Cargando…

Association of genetic variations and gene expression in a family-based study

BACKGROUND: Expression quantitative trait locus (eQTL) maps are considered a valuable resource in studying complex diseases. The availability of gene expression data from the Genetic Analysis Workshop 19 (GAW19) provides a great opportunity to investigate the association of gene expression with gene...

Descripción completa

Detalles Bibliográficos
Autores principales: Pitsillides, Achilleas N., Choi, Seung-Hoan, Hogan, John D., Hong, Jaeyoung, Lin, Honghuang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133483/
https://www.ncbi.nlm.nih.gov/pubmed/27980620
http://dx.doi.org/10.1186/s12919-016-0014-0
_version_ 1782471271335854080
author Pitsillides, Achilleas N.
Choi, Seung-Hoan
Hogan, John D.
Hong, Jaeyoung
Lin, Honghuang
author_facet Pitsillides, Achilleas N.
Choi, Seung-Hoan
Hogan, John D.
Hong, Jaeyoung
Lin, Honghuang
author_sort Pitsillides, Achilleas N.
collection PubMed
description BACKGROUND: Expression quantitative trait locus (eQTL) maps are considered a valuable resource in studying complex diseases. The availability of gene expression data from the Genetic Analysis Workshop 19 (GAW19) provides a great opportunity to investigate the association of gene expression with genetic variants in blood. METHODS: A total of 267 samples with gene expression and whole genome sequencing data were employed in this study. We used linear mixed models with genetic random effects along with a permutation procedure to create an eQTL map. The eQTL map was further tested in terms of functional implication, including the enrichment in disease-related variants and in regulatory regions. RESULTS: We identified 22,869 significant eQTLs from the GAW19 data set. These eQTLs were highly enriched with genetic loci associated with blood pressure and DNase hypersensitive regions. In addition, the majority of genes associated with eQTLs showed moderate to high heritability (h (2) > 0.4). CONCLUSIONS: We successfully created an eQTL map from the GAW19 data set. Our study indicated that the eQTLs were enriched within regulatory regions, and tended to have relatively high heritability.
format Online
Article
Text
id pubmed-5133483
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-51334832016-12-15 Association of genetic variations and gene expression in a family-based study Pitsillides, Achilleas N. Choi, Seung-Hoan Hogan, John D. Hong, Jaeyoung Lin, Honghuang BMC Proc Proceedings BACKGROUND: Expression quantitative trait locus (eQTL) maps are considered a valuable resource in studying complex diseases. The availability of gene expression data from the Genetic Analysis Workshop 19 (GAW19) provides a great opportunity to investigate the association of gene expression with genetic variants in blood. METHODS: A total of 267 samples with gene expression and whole genome sequencing data were employed in this study. We used linear mixed models with genetic random effects along with a permutation procedure to create an eQTL map. The eQTL map was further tested in terms of functional implication, including the enrichment in disease-related variants and in regulatory regions. RESULTS: We identified 22,869 significant eQTLs from the GAW19 data set. These eQTLs were highly enriched with genetic loci associated with blood pressure and DNase hypersensitive regions. In addition, the majority of genes associated with eQTLs showed moderate to high heritability (h (2) > 0.4). CONCLUSIONS: We successfully created an eQTL map from the GAW19 data set. Our study indicated that the eQTLs were enriched within regulatory regions, and tended to have relatively high heritability. BioMed Central 2016-10-18 /pmc/articles/PMC5133483/ /pubmed/27980620 http://dx.doi.org/10.1186/s12919-016-0014-0 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Pitsillides, Achilleas N.
Choi, Seung-Hoan
Hogan, John D.
Hong, Jaeyoung
Lin, Honghuang
Association of genetic variations and gene expression in a family-based study
title Association of genetic variations and gene expression in a family-based study
title_full Association of genetic variations and gene expression in a family-based study
title_fullStr Association of genetic variations and gene expression in a family-based study
title_full_unstemmed Association of genetic variations and gene expression in a family-based study
title_short Association of genetic variations and gene expression in a family-based study
title_sort association of genetic variations and gene expression in a family-based study
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133483/
https://www.ncbi.nlm.nih.gov/pubmed/27980620
http://dx.doi.org/10.1186/s12919-016-0014-0
work_keys_str_mv AT pitsillidesachilleasn associationofgeneticvariationsandgeneexpressioninafamilybasedstudy
AT choiseunghoan associationofgeneticvariationsandgeneexpressioninafamilybasedstudy
AT hoganjohnd associationofgeneticvariationsandgeneexpressioninafamilybasedstudy
AT hongjaeyoung associationofgeneticvariationsandgeneexpressioninafamilybasedstudy
AT linhonghuang associationofgeneticvariationsandgeneexpressioninafamilybasedstudy