A new test for linkage in affected sib pairs

Abstract

In affected sib pair linkage methods the mean proportion of marker alleles shared identical by descent (ibd) among affected sib pairs has been shown to be a powerful test for detecting linkage compared with other tests for most situations. However, it is not always possible to estimate identity by descent sharing between sibs unambiguously, even when the parental genotypes are known. Here we define a measure of informativity for scoring ibd sharing based on the parental mating and sib pair genotypes. This measure reflects the precision with which one can obtain the ibd sharing information between sibs based on family data. Then we define a new weighted mean proportion of alleles shared ibd by sib pairs test statistics. In this study we assign precision for estimating the ibd sharing as weights to the proportion of alleles shared ibd by affected sib pairs. However, the simulation results showed that there is no significant gain in power using the weighted mean proportion test. Implications of this observation are discussed.