ArticleScientific reports2017
Allelic imbalance of somatic mutations in cancer genomes and transcriptomes.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 48 citations in OpenAlex.
- Mutations in the pancreatic secretory enzymesProceedings of the National Academy of Sciences of the United States of America · 2018Trial
- Allelic Imbalance and Chromothripsis Lead to Diversity in Japanese Tumor Genomes With Whole-Genome Duplication.Cancer science · 2025Article
- Nonsense-Mediated mRNA Decay in Human Health and Diseases: Current Understanding, Regulatory Mechanisms and Future Perspectives.Molecular biotechnology · 2025Review
- Development and validation of mRNA expression-based classifiers to predict low-risk thyroid tumors.Frontiers in endocrinology · 2025Article
- A spectrum of nonsense-mediated mRNA decay efficiency along the degree of mutational constraint.Communications biology · 2024Article
- Review
- Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies.Journal of personalized medicine · 2022Article
- Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant.NPJ breast cancer · 2022Article
- Article
- Genetic Alterations in Preinvasive Lung Synchronous Lesions.Cancer research and treatment · 2020Article
- POLE Mutation Spectra Are Shaped by the Mutant Allele Identity, Its Abundance, and Mismatch Repair Status.Molecular cell · 2020Article
- Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.Cell systems · 2020Article
- Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia.Scientific reports · 2019Article
- Article
- Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes.Cancer cell international · 2019Article
- Systematic pan-cancer analysis of somatic allele frequency.Scientific reports · 2018Article
- Comprehensive genomic transcriptomic tumor-normal gene panel analysis for enhanced precision in patients with lung cancer.Oncotarget · 2018Article
- Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients.BMC bioinformatics · 2018Article
- Article
- Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder.American journal of human genetics · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Somatic mutations in cancer genomes often show allelic imbalance (AI) of mutation abundance between the genome and transcriptome, but there is not yet a systematic understanding of AI. In this study, we performed large-scale DNA and RNA AI analyses of >100,000 somatic mutations in >2,000 cancer specimens across five tumor types using the exome and transcriptome sequencing data of the Cancer Genome Atlas consortium. First, AI analysis of nonsense mutations and frameshift indels revealed that nonsense-mediated decay is typical in cancer genomes, and we identified the relationship between the extent of AI and the location of mutations in addition to the well-recognized 50-nt rules. Second, the AI with splice site mutations may reflect the extent of intron retention and is frequently observed in known tumor suppressor genes. For missense mutations, we observed that mutations frequently subject to AI are enriched to genes related to cancer, especially those of apoptosis and the extracellular matrix, and C:G > A:T transversions. Our results suggest that mutations in known cancer-related genes and their transcripts are subjected to different levels of transcriptional or posttranscriptional regulation compared to wildtype alleles and may add an additional regulatory layer to the functions of cancer-relevant genes.
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