Overexpressed somatic alleles are enriched in functional elements in Breast Cancer

Abstract Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant...

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Autores principales:	Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, Anelia Horvath
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/de12aae9e1cb49908e4868f2314b57c1
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spelling	oai:doaj.org-article:de12aae9e1cb49908e4868f2314b57c12021-12-02T12:32:32ZOverexpressed somatic alleles are enriched in functional elements in Breast Cancer10.1038/s41598-017-08416-w2045-2322https://doaj.org/article/de12aae9e1cb49908e4868f2314b57c12017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08416-whttps://doaj.org/toc/2045-2322Abstract Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC). We document significant allele-preferential expression of functional variants in CGC genes and across the entire dataset. Notably, we find frequent allele-specific overexpression of variants in tumor-suppressor genes. We also report a list of over-expressed variants from non-CGC genes. Overall, our analysis presents an integrated set of features of somatic allele expression and points to the vast information content of the asymmetric alleles in the cancer transcriptome.Paula RestrepoMercedeh MovassaghNawaf AlomranChristian MillerMuzi LiChris TrenkovYulian ManchevSonali BahlStephanie WarnkenLiam SpurrTatiyana ApanasovichKeith CrandallNathan EdwardsAnelia HorvathNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Paula Restrepo Mercedeh Movassagh Nawaf Alomran Christian Miller Muzi Li Chris Trenkov Yulian Manchev Sonali Bahl Stephanie Warnken Liam Spurr Tatiyana Apanasovich Keith Crandall Nathan Edwards Anelia Horvath Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
description	Abstract Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC). We document significant allele-preferential expression of functional variants in CGC genes and across the entire dataset. Notably, we find frequent allele-specific overexpression of variants in tumor-suppressor genes. We also report a list of over-expressed variants from non-CGC genes. Overall, our analysis presents an integrated set of features of somatic allele expression and points to the vast information content of the asymmetric alleles in the cancer transcriptome.
format	article
author	Paula Restrepo Mercedeh Movassagh Nawaf Alomran Christian Miller Muzi Li Chris Trenkov Yulian Manchev Sonali Bahl Stephanie Warnken Liam Spurr Tatiyana Apanasovich Keith Crandall Nathan Edwards Anelia Horvath
author_facet	Paula Restrepo Mercedeh Movassagh Nawaf Alomran Christian Miller Muzi Li Chris Trenkov Yulian Manchev Sonali Bahl Stephanie Warnken Liam Spurr Tatiyana Apanasovich Keith Crandall Nathan Edwards Anelia Horvath
author_sort	Paula Restrepo
title	Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
title_short	Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
title_full	Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
title_fullStr	Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
title_full_unstemmed	Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
title_sort	overexpressed somatic alleles are enriched in functional elements in breast cancer
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/de12aae9e1cb49908e4868f2314b57c1
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Overexpressed somatic alleles are enriched in functional elements in Breast Cancer

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