ArticleNucleic acids research2015
Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Comparative RNA-Seq Analysis of Colon Spheroids and Patient-derived Tissues Identifies Non-Canonical Transcript Isoforms of Protein-Coding Genes Implicated in Colon Carcinogenesis.Cancer informatics · 2025Article
- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.Cellular and molecular life sciences : CMLS · 2024Review
- Article
- Genomic basis for RNA alterations in cancer.Nature · 2020Article
- Mutational signatures and mutable motifs in cancer genomes.Briefings in bioinformatics · 2018Review
- Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations.Nucleic acids research · 2018Article
- RBM10: Harmful or helpful-many factors to consider.Journal of cellular biochemistry · 2018Review
- Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.NPJ genomic medicine · 2018Article
- Nuclear topology modulates the mutational landscapes of cancer genomes.Nature structural & molecular biology · 2017Article
- Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma.Scientific reports · 2017Article
- Article
- RBM10 promotes transformation-associated processes in small cell lung cancer and is directly regulated by RBM5.PloS one · 2017Article
- Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers.Scientific reports · 2016Article
- Exome-based Variant Detection in Core Promoters.Scientific reports · 2016Article
- OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.Genome biology · 2016Article
- Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer.PLoS genetics · 2016Review
- Role of non-coding sequence variants in cancer.Nature reviews. Genetics · 2016Review
- TERT promoter mutations and monoallelic activation of TERT in cancer.Oncogenesis · 2015Article
- The search for cis-regulatory driver mutations in cancer genomes.Oncotarget · 2015Review
- Anticancer Effect of Lycopene in Gastric Carcinogenesis.Journal of cancer prevention · 2015Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Cancer-associated somatic mutations outside protein-coding regions remain largely unexplored. Analyses of the TERT locus have indicated that non-coding regulatory mutations can be more frequent than previously suspected and play important roles in oncogenesis. Using a computational method called SASE-hunter, developed here, we identified a novel signature of accelerated somatic evolution (SASE) marked by a significant excess of somatic mutations localized in a genomic locus, and prioritized those loci that carried the signature in multiple cancer patients. Interestingly, even when an affected locus carried the signature in multiple individuals, the mutations contributing to SASE themselves were rarely recurrent at the base-pair resolution. In a pan-cancer analysis of 906 samples from 12 tumor types, we detected SASE in the promoters of several genes, including known cancer genes such as MYC, BCL2, RBM5 and WWOX. Nucleotide substitution patterns consistent with oxidative DNA damage and local somatic hypermutation appeared to contribute to this signature in selected gene promoters (e.g. MYC). SASEs in selected cancer gene promoters were associated with over-expression, and also correlated with the age of onset of cancer, aggressiveness of the disease and survival. Taken together, our work detects a hitherto under-appreciated and clinically important class of regulatory changes in cancer genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.