Research
Print page Print page
Switch language
The Capital Region of Denmark - a part of Copenhagen University Hospital
Published

WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

APA

CBE

MLA

Vancouver

Author

Bibtex

@article{5a2c50eb605d4ff8ba80aef0bee1fc8a,
title = "WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases",
abstract = "BACKGROUND: Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this context, epistasis is generally ignored. Data complexity and interpretation issues make it difficult to process and interpret epistasis. As the number of interaction grows exponentially with the number of variants, computational limitation is a bottleneck. Gene Network based strategies have been successful in integrating biological data and identifying relevant hub genes and pathways related to complex traits. In this study, epistatic interactions and network-based analysis are combined in the Weighted Interaction SNP hub (WISH) method and implemented in an efficient and easy to use R package.RESULTS: The WISH R package (WISH-R) was developed to calculate epistatic interactions on a genome-wide level based on genomic data. It is easy to use and install, and works on regular genomic data. The package filters data based on linkage disequilibrium and calculates epistatic interaction coefficients between SNP pairs based on a parallelized efficient linear model and generalized linear model implementations. Normalized epistatic coefficients are analyzed in a network framework, alleviating multiple testing issues and integrating biological signal to identify modules and pathways related to complex traits. Functions for visualizing results and testing runtimes are also provided.CONCLUSION: The WISH-R package is an efficient implementation for analyzing genome-wide epistasis for complex diseases and traits. It includes methods and strategies for analyzing epistasis from initial data filtering until final data interpretation. WISH offers a new way to analyze genomic data by combining epistasis and network based analysis in one method and provides options for visualizations. This alleviates many of the existing hurdles in the analysis of genomic interactions.",
author = "Carmelo, {Victor A O} and Kogelman, {Lisette J A} and Madsen, {Majbritt Busk} and Kadarmideen, {Haja N}",
year = "2018",
month = "7",
day = "31",
doi = "10.1186/s12859-018-2291-2",
language = "English",
volume = "19",
pages = "277",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central Ltd",
number = "1",

}

RIS

TY - JOUR

T1 - WISH-R- a fast and efficient tool for construction of epistatic networks for complex traits and diseases

AU - Carmelo, Victor A O

AU - Kogelman, Lisette J A

AU - Madsen, Majbritt Busk

AU - Kadarmideen, Haja N

PY - 2018/7/31

Y1 - 2018/7/31

N2 - BACKGROUND: Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this context, epistasis is generally ignored. Data complexity and interpretation issues make it difficult to process and interpret epistasis. As the number of interaction grows exponentially with the number of variants, computational limitation is a bottleneck. Gene Network based strategies have been successful in integrating biological data and identifying relevant hub genes and pathways related to complex traits. In this study, epistatic interactions and network-based analysis are combined in the Weighted Interaction SNP hub (WISH) method and implemented in an efficient and easy to use R package.RESULTS: The WISH R package (WISH-R) was developed to calculate epistatic interactions on a genome-wide level based on genomic data. It is easy to use and install, and works on regular genomic data. The package filters data based on linkage disequilibrium and calculates epistatic interaction coefficients between SNP pairs based on a parallelized efficient linear model and generalized linear model implementations. Normalized epistatic coefficients are analyzed in a network framework, alleviating multiple testing issues and integrating biological signal to identify modules and pathways related to complex traits. Functions for visualizing results and testing runtimes are also provided.CONCLUSION: The WISH-R package is an efficient implementation for analyzing genome-wide epistasis for complex diseases and traits. It includes methods and strategies for analyzing epistasis from initial data filtering until final data interpretation. WISH offers a new way to analyze genomic data by combining epistasis and network based analysis in one method and provides options for visualizations. This alleviates many of the existing hurdles in the analysis of genomic interactions.

AB - BACKGROUND: Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this context, epistasis is generally ignored. Data complexity and interpretation issues make it difficult to process and interpret epistasis. As the number of interaction grows exponentially with the number of variants, computational limitation is a bottleneck. Gene Network based strategies have been successful in integrating biological data and identifying relevant hub genes and pathways related to complex traits. In this study, epistatic interactions and network-based analysis are combined in the Weighted Interaction SNP hub (WISH) method and implemented in an efficient and easy to use R package.RESULTS: The WISH R package (WISH-R) was developed to calculate epistatic interactions on a genome-wide level based on genomic data. It is easy to use and install, and works on regular genomic data. The package filters data based on linkage disequilibrium and calculates epistatic interaction coefficients between SNP pairs based on a parallelized efficient linear model and generalized linear model implementations. Normalized epistatic coefficients are analyzed in a network framework, alleviating multiple testing issues and integrating biological signal to identify modules and pathways related to complex traits. Functions for visualizing results and testing runtimes are also provided.CONCLUSION: The WISH-R package is an efficient implementation for analyzing genome-wide epistasis for complex diseases and traits. It includes methods and strategies for analyzing epistasis from initial data filtering until final data interpretation. WISH offers a new way to analyze genomic data by combining epistasis and network based analysis in one method and provides options for visualizations. This alleviates many of the existing hurdles in the analysis of genomic interactions.

U2 - 10.1186/s12859-018-2291-2

DO - 10.1186/s12859-018-2291-2

M3 - Journal article

VL - 19

SP - 277

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - 1

ER -

ID: 54944323