PO.BCS01.12 · 生物信息与计算

Cancer epitope prediction tools & analysis pipelines in CEDAR

海报缩略图:Cancer epitope prediction tools & analysis pipelines in CEDAR
编号 5503 展板 8 🕑 4/21 02:00–05:00 📍 Section 4 主讲 Ibel Carri, PhD
分会场 New Software Tools for Data Analysis
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作者与单位 Authors & Affiliations

Ibel Carri1, Jason Greenbaum2, Zhen Yan2, Kevin Kim2, Haeuk Kim2, Ashmitaa Logandha Ramamoorthy Premlal2, Daniel Marrama1, Nina Blazeska3, Hannah K. Carter4, Morten Nielsen5, Alessandro Sette1, Bjoern Peters1, Zeynep Kosaloglu-Yalcin3

1La Jolla Institute for Immunology, La Jolla, CA,2Bioinformatics Core, La Jolla Institute for Immunology, La Jolla, CA,3La Jolla Institute for Immunology, San Diego, CA,4UC San Diego, La Jolla, CA,5Department of Health Technology, Technical University of Denmark, Lyngby, Denmark

摘要 Abstract

The identification of immunogenic cancer epitopes, including patient-specific neoepitopes and shared tumor-associated antigens (TAAs), is a central challenge for the development of effective cancer immunotherapies. To accelerate their discovery, the Cancer Epitope Database and Analysis Resource (CEDAR), a comprehensive resource for immuno-oncology, curates epitope data from the literature and develops tailored computational tools. Building on this foundation, we introduce the modular Next-Generation IEDB Tools (NGT) platform (nextgen-tools.iedb.org/) that integrates a wide array of cancer-focused computational tools. The NGT platform allows users to construct, save, and share customized, reproducible, end-to-end computational pipelines for tumor antigen discovery. This architecture enables systematic prioritization of epitope candidates by applying multiple, sequential filtering criteria based on predicted and calculated relevant immune features, such as antigen expression, antigen presentation, self-similarity, and immunogenicity. Key tools include the Mutated Peptide Generator (MPG), which translates genomic variants (e.g., SNVs, indels) into candidate neoepitope sequences; Peptide Expression Annotation (PepX), which integrates public RNA-Seq data from resources like TCGA and GTEx to quantify antigen-encoding transcript abundance in tumor tissue; the Patient-Specific Presentation Metric (PHBR), a metric that estimates the likelihood of a mutation being presented by a patient's specific MHC Class I alleles; ICERFIRE (via Peptide Variant Comparison, PVC), a robust immunogenicity model that predicts the T-cell recognition potential of neoepitopes; PEPMatch, a tool to filter out candidate neoepitopes that are highly similar to self-peptides, which can indicate potential tolerance or autoimmunity risks; and Cluster, which groups highly similar peptide sequences to reduce redundancy and focus on the most representative candidates for experimental validation. The CEDAR computational tools and integrated pipeline architecture on the NGT platform provide cancer immunologists with a flexible, user-friendly, and state-of-the-art resource. This comprehensive framework accelerates the translation of genomic and transcriptomic sequencing data into clinically actionable epitope candidates. Here, we present how these integrated tools can be applied to patient-level analyses, enabling personalized identification and prioritization of tumor epitopes to guide cancer vaccine design and immunotherapy development.
利益披露 Disclosure
I. Carri, None.. J. Greenbaum, None.. Z. Yan, None.. K. Kim, None.. H. Kim, None.. A. L. R. Premlal, None.. D. Marrama, None.. N. Blazeska, None.. M. Nielsen, None.. A. Sette, None. B. Peters, Amgen Other, Speaker, consultant. Sanofi Other, Speaker, consultant.

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