A tool for detecting complementary single nucleotide polymorphism pairs in genome-wide association studies for epistasis testing

Caylak, Gizem and Taştan, Öznur and Cicek, A. Ercument (2021) A tool for detecting complementary single nucleotide polymorphism pairs in genome-wide association studies for epistasis testing. Journal of Computational Biology, 28 (4). pp. 378-380. ISSN 1066-5277 (Print) 1557-8666 (Online)

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Abstract

Detecting interacting loci pairs has been instrumental to understand disease etiology when single locus associations do not fully account for the underlying heritability. However, the number of loci to test is prohibitively large. Epistasis test prioritization algorithms rank likely epistatic single nucleotide polymorphism (SNP) pairs to limit the number of statistical tests. Potpourri detects epistatic SNP pairs by diversifying the selected SNPs' genomic regions and investigating their co-occurrence patterns over the case cohort. It can also input and further prioritize SNPs in regulatory or coding regions. The program identifies and returns a list of prioritized SNP pairs for epistasis testing. This article describes how to use the program and the details of the input and output data.
Item Type: Article
Uncontrolled Keywords: complementation; diversification; epistasis test prioritization; population cover; submodular optimization
Divisions: Faculty of Engineering and Natural Sciences
Depositing User: Öznur Taştan
Date Deposited: 03 Sep 2022 18:40
Last Modified: 03 Sep 2022 18:40
URI: https://research.sabanciuniv.edu/id/eprint/43437

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