500K, and Illumina 550K arrays for regions on chromosomes 2 and 7 of 90 individuals were assessed to investigate genotype accordance between the platforms. The common SNPs in TG the Affymetrix and Illumina arrays showed similar genotype accordance. The consistency rate of the Illumina array to consensus genotypes, i.e., identically called by more than two platforms, was the highest, and that of the Affymetrix array was the lowest. The TG array data showed high accordance and reasonable consistency between platforms.