ArticleGenome research2018
A comprehensive characterization of
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
51 citing papers in PubMed, 77 citations in OpenAlex.
- Condensates and cell states: A new paradigm for understanding tumor biology.Biophysical journal · 2026Review
- Pathogenicity prediction for noncanonical splice-altering variants based on multimodal feature fusion.Briefings in bioinformatics · 2026Article
- Identification of Intronic Variants inNeurology. Genetics · 2026Article
- Article
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- Unveiling splicing disruptions due to common somatic variants in acute myeloid leukemia.Human genomics · 2025Article
- Epitranscriptomic sculpting: the role of mMedical oncology (Northwood, London, England) · 2025Review
- Alternative Splicing in Tumorigenesis and Cancer Therapy.Biomolecules · 2025Review
- RNA splicing: Novel star in pulmonary diseases with a treatment perspective.Acta pharmaceutica Sinica. B · 2025Review
- Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data.Nature communications · 2025Article
- Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies.Human vaccines & immunotherapeutics · 2024Review
- SpliceVarDB: A comprehensive database of experimentally validated human splicing variants.American journal of human genetics · 2024Article
- Novel ERBB2 Variant Potentially Associated with Resistance against Anti-HER2 Monoclonal Antibody-Based Therapy in ERBB2-Amplified Metastatic Colorectal Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Non-genetic heterogeneity and immune subtyping in breast cancer: Implications for immunotherapy and targeted therapeutics.Translational oncology · 2024Article
- Activation-induced cytidine deaminase causes recurrent splicing mutations in diffuse large B-cell lymphoma.Molecular cancer · 2024Article
- Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes.NPJ genomic medicine · 2024Article
- Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers.British journal of cancer · 2023Article
- Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv.Nucleic acids research · 2023Article
- Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.Genome biology · 2023Article
- Multiancestry genomic and transcriptomic analysis of gastric cancer.Nature genetics · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although many driver mutations are thought to promote carcinogenesis via abnormal splicing, the landscape of splicing-associated variants (SAVs) remains unknown due to the complexity of splicing abnormalities. Here, we developed a statistical framework to systematically identify SAVs disrupting or newly creating splice site motifs and applied it to matched whole-exome and transcriptome sequencing data from 8976 samples across 31 cancer types, generating a catalog of 14,438 SAVs. Such a large collection of SAVs enabled us to characterize their genomic features, underlying mutational processes, and influence on cancer driver genes. In fact, ∼50% of SAVs identified were those disrupting noncanonical splice sites (non-GT-AG dinucleotides), including the third and fifth intronic bases of donor sites, or newly creating splice sites. Mutation signature analysis revealed that tobacco smoking is more strongly associated with SAVs, whereas ultraviolet exposure has less impact. SAVs showed remarkable enrichment of cancer-related genes, and as many as 14.7% of samples harbored at least one SAVs affecting them, particularly in tumor suppressors. In addition to intron retention, whose association with tumor suppressor inactivation has been previously reported, exon skipping and alternative splice site usage caused by SAVs frequently affected tumor suppressors. Finally, we described high-resolution distributions of SAVs along the gene and their splicing outcomes in commonly disrupted genes, including
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Registered trials
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 OpenQuestion graph.