Estimating genotyping error rate in a fine-mapping project

Abstract

Genotyping errors may be problematic with microsatellite markers selected for fine mapping. We studied errors in 22,500 genotypes of 60 such markers using semi-automated fluorescent methods, with 4,488 (20%) genotypes duplicated separately. DNA was available for affected individuals plus parents and/or siblings. In the entire panel, inheritance error-checking detected 25 microsatellite mutations (0.056% of alleles) and 16 priming site mutations (0.037%); 64 sample swap errors; and 203 missed alleles or call errors (0.9%), of which 110 were due to three markers with disproportionate amplification. For the remaining 57 markers, 93 erroneous calls (0.44%) were detected. Discordancies (other tha..