Malaspinas, Anna-Sapfo Creator Faculty cuhler@mit.edu Uhler, Caroline Creator MATH / Applied Mathematics Illinois Institute of Technology Affiliated department Epistasis Markov basis association studies sparse contingency tables Fisher’s exact test 2011 2011 Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher’s exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs). Article

born digital application/pdf en https://doi.org/10.18409/jas.v2i1.27 2 Open Access eng http://hdl.handle.net/10560/islandora:1007830