ArticleNature genetics2019
Accounting for proximal variants improves neoantigen prediction.
Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 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
- Neoadjuvant PD-L1 plus CTLA-4 blockade in patients with cisplatin-ineligible operable high-risk urothelial carcinoma.Nature medicine · 2020Trial
- Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer.NPJ precision oncology · 2026Article
- Computational Methods for Cancer Neoantigen Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials.ArXiv · 2025Article
- Review
- Genomic landscape of diffuse glioma revealed by whole genome sequencing.Nature communications · 2025Article
- Leveraging mRNA technology for antigen based immuno-oncology therapies.Journal for immunotherapy of cancer · 2025Review
- Article
- Multi-omics indicators of long-term survival benefits after immune checkpoint inhibitor therapy.Cell reports methods · 2023Article
- Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.Journal for immunotherapy of cancer · 2023Review
- Article
- Identification of neoantigens in oesophageal adenocarcinoma.Immunology · 2023Article
- Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling.Frontiers in immunology · 2023Article
- Designing neoantigen cancer vaccines, trials, and outcomes.Frontiers in immunology · 2023Review
- Article
- Engineering neoantigen vaccines to improve cancer personalized immunotherapy.International journal of biological sciences · 2022Review
- Identification of Neoantigens in Two Murine Gastric Cancer Cell Lines Leading to the Neoantigen-Based Immunotherapy.Cancers · 2021Article
- Article
- Whole exome and transcriptome sequencing reveal clonal evolution and exhibit immune-related features in metastatic colorectal tumors.Cell death discovery · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Recent efforts to design personalized cancer immunotherapies use predicted neoantigens, but most neoantigen prediction strategies do not consider proximal (nearby) variants that alter the peptide sequence and may influence neoantigen binding. We evaluated somatic variants from 430 tumors to understand how proximal somatic and germline alterations change the neoantigenic peptide sequence and also affect neoantigen binding predictions. On average, 241 missense somatic variants were analyzed per sample. Of these somatic variants, 5% had one or more in-phase missense proximal variants. Without incorporating proximal variant correction for major histocompatibility complex class I neoantigen peptides, the overall false discovery rate (incorrect neoantigens predicted) and the false negative rate (strong-binding neoantigens missed) across peptides of lengths 8-11 were estimated as 0.069 (6.9%) and 0.026 (2.6%), respectively.
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Registered trials
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