BRASS: Permutation methods for binary traits in genetic association studies with structured samples

In genetic association analysis of complex traits, permutation testing can be a valuable tool for assessing significance when the distribution of the test statistic is unknown or not well-approximated. This commonly arises, e.g, in tests of gene-set, pathway or genome-wide significance, or when the statistic is formed by machine learning or data adaptive methods. Existing applications include eQTL mapping, association testing with rare variants, inclusion of admixed individuals in genetic association analysis, and epistasis detection among many others. For genetic association testing in samples with population structure and/or relatedness, use of naive permutation can lead to inflated type 1 error. To address this in quantitative traits, the MVNpermute method was developed. However, for association mapping of a binary trait, the relationship between the mean and variance makes both naive permutation and the MVNpermute method invalid. We propose BRASS, a permutation method for binary traits, for use in association mapping in structured samples. In addition to modeling structure in the sample, BRASS allows for covariates, ascertainment and simultaneous testing of multiple markers, and it accommodates a wide range of test statistics. In simulation studies, we compare BRASS to other permutation and resampling-based methods in a range of scenarios that include population structure, familial relatedness, ascertainment and phenotype model misspecification. In these settings, we demonstrate the superior control of type 1 error by BRASS compared to the other 6 methods considered. We apply BRASS to assess genome-wide significance for association analyses in domestic dog for elbow dysplasia (ED) and idiopathic epilepsy (IE). For both traits we detect previously identified associations, and in addition, for ED, we detect significant association with a SNP on chromosome 35 that was not detected by previous analyses, demonstrating the potential of the method.Author summary: To determine whether genetic association with a trait is significant, permutation methods are an attractive and popular approach when analytic methods based on distributional assumptions are not available, e.g., when applying machine learning or data adaptive methods, or when performing a multiple testing correction, e.g., to assess region-wide or genome-wide significance in association mapping studies. Existing applications include eQTL mapping, association testing with rare variants, inclusion of admixed individuals in genetic association analysis, and detection of genetic interaction among many others. However, when there is population structure in the sample, naive permutation of the data can lead to inflated significance of the association results. For continuous traits, linear mixed-model based approaches have been proposed for permutation-based tests that can also adjust for sample structure; however, these do not remain valid when applied to binary traits, as key features of binary data are not well accounted for. We propose BRASS, a permutation-based testing method for binary data that incorporates important characteristics of binary data in the trait model, can accommodate relevant covariates and ascertainment, and adjusts for the presence of structure in the sample. In simulations, we demonstrate the superior control of type 1 error by BRASS compared to other methods, and we apply BRASS in the context of correcting for multiple testing in two genome-wide association studies in domestic dog: one for elbow dysplasia and one for idiopathic epilepsy.