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PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs
Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661514/ https://www.ncbi.nlm.nih.gov/pubmed/26612672 http://dx.doi.org/10.1038/srep17302 |
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author | Cheng, Zhongshan Chu, Hin Fan, Yanhui Li, Cun Song, You-Qiang Zhou, Jie Yuen, Kwok-Yung |
author_facet | Cheng, Zhongshan Chu, Hin Fan, Yanhui Li, Cun Song, You-Qiang Zhou, Jie Yuen, Kwok-Yung |
author_sort | Cheng, Zhongshan |
collection | PubMed |
description | Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. |
format | Online Article Text |
id | pubmed-4661514 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-46615142015-12-02 PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs Cheng, Zhongshan Chu, Hin Fan, Yanhui Li, Cun Song, You-Qiang Zhou, Jie Yuen, Kwok-Yung Sci Rep Article Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets. Nature Publishing Group 2015-11-27 /pmc/articles/PMC4661514/ /pubmed/26612672 http://dx.doi.org/10.1038/srep17302 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Cheng, Zhongshan Chu, Hin Fan, Yanhui Li, Cun Song, You-Qiang Zhou, Jie Yuen, Kwok-Yung PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title_full | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title_fullStr | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title_full_unstemmed | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title_short | PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs |
title_sort | pexfins: an integrative post-gwas explorer for functional indels and snps |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661514/ https://www.ncbi.nlm.nih.gov/pubmed/26612672 http://dx.doi.org/10.1038/srep17302 |
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