ArticleScientific reports2018
Systematic pan-cancer analysis of somatic allele frequency.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
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- Biased expression of mutant alleles in cancer-related genes in esophageal squamous cell carcinoma.Esophagus : official journal of the Japan Esophageal Society · 2022Article
- Whole exome sequencing of high-risk neuroblastoma identifies novel non-synonymous variants.PloS one · 2022Article
- Nucleotide-based genetic networks: Methods and applications.Journal of biosciences · 2022Article
- NSD1: A Lysine Methyltransferase between Developmental Disorders and Cancer.Life (Basel, Switzerland) · 2021Review
- Machine learning algorithm improved automated droplet classification of ddPCR for detection of BRAF V600E in paraffin-embedded samples.Scientific reports · 2021Article
- The Impact of Variant Allele Frequency in EGFR Mutated NSCLC Patients on Targeted Therapy.Frontiers in oncology · 2021Article
- Toward a More Precise Future for Oncology.Cancer cell · 2020Article
- Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.Cell systems · 2020Article
- Estimating the Allele-Specific Expression of SNVs From 10× Genomics Single-Cell RNA-Sequencing Data.Genes · 2020Article
- Evidence for Etiologic Subtypes of Breast Cancer in the Carolina Breast Cancer Study.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2019Article
- Review
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correlation between allele frequency of somatic variants and total gene expression of their harboring gene, we used the unique data set of matched tumor and normal RNA and DNA sequencing data of 5523 distinct single nucleotide variants in 381 individuals across 10 cancer types obtained from The Cancer Genome Atlas (TCGA). We analyzed the allele frequency in the context of the variant and gene functional features and linked it with changes in the total gene expression. We documented higher allele frequency of somatic variants in cancer-implicated genes (Cancer Gene Census, CGC). Furthermore, somatic alleles bearing premature terminating variants (PTVs), when positioned in CGC genes, appeared to be less frequently degraded via nonsense-mediated mRNA decay, indicating possible favoring of truncated proteins by the tumor transcriptome. Among the genes with multiple PTVs with high allele frequency, ARID1, TP53 and NSD1 were known key cancer genes. All together, our analyses suggest that high allele frequency of tumor somatic variants can indicate driving functionality and can serve to identify potential cancer-implicated genes.
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