A vast resource of allelic expression data spanning human tissues

Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153...

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Autores principales: Castel, Stephane E., Aguet, François, Mohammadi, Pejman, Ardlie, Kristin G., Lappalainen, Tuuli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488534/
https://www.ncbi.nlm.nih.gov/pubmed/32912332
http://dx.doi.org/10.1186/s13059-020-02122-z
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author Castel, Stephane E.
Aguet, François
Mohammadi, Pejman
Ardlie, Kristin G.
Lappalainen, Tuuli
author_facet Castel, Stephane E.
Aguet, François
Mohammadi, Pejman
Ardlie, Kristin G.
Lappalainen, Tuuli
author_sort Castel, Stephane E.
collection PubMed
description Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.
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spelling pubmed-74885342020-09-15 A vast resource of allelic expression data spanning human tissues Castel, Stephane E. Aguet, François Mohammadi, Pejman Ardlie, Kristin G. Lappalainen, Tuuli Genome Biol Short Report Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues. BioMed Central 2020-09-11 /pmc/articles/PMC7488534/ /pubmed/32912332 http://dx.doi.org/10.1186/s13059-020-02122-z Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
spellingShingle Short Report
Castel, Stephane E.
Aguet, François
Mohammadi, Pejman
Ardlie, Kristin G.
Lappalainen, Tuuli
A vast resource of allelic expression data spanning human tissues
title A vast resource of allelic expression data spanning human tissues
title_full A vast resource of allelic expression data spanning human tissues
title_fullStr A vast resource of allelic expression data spanning human tissues
title_full_unstemmed A vast resource of allelic expression data spanning human tissues
title_short A vast resource of allelic expression data spanning human tissues
title_sort vast resource of allelic expression data spanning human tissues
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488534/
https://www.ncbi.nlm.nih.gov/pubmed/32912332
http://dx.doi.org/10.1186/s13059-020-02122-z
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