%0 Generic %A T.J., Hoffmann %A C., Lange %A S., Vansteelandt %A B.A., Raby %A D.L., DeMeo %A E.K., Silverman %A S.T., Weiss %A N.M., Laird %D 2009 %T Supplementary Material for: Parsing the Effects of Individual SNPs in Candidate Genes with Family Data %U https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Parsing_the_Effects_of_Individual_SNPs_in_Candidate_Genes_with_Family_Data/5120932 %R 10.6084/m9.figshare.5120932.v1 %2 https://karger.figshare.com/ndownloader/files/8705281 %K Binary trait %K Candidate gene analysis %K Family-based association tests %K FBAT-C %K Linkage disequilibrium (LD) %K Model-based test %K Model-free test %K Nuclear families %K Quantitative trait %X We introduce a stepwise approach for family-based designs for selecting a set of markers in a gene that are independently associated with the disease. The approach is based on testing the effect of a set of markers conditional on another set of markers. Several likelihood-based approaches have been proposed for special cases, but no model-free based tests have been proposed. We propose two types of tests in a family-based framework that are applicable to arbitrary family structures and completely robust to population stratification. We propose methods for ascertained dichotomous traits and unascertained quantitative traits. We first propose a completely model-free extension of the FBAT main genetic effect test. Then, for power issues, we introduce two model-based tests, one for dichotomous traits and one for continuous traits. Lastly, we utilize these tests to analyze a continuous lung function phenotype as a proxy for asthma in the Childhood Asthma Management Program. The methods are implemented in the free R package fbati. %I Karger Publishers