---
_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'
...