Document Type
Journal Article
Publication Date
8-15-2017
Journal
Scientific Reports
Volume
7
Issue
1
DOI
10.1038/s41598-017-08416-w
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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
APA Citation
Restrepo, P., Movassagh, M., Alomran, N., Miller, C., Li, M., Trenkov, C., Manchev, Y., Bahl, S., Warnken, S., Spurr, L., Apanasovich, T., Crandall, K., Edwards, N., & Horvath, A. (2017). Overexpressed Somatic Alleles are Enriched in Functional Elements in Breast Cancer.. Scientific Reports, 7 (1). http://dx.doi.org/10.1038/s41598-017-08416-w
Peer Reviewed
1
Open Access
1
Included in
Medical Pharmacology Commons, Medical Physiology Commons, Pharmacology Commons, Physiology Commons
Comments
Reproduced with permission of Macmillan Publishers Limited. Scientific Reports