Supplementary Material for: Parsing the Effects of Individual SNPs in Candidate Genes with Family Data Hoffmann T.J. Lange C. Vansteelandt S. Raby B.A. DeMeo D.L. Silverman E.K. Weiss S.T. Laird N.M. 10.6084/m9.figshare.5120932.v1 https://karger.figshare.com/articles/dataset/Supplementary_Material_for_Parsing_the_Effects_of_Individual_SNPs_in_Candidate_Genes_with_Family_Data/5120932 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. 2009-12-04 00:00:00 Binary trait Candidate gene analysis Family-based association tests FBAT-C Linkage disequilibrium (LD) Model-based test Model-free test Nuclear families Quantitative trait