ArticleNature communications2020
Discovery of driver non-coding splice-site-creating mutations in cancer.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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.
The trial behind it
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
23 citing papers in PubMed, 40 citations in OpenAlex.
- To be or not to be a protein coding mutation, that's the question!NAR genomics and bioinformatics · 2025Review
- Alternative splicing: from tumorigenesis to neoantigen-mediated cancer immunotherapy.Biomarker research · 2025Review
- Targeting a pathogenic cryptic exon that drives HLRCC to induce exon skipping.Molecular therapy. Nucleic acids · 2025Article
- Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data.Nature communications · 2025Article
- Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations.Nature genetics · 2025Article
- Article
- SpliceVarDB: A comprehensive database of experimentally validated human splicing variants.American journal of human genetics · 2024Article
- MAP3K4 kinase action and dual role in cancer.Discover oncology · 2024Review
- Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing.NPJ systems biology and applications · 2024Article
- Novel insights into the pathogenesis of follicular lymphoma by molecular profiling of localized and systemic disease forms.Leukemia · 2023Article
- Discovering cryptic splice mutations in cancers via a deep neural network framework.NAR cancer · 2023Article
- Alternative splicing: a new breakthrough for understanding tumorigenesis and potential clinical applications.Genes & genomics · 2023Review
- Genome-wide mapping of somatic mutation rates uncovers drivers of cancer.Nature biotechnology · 2022Article
- Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data.Nature communications · 2022Article
- Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites.Nucleic acids research · 2022Article
- Dysregulation and therapeutic targeting of RNA splicing in cancer.Nature cancer · 2022Review
- Micropeptides translated from putative long non-coding RNAs.Acta biochimica et biophysica Sinica · 2022Review
- Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders.NPJ genomic medicine · 2022Article
- Leveraging Allele-Specific Expression for Therapeutic Response Gene Discovery in Glioblastoma.Cancer research · 2022Article
- Genome-wide identification of exon extension/shrinkage events induced by splice-site-creating mutations.RNA biology · 2022Article
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
Abstract
Non-coding mutations can create splice sites, however the true extent of how such somatic non-coding mutations affect RNA splicing are largely unexplored. Here we use the MiSplice pipeline to analyze 783 cancer cases with WGS data and 9494 cases with WES data, discovering 562 non-coding mutations that lead to splicing alterations. Notably, most of these mutations create new exons. Introns associated with new exon creation are significantly larger than the genome-wide average intron size. We find that some mutation-induced splicing alterations are located in genes important in tumorigenesis (ATRX, BCOR, CDKN2B, MAP3K1, MAP3K4, MDM2, SMAD4, STK11, TP53 etc.), often leading to truncated proteins and affecting gene expression. The pattern emerging from these exon-creating mutations suggests that splice sites created by non-coding mutations interact with pre-existing potential splice sites that originally lacked a suitable splicing pair to induce new exon formation. Our study suggests the importance of investigating biological and clinical consequences of noncoding splice-inducing mutations that were previously neglected by conventional annotation pipelines. MiSplice will be useful for automatically annotating the splicing impact of coding and non-coding mutations in future large-scale analyses.
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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.