The impact of marker allele frequency misspecification in variance components quantitative trait locus analysis using sibship data

In cases where sibship data are collected for a quantitative trait locus (QTL) linkage study without access to parental genotypes, the proportion of genes shared identical by descent must be estimated using the marker allele frequencies. No systematic study has been conducted to date to evaluate the effect of misspecification of these frequencies on a test of quantitative trait linkage. Analysis of both simulated and actual data on quantitative traits was carried out under various sets of allele frequency estimates. While correctly specifying the allele frequency distribution led to a slightly more powerful test and higher lod scores, the differences were small and would not likely alter the conclusion of a study. These results suggest that, at least for QTL analysis, there is a great deal of tolerance for misspecifying marker allele frequencies with little, if any, appreciable effect on the linkage test. However, the observed variations may be sufficiently large to alter the priority one might give to a positive finding for follow up.