ArticleGenome medicine2017
The neoepitope landscape in pediatric cancers.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it, 96 citations in OpenAlex.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Preclinical proof of concept for a personalized SNAP™-TIL (Specific Neo-Antigen Peptides-TIL) therapy platform.Oncoimmunology · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- The promises and challenges of neoantigen cancer vaccines.Nature biotechnology · 2026Review
- The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer.iScience · 2026Article
- Article
- Somatic Mutations in DNA Mismatch Repair Genes, Mutation Rate and Neoantigen Load in Acute Lymphoblastic Leukemia.Pharmaceuticals (Basel, Switzerland) · 2025Article
- RBM39 degrader invigorates innate immunity to eradicate neuroblastoma despite cancer cell plasticity.Nature communications · 2025Article
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Preclinical and Clinical-Scale Magnetic Particle Imaging of Natural Killer Cells: in vitro and ex vivo Demonstration of Cellular Sensitivity, Resolution, and Quantification.Molecular imaging and biology · 2025Article
- T cell exhaustion in pediatric B-ALL: current knowledge and future perspectives.Frontiers in immunology · 2025Review
- Identification of tumor rejection antigens and the immunologic landscape of medulloblastoma.Genome medicine · 2024Article
- DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma.Cell reports. Medicine · 2024Article
- FusionNeoAntigen: a resource of fusion gene-specific neoantigens.Nucleic acids research · 2024Article
- The dark side of stemness - the role of hematopoietic stem cells in development of blood malignancies.Frontiers in oncology · 2024Review
- Adoptive cell therapy in paediatric extracranial solid tumours: current approaches and future challenges.European journal of cancer (Oxford, England : 1990) · 2023Review
- Prospective Identification of Prognostic Hot-Spot Mutant Gene Signatures for Leukemia: A Computational Study Based on Integrative Analysis of TCGA and cBioPortal Data.Molecular biotechnology · 2023Article
- A Kmer-based paired-end readiScience · 2023Article
- mRNA-Based Therapeutics in Cancer Treatment.Pharmaceutics · 2023Review
- Decreased expression ofFrontiers in oncology · 2023Article
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Authors and funding
16 authors at 1 institution in 1 country.
Funding
Abstract
backgroundNeoepitopes derived from tumor-specific somatic mutations are promising targets for immunotherapy in childhood cancers. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of the neoepitope landscape in childhood cancer. Studies to date have focused primarily on missense mutations without exploring gene fusions, which are a major class of oncogenic drivers in pediatric cancer.
methodsWe developed an analytical workflow for identification of putative neoepitopes based on somatic missense mutations and gene fusions using whole-genome sequencing data. Transcriptome sequencing data were incorporated to interrogate the expression status of the neoepitopes.
resultsWe present the neoepitope landscape of somatic alterations including missense mutations and oncogenic gene fusions identified in 540 childhood cancer genomes and transcriptomes representing 23 cancer subtypes. We found that 88% of leukemias, 78% of central nervous system tumors, and 90% of solid tumors had at least one predicted neoepitope. Mutation hotspots in KRAS and histone H3 genes encode potential epitopes in multiple patients. Additionally, the ETV6-RUNX1 fusion was found to encode putative neoepitopes in a high proportion (69.6%) of the pediatric leukemia harboring this fusion.
conclusionsOur study presents a comprehensive repertoire of potential neoepitopes in childhood cancers, and will facilitate the development of immunotherapeutic approaches designed to exploit them. The source code of the workflow is available at GitHub ( https://github.com/zhanglabstjude/neoepitope ).
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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 OpenQuestion graph.