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Overexpressed somatic alleles are enriched in functional elements in Breast Cancer

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 f...

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Detalles Bibliográficos
Autores principales: Restrepo, Paula, Movassagh, Mercedeh, Alomran, Nawaf, Miller, Christian, Li, Muzi, Trenkov, Chris, Manchev, Yulian, Bahl, Sonali, Warnken, Stephanie, Spurr, Liam, Apanasovich, Tatiyana, Crandall, Keith, Edwards, Nathan, Horvath, Anelia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557904/
https://www.ncbi.nlm.nih.gov/pubmed/28811643
http://dx.doi.org/10.1038/s41598-017-08416-w
Descripción
Sumario: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.