Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster

Abstract The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal g...

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Autores principales:	Izel Fourie Sørensen, Stefan M. Edwards, Palle Duun Rohde, Peter Sørensen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b731d87ff1264fb19669b12720282bca
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spelling	oai:doaj.org-article:b731d87ff1264fb19669b12720282bca2021-12-02T12:32:58ZMultiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster10.1038/s41598-017-02281-32045-2322https://doaj.org/article/b731d87ff1264fb19669b12720282bca2017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02281-3https://doaj.org/toc/2045-2322Abstract The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal genetic variants. We aimed at searching for patterns in GBLUP-derived single-marker statistics, by including them in genetic marker set tests, that could reveal associations between a set of genetic markers (genomic feature) and a complex trait. GBLUP-derived set tests proved to be powerful for detecting genomic features, here defined by gene ontology (GO) terms, enriched for causal variants affecting a quantitative trait in a population with low degree of relatedness. Different set test approaches were compared using simulated data illustrating the impact of trait- and genomic feature-specific factors on detection power. We extended the most powerful single trait set test, covariance association test (CVAT), to a multiple trait setting. The multiple trait CVAT (MT-CVAT) identified functionally relevant GO categories associated with the quantitative trait, chill coma recovery time, in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel.Izel Fourie SørensenStefan M. EdwardsPalle Duun RohdePeter SørensenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-17 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Izel Fourie Sørensen Stefan M. Edwards Palle Duun Rohde Peter Sørensen Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
description	Abstract The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal genetic variants. We aimed at searching for patterns in GBLUP-derived single-marker statistics, by including them in genetic marker set tests, that could reveal associations between a set of genetic markers (genomic feature) and a complex trait. GBLUP-derived set tests proved to be powerful for detecting genomic features, here defined by gene ontology (GO) terms, enriched for causal variants affecting a quantitative trait in a population with low degree of relatedness. Different set test approaches were compared using simulated data illustrating the impact of trait- and genomic feature-specific factors on detection power. We extended the most powerful single trait set test, covariance association test (CVAT), to a multiple trait setting. The multiple trait CVAT (MT-CVAT) identified functionally relevant GO categories associated with the quantitative trait, chill coma recovery time, in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel.
format	article
author	Izel Fourie Sørensen Stefan M. Edwards Palle Duun Rohde Peter Sørensen
author_facet	Izel Fourie Sørensen Stefan M. Edwards Palle Duun Rohde Peter Sørensen
author_sort	Izel Fourie Sørensen
title	Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
title_short	Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
title_full	Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
title_fullStr	Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
title_full_unstemmed	Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
title_sort	multiple trait covariance association test identifies gene ontology categories associated with chill coma recovery time in drosophila melanogaster
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b731d87ff1264fb19669b12720282bca
work_keys_str_mv	AT izelfouriesørensen multipletraitcovarianceassociationtestidentifiesgeneontologycategoriesassociatedwithchillcomarecoverytimeindrosophilamelanogaster AT stefanmedwards multipletraitcovarianceassociationtestidentifiesgeneontologycategoriesassociatedwithchillcomarecoverytimeindrosophilamelanogaster AT palleduunrohde multipletraitcovarianceassociationtestidentifiesgeneontologycategoriesassociatedwithchillcomarecoverytimeindrosophilamelanogaster AT petersørensen multipletraitcovarianceassociationtestidentifiesgeneontologycategoriesassociatedwithchillcomarecoverytimeindrosophilamelanogaster
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Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster

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