ArticleNature genetics2020
Identification of cancer driver genes based on nucleotide context.
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers, 2 of them syntheses that pooled it.
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Who cites it
149 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Uncovering Oncogenic Mechanisms of Tumor Suppressor Genes in Breast Cancer Multi-Omics Data.International journal of molecular sciences · 2022Pooled it
- Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes.Genome medicine · 2022Pooled it
- Impact of Tumor Genomic Profile on Adjuvant Chemotherapy Efficacy in Resected Pancreatic Adenocarcinoma: Results From the PRODIGE-24/CCTG PA6 Study.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026Article
- ExIR enables prioritizing driver and biomarker genes from omics data in a reference free manner.iScience · 2026Article
- Article
- Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution.Genome research · 2026Article
- Integrated mutational landscape analysis of endometrial stromal sarcoma.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A panel of four autoantibodies to tumour-associated antigens in patients with prostate cancer and its potential for multi-cancer detection.British journal of cancer · 2026Article
- Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility.Nature communications · 2026Article
- Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention.American journal of human genetics · 2026Article
- Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT).Environmental and molecular mutagenesis · 2025Review
- Germline variant spectrum of hereditary cancer susceptibility genes in a Chinese cohort.Human genomics · 2025Article
- Transcription start sites experience a high influx of heritable variants fueled by early development.Nature communications · 2025Article
- Mutation of CMTR2 in Lung Adenocarcinoma Alters RNA Alternative Splicing and Reveals Therapeutic Vulnerabilities.Nature communications · 2025Article
- Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals.Genome biology · 2025Article
- Analysis of IDH1 and IDH2 mutations as causes of the hypermethylator phenotype in colorectal cancer.The Journal of pathology · 2025Article
- Synchronous endometrial/cervical and ovarian/fallopian tube carcinoma: a genome-wide mutation analysis.The journal of pathology. Clinical research · 2025Article
- Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection.Nucleic acids research · 2025Article
- Transcriptome-wide association study of alternative polyadenylation identifies susceptibility genes in non-small cell lung cancer.Oncogene · 2025Article
- Cancer gene identification from RNA variant allelic frequencies using RVdriver.Genome biology · 2025Article
89 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Cancer genomes contain large numbers of somatic mutations but few of these mutations drive tumor development. Current approaches either identify driver genes on the basis of mutational recurrence or approximate the functional consequences of nonsynonymous mutations by using bioinformatic scores. Passenger mutations are enriched in characteristic nucleotide contexts, whereas driver mutations occur in functional positions, which are not necessarily surrounded by a particular nucleotide context. We observed that mutations in contexts that deviate from the characteristic contexts around passenger mutations provide a signal in favor of driver genes. We therefore developed a method that combines this feature with the signals traditionally used for driver-gene identification. We applied our method to whole-exome sequencing data from 11,873 tumor-normal pairs and identified 460 driver genes that clustered into 21 cancer-related pathways. Our study provides a resource of driver genes across 28 tumor types with additional driver genes identified according to mutations in unusual nucleotide contexts.
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