NDLI: Comparison of Strategies to Detect Epistasis from eQTL Data

Content Provider	PubMed Central
Author	Kapur, Karen Schüpbach, Thierry Xenarios, Ioannis Kutalik, Zoltán Bergmann, Sven
Editor	Xiong, Momiao
Copyright Year	2011
Abstract	Genome-wide association studies have been instrumental in identifying genetic variants associated with complex traits such as human disease or gene expression phenotypes. It has been proposed that extending existing analysis methods by considering interactions between pairs of loci may uncover additional genetic effects. However, the large number of possible two-marker tests presents significant computational and statistical challenges. Although several strategies to detect epistasis effects have been proposed and tested for specific phenotypes, so far there has been no systematic attempt to compare their performance using real data. We made use of thousands of gene expression traits from linkage and eQTL studies, to compare the performance of different strategies. We found that using information from marginal associations between markers and phenotypes to detect epistatic effects yielded a lower false discovery rate (FDR) than a strategy solely using biological annotation in yeast, whereas results from human data were inconclusive. For future studies whose aim is to discover epistatic effects, we recommend incorporating information about marginal associations between SNPs and phenotypes instead of relying solely on biological annotation. Improved methods to discover epistatic effects will result in a more complete understanding of complex genetic effects.
Related Links	http://dx.doi.org/10.1371/journal.pone.0028415
Starting Page	28415
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	12
Volume Number	6
Language	English
Publisher	Public Library of Science
Publisher Date	2011-12-19
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

eQTL Epistasis – Challenges and Computational Approaches

Model-Based Multifactor Dimensionality Reduction to detect epistasis for quantitative traits in the presence of error-free and noisy data

Perceptual Strategies of Pigeons to Detect a Rotational Centre—A Hint for Star Compass Learning?

Comparison of model-based tests and selection strategies to detect genetic polymorphisms influencing pharmacokinetic parameters

An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies

A comparison of methods to detect urinary tract infections using electronic data

A practical method to detect SNVs and indels from whole genome and exome sequencing data

Data from: Negative epistasis between beneficial mutations in an evolving bacterial population (Dataset)

Two-stage strategies to detect gene × gene interactions in case-control data

Comparison of Strategies to Detect Epistasis from eQTL Data

Similar Documents

eQTL Epistasis – Challenges and Computational Approaches

Model-Based Multifactor Dimensionality Reduction to detect epistasis for quantitative traits in the presence of error-free and noisy data

Perceptual Strategies of Pigeons to Detect a Rotational Centre—A Hint for Star Compass Learning?

Comparison of model-based tests and selection strategies to detect genetic polymorphisms influencing pharmacokinetic parameters

An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies

A comparison of methods to detect urinary tract infections using electronic data

A practical method to detect SNVs and indels from whole genome and exome sequencing data

Data from: Negative epistasis between beneficial mutations in an evolving bacterial population (Dataset)

Two-stage strategies to detect gene × gene interactions in case-control data

Comparison of Strategies to Detect Epistasis from eQTL Data