--- _id: '2961' abstract: - lang: eng text: |- 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 specic 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). acknowledgement: Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship. Caroline Uhler is supported by an International Fulbright Science and Technology Fellowship. author: - first_name: Anna full_name: 'Malaspinas, Anna-Sapfo ' last_name: Malaspinas - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Malaspinas A, Uhler C. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2011;2(1):36-53. doi:http://dx.doi.org/10.18409/jas.v2i1.27 apa: Malaspinas, A., & Uhler, C. (2011). Detecting epistasis via Markov bases. Journal of Algebraic Statistics. Public Knowledge Project. http://dx.doi.org/10.18409/jas.v2i1.27 chicago: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics. Public Knowledge Project, 2011. http://dx.doi.org/10.18409/jas.v2i1.27. ieee: A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” Journal of Algebraic Statistics, vol. 2, no. 1. Public Knowledge Project, pp. 36–53, 2011. ista: Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2(1), 36–53. mla: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics, vol. 2, no. 1, Public Knowledge Project, 2011, pp. 36–53, doi:http://dx.doi.org/10.18409/jas.v2i1.27. short: A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53. date_created: 2018-12-11T12:00:34Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' doi: http://dx.doi.org/10.18409/jas.v2i1.27 extern: 1 intvolume: ' 2' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.4929 month: '01' oa: 1 page: 36 - 53 publication: Journal of Algebraic Statistics publication_status: published publisher: Public Knowledge Project publist_id: '3764' quality_controlled: 0 status: public title: Detecting epistasis via Markov bases type: journal_article volume: 2 year: '2011' ...