The QTDT approach accommodates data not only from parents and siblings, but also from all available relatives. This test is also robust to population stratification. However, when population stratification is absent, it is possible to utilize even more information, namely the additional information contained in the founder genotypes. In this paper, we introduce a simple modification of the allelic transmission scoring scheme of Abecasis et al. that results in a more powerful test of linkage disequilibrium, but is only applicable in the absence of population stratification. This test, the quantitative trait linkage disequilibrium (QTLD) test, has been incorporated into a new procedure in the statistical genetics computer package SOLAR [5]. Like the QTDT, the QTLD is a direct test of linkage disequilibrium whose type I error rate is not inflated in the presence of linkage. Thus, it can be used to partition the total evidence into independent linkage and linkage disequilibrium components. We apply this procedure in a linkage/association analysis of an electrophysiological measurement previously shown to be related to alcoholism. We also demonstrate by simulation the increase in power obtained with the QTLD test, relative to the QTDT, when a true association exists between a marker and a QTL.
