ArticleCell reports2018
Systematic Analysis of Splice-Site-Creating Mutations in Cancer.
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Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers, 1 of them a synthesis that pooled it.
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160citing papers in PubMed, 1 pooled it
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Who cites it
160 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group.Annals of oncology : official journal of the European Society for Medical Oncology · 2020Pooled it
- DRIVE: a comprehensive resource deciphering drug-induced transcriptomic and splicing response in cancer cell.Neoplasia (New York, N.Y.) · 2026Article
- Review
- Decoding neoantigen-encoding tumor-specific transcripts unveils a shared target reservoir for immunotherapy in hepatocellular carcinoma.Journal for immunotherapy of cancer · 2026Article
- Splicing-driven post-translational dysregulation: a new frontier for precision cancer medicine and immunotherapy.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- Systematic Evaluation of Peptidomimetic Modifications in a Major Histocompatibility Complex Class I Model Epitope: A Framework for Immunogenic Antigen Design.ACS chemical biology · 2026Article
- RNA splicing in cancer cell death regulation: shedding light on the molecular mechanisms and potential clinical applications.Cell death & disease · 2026Review
- Pathogenicity prediction for noncanonical splice-altering variants based on multimodal feature fusion.Briefings in bioinformatics · 2026Article
- Mapping glioblastoma's isoform diversity using long-read single-cell analysis.Nature communications · 2026Article
- Antigen Remodeling in Colorectal Cancer: How Radiotherapy and Chemotherapy Enhance Immunotherapy Responsiveness.Cancers · 2026Review
- Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.iScience · 2026Article
- CoREST complex inhibition alters RNA splicing to promote neoantigen expression and enhance tumor immunity.JCI insight · 2026Article
- Review
- A data-driven pan-cancer proteogenomic analysis reveals the characteristics of human cancer protein expression.iScience · 2026Article
- Predominant mutated non-canonical tumor-specific antigens identified by proteogenomics demonstrate immunogenicity and tumor suppression in CRC.Cell genomics · 2026Article
- mRNA processing in cancer immunotherapy: emerging targets, resistance mechanisms, and therapeutic opportunities.Frontiers in immunology · 2026Review
- Non-canonical and induced neoantigens as emerging sources of cancer-specific immunotherapy targets.Frontiers in immunology · 2026Review
- 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
- Unveiling splicing disruptions due to common somatic variants in acute myeloid leukemia.Human genomics · 2025Article
100 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors.
Reyka G JayasingheDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Song CaoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Qingsong GaoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Michael C WendlMcDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA.
Nam Sy VoDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Sheila M ReynoldsInstitute for Systems Biology, Seattle, WA 98109, USA.
Yanyan ZhaoDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Héctor Climente-GonzálezInstitut Curie, 75248 Paris Cedex, France; MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 77300 Fontainebleau, France; INSERM U900, 75248 Paris Cedex, France.
Shengjie ChaiLineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Fang WangDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Rajees VargheseDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Mo HuangDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
Wen-Wei LiangDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Matthew A WyczalkowskiDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Sohini SenguptaDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Zhi LiDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA.
Samuel H PayneBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
David FenyöDepartment of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA.
Jeffrey H MinerDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA.
Matthew J WalterDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
Cancer Genome Atlas Research Network
Benjamin VincentLineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Eduardo EyrasCatalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Computational RNA Biology Group, Pompeu Fabra University (UPF), 08003 Barcelona, Spain.
Ken ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Ilya ShmulevichInstitute for Systems Biology, Seattle, WA 98109, USA. Electronic address: ilya.shmulevich@systemsbiology.org.
Feng ChenDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address: fchen@wustl.edu.
Li DingDepartment of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address: lding@wustl.edu.
Funding
Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6MLarge Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7MThe Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3MTumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI DIANE BODURKA · 1985 to 2026
$290.8MVirology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5MGene Expression Patterns in Human Tumors Identified Using Transcript SequencingU24CA143848 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, PEROU, CHARLES M · 2009 to 2016
$20.8MGenome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0MThe Cancer Genome Atlas Data Analysis CenterU24CA143845 · NCI · BROAD INSTITUTE, INC. · PI CHIN, LYNDA, GETZ, GAD A · 2009 to 2016
$16.0MHarvard Genome Characterization CenterU24CA144025 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHERLAPATI, RAJU S. · 2009 to 2016
$14.0MThe USC-JHU Cancer Epigenome Characterization CenterU24CA143882 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BAYLIN, STEPHEN B., WEISENBERGER, DANIEL JOSEPH · 2009 to 2016
$13.3MMSKCC Center for Translational Cancer Genomic AnalysisU24CA143840 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI LADANYI, MARC, SANDER, CHRIS · 2009 to 2016
$11.5MCancer transcriptome characterization using massively parallel DNA sequencingU24CA143866 · NCI · BRITISH COLUMBIA CANCER AGENCY · PI MARRA, MARCO ANTONIO · 2009 to 2015
$10.9MNCI NIH HHS P30 CA016086NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA163722NCI NIH HHS R01 CA178383NCI NIH HHS R01 CA180006NCI NIH HHS U24 CA143799NCI NIH HHS U24 CA143835NCI NIH HHS U24 CA143840NCI NIH HHS U24 CA143843NCI NIH HHS U24 CA143845NCI NIH HHS U24 CA143848NCI NIH HHS U24 CA143858NCI NIH HHS U24 CA143866NCI NIH HHS U24 CA143867NCI NIH HHS U24 CA143882NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA144025NCI NIH HHS U24 CA210950NCI NIH HHS U24 CA210957NCI NIH HHS U24 CA210972NCI NIH HHS U24 CA210990NCI NIH HHS U24 CA211006NHGRI NIH HHS R01 HG009711NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG003273
Abstract
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.
Indexed as
MutationRNA Splice SitesBRCA1 ProteinGATA3 Transcription FactorHEK293 CellsHumansNeoplasmsPoly (ADP-Ribose) Polymerase-1Programmed Cell Death 1 ReceptorTumor Suppressor Protein p53X-linked Nuclear ProteinATRX protein, humanBRCA1 ProteinBRCA1 protein, humanGATA3 protein, humanGATA3 Transcription FactorPARP1 protein, humanPoly (ADP-Ribose) Polymerase-1Programmed Cell Death 1 ReceptorRNA Splice SitesTP53 protein, humanTumor Suppressor Protein p53X-linked Nuclear Proteinmutations of clinical relevanceRNAsplicing
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