805. Genotyping errors in SNP markers: types, consequences, and a novel detection method

Abstract

Genotyping errors consist in misclassification of genotypes at a genetic marker. Most research using genotyping arrays only report generic screening of SNPs due to low calling rate, departures of Hardy-Weinberg equilibrium or because of reduced allele frequency (Minimum Allele Frequency, MAF). Detection of genotyping errors for a particular experimental dataset remains generally unreported. We propose to relate the probability of genotyping errors to the probability of the rate of rejection of true parent-offspring. Only single nucleotide polymorphisms (SNPs) at intermediate frequencies are useful to determine genotyping errors. Genotyping errors are detected mostly for SNPs at allele frequencies between 0.18 and 0.50. Our method can estimate the probability of generic (across all SNPs) and specific (affecting some SNPs) genotyping errors. For the rate of rejection of 0.000735 in a porcine HD array we estimated a genotyping error of 6 out of 1000 SNPs.