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.
Saunders
Ian W
IW
Preventative Health National Research Flagship, Private Bag No. 2, Glen Osmond, SA 5064, Australia. Ian.Saunders@csiro.au
Brohede
Jesper
J
Hannan
Garry N
GN
D000465:Algorithms; D001315:Australia; D005192:Family Health; D005821:Genetic Techniques; D005820:Genetic Testing; D016678:Genome; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D015203:Reproducibility of Results