Detecting epistasis via Markov bases

DOI10.18409/JAS.V2I1.27zbMATH Open1395.62345arXiv1006.4929OpenAlexW2963841409MaRDI QIDQ2819989FDOQ2819989

Authors: Anna-Sapfo Malaspinas, Caroline Uhler 

Publication date: 13 September 2016

Published in: Journal of Algebraic Statistics (Search for Journal in Brave)

Abstract: 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 SNPs.

Full work available at URL: https://arxiv.org/abs/1006.4929

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zbMATH Keywords

epistasisFisher's exact testsparse contingency tablesMarkov basisassociation studies

Mathematics Subject Classification ID

Parametric hypothesis testing (62F03) Applications of statistics to biology and medical sciences; meta analysis (62P10) Contingency tables (62H17) Protein sequences, DNA sequences (92D20)

Cited In (2)

• Algebraic methods for studying interactions between epidemiological variables
• Block-based Bayesian epistasis association mapping with application to WTCCC type 1 diabetes data

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