As there are many publications on the effect of sample correlation on association analysis, and on using pedigrees in association studies, related questions that are not addressed here include: (1) combining linkage and association signals (Göring and Terwilliger, 2000; Li et al., 2005); (2) family-based associations such as transmission disequilibrium test (TDT) and its extensions (Nagelkerke et al., 2004; Allen-Brady et al., 2005; Gray et al., 2009); (3) association using multiple family members with novel test statistics instead of the standard chi-square test (Risch and Teng, 1998; Teng and Risch, 1999; Li et al., 2000); (4) association with unknown (“cryptic”) correlations (Voight and Pritchard, 2005; Astle and Blading, 2009; Rakovski and Stram, 2009; Thornton and McPeek, 2010; Sillanpää, 2011) where the relativeness between samples is detected instead of given (Weir et al., 2006; Choi et al., 2009). This paper is about a simple and accessible method to incorporate sample correlations in genetic case-control studies within the standard chi-square test framework.
