Hardy–Weinberg quality control


N. Morton, Human Genetics, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, U.K. Tel: +44 (0) 23 8079 6535; Fax: +44 (0) 23 8079 4264. E-mail: nem@soton.ac.uk


An efficient test of deviation from Hardy–Weinberg frequencies with one degree of freedom was applied to 44 marker loci in a genome scan, and 7 loci had a significant excess of apparent homozygotes (χ2(1) > 6) suggestive of typing error. In this example evidence for linkage did not increase when outliers were censored. Statistical quality control is an essential part of genotyping, and the effect of mistyping and map error should be considered in evaluating any genome scan.