Population-based association study using unrelated individuals is a powerful strategy (Risch and Merikangas, 1996; Risch, 2000) for detecting association between markers and quantitative trait loci (QTLs). However, association test using unrelated individuals may suffer from confounding due to population structure. In this paper, we examine the impact of confounding due to population substructure on commonly used statistical procedures. Two study designs for genetic association study are considered: 1) retrospective sampling of cases and controls according to two cutoff points of the quantitat...
