Power of TDT The Power of Transmission Disequilibrium Tests for Quantitative Traits Jinming Li † , Dai Wang † , Jianping Dong, Renfang Jiang, Kui Zhang, Shuanglin Zhang, Hongyu Zhao, Fengzhu Sun * Department of Epidemiology and Public Health, Yale University School of Medicine, New Heaven, Connecticut (J.L., K.Z., S.Z., H.Z.), Department of Mathematics, University of Southern California, Los Angeles, California (D.W., K.Z., F.S.), Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan (J.D., R.J.) We develop a score statistic to test for linkage in the presence of linkage disequilibrium for quantitative traits. We then extend this method to analyze multiple tightly linked markers. One potential limitation with the use of many genetic markers is the large number of degrees of freedom involved that may reduce the overall power to detect linkage. To overcome this limitation, we propose to group haplotypes on the basis of haplotype similarity before performing transmission disequilibrium tests. Finally, we apply these methods to the GAW12 simulated data and compare their power. Key words: transmission/disequilibrium test, quantitative trait, haplotype INTRODUCTION The transmission disequilibrium test (TDT) for linkage introduced by Spielman et al. [1993] employs a family-based design and is robust to population stratification. Schaid [1996] proposed a general score statistic for the TDT. In this article, we extend Schaid’s results and develop a score statistic for quantitative traits. We show that the tests for † These authors contributed equally to this work. * Correspondence to: Dr. Fengzhu Sun, Department of Mathematics, University of Southern California, Los Angeles, CA 90089. Fax: 213-740-2424. E-mail: fsun@hto.usc.edu 1