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  • Title: Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference.
    Author: Saunders IW, Brohede J, Hannan GN.
    Journal: Genomics; 2007 Sep; 90(3):291-6. PubMed ID: 17587543.
    Abstract:
    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.
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