Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference

A simple method of inferring the genotyping error rate of SNP arrays and similar high-throughput genotyping methods from Mendelian errors is described. Application to genotypes from small families using the Affymetrix GeneChip Human Mapping 50 k Array indicates an error rate of about 0.1%, and this rate can be reduced by increasing the quality criterion for calls, though at the cost of a reduced genotype call rate, which limits the benefit available. Simulated data are used to show that the number of SNPs on this array is sufficient for such a low error rate to have little impact on identical by descent-based inference for disease linkage in sib-pair studies.