Dataset Information

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 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.

SUBMITTER: Restrepo P

PROVIDER: S-EPMC5557904 | biostudies-other | 2017 Aug

REPOSITORIES: biostudies-other

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Overexpressed somatic alleles are enriched in functional elements in Breast Cancer.

Restrepo Paula P Movassagh Mercedeh M Alomran Nawaf N Miller Christian C Li Muzi M Trenkov Chris C Manchev Yulian Y Bahl Sonali S Warnken Stephanie S Spurr Liam L Apanasovich Tatiyana T Crandall Keith K Edwards Nathan N Horvath Anelia A

Scientific reports 20170815 1

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 functionali ...[more]

PMID: 28811643

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Dataset Information

Overexpressed somatic alleles are enriched in functional elements in Breast Cancer.

Publications

Overexpressed somatic alleles are enriched in functional elements in Breast Cancer.

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