TDT statistics for mapping quantitative trait loci

The original transmission disequilibrium test (TDT), was introduced to test for linkage between a marker and a disease‐susceptibility locus (Spielman et al. 1993). Allison (1997) extended the TDT procedure to quantitative traits. Allison's test, however, is restrictive in that it requires family trios consisting of one heterozygous parent, one homozygous parent and one child, and considers only the situation where the marker locus is analogous to the quantitative trait locus itself. In this paper, we propose, investigate and apply a general TDT for quantitative traits that permits more than one child per family, does not require only one parent to be heterozygous, and allows for the fact that the various alleles at the marker and trait loci may be at varying degree of linkage disequilibrium. We also show that this TDT for quantitative traits is still a valid test of linkage in the presence of population substructure. To provide guidelines for study design, we develop analytic formulae for calculation of the power of the TDT for mapping quantitative trait loci and investigate the impact of various factors on the power. Power calculations show that the proposed TDT for quantitative traits is more powerful than Allison's basic test statistic and the extreme discordant sib pair linkage method. The proposed TDT statistic for quantitative traits is applied to systolic blood pressure variation in the Rochester Family Heart Study using an extremely discordant sibling pair design.