We have introduced the QTLD test, a novel approach for detecting association due to linkage disequilibrium in the absence of population stratification. We have confirmed in our simulations that the QTLD test provides a significant increase, relative to the QTDT, in power to detect an allelic association. Investigators can now use SOLAR to conduct a combined linkage and association analysis, using pedigrees of arbitrary size and complexity, that includes a test for population stratification along with several tests of association: measured genotype, QTDT, and, where appropriate, the QTLD test. Our application of this procedure to the COGA data for TTTH1 identified several SNPs under the chromosome 7 linkage peak which exhibit suggestive levels of association, although none were statistically significant after correction for multiple testing.
