A unified Haseman-Elston method for testing linkage with quantitative traits

Abstract

The Haseman and Elston (H-E) method uses a simple linear regression to model the squared trait difference of sib pairs with the shared allele identical by descent (IBD) at marker locus for linkage testing. Under this setting, the squared mean-corrected trait sum is also linearly related to the IBD sharing. However, the resulting slope estimate for either model is not efficient. In this report, we propose a simple linkage test that optimally uses information from the estimates of both models. We also demonstrate that the new test is more powerful than both the traditional one and the recently revisited H-E methods.

Figure 1

Power comparisons between the new procedure and the two H-E tests for linkage. A, Additive-trait locus with P=.1. B, Dominant-trait locus with P=.1. C, Recessive trait with P=.2. The average Z scores using traditional (model [1]), revisited (model [3]), and unified H-E methods are represented by dotted, dashed, and solid lines, respectively. Locus-specific heritability is h=.1 (circle), .2 (square), .3 (triangle), and .4 (diamond).