pVACtools: a computational toolkit to identify and visualize cancer neoantigens

J Hundal, S Kiwala, J McMichael, CA Miller, H Xia… - Cancer immunology …, 2020 - AACR
Identification of neoantigens is a critical step in predicting response to checkpoint blockade
therapy and design of personalized cancer vaccines. This is a cross-disciplinary challenge …

Computational prediction of MHC anchor locations guides neoantigen identification and prioritization

H Xia, J McMichael, M Becker-Hapak… - Science …, 2023 - science.org
Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic
DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they …

Neoantigen dissimilarity to the self-proteome predicts immunogenicity and response to immune checkpoint blockade

LP Richman, RH Vonderheide, AJ Rech - Cell systems, 2019 - cell.com
Despite improved methods for MHC affinity prediction, the vast majority of computationally
predicted tumor neoantigens are not immunogenic experimentally, indicating that high …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H Xia, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

[HTML][HTML] Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group

L De Mattos-Arruda, M Vazquez, F Finotello, R Lepore… - Annals of oncology, 2020 - Elsevier
Background The use of next-generation sequencing technologies has enabled the rapid
identification of non-synonymous somatic mutations in cancer cells. Neoantigens are …

'Hotspots' of antigen presentation revealed by human leukocyte antigen ligandomics for neoantigen prioritization

M Müller, D Gfeller, G Coukos… - Frontiers in …, 2017 - frontiersin.org
The remarkable clinical efficacy of the immune checkpoint blockade therapies has motivated
researchers to discover immunogenic epitopes and exploit them for personalized vaccines …

Machine-learning prediction of tumor antigen immunogenicity in the selection of therapeutic epitopes

CC Smith, S Chai, AR Washington, SJ Lee… - Cancer immunology …, 2019 - AACR
Current tumor neoantigen calling algorithms primarily rely on epitope/major
histocompatibility complex (MHC) binding affinity predictions to rank and select for potential …

Neoantigen-based personalized cancer vaccines: the emergence of precision cancer immunotherapy

G Richard, MF Princiotta, D Bridon… - Expert Review of …, 2022 - Taylor & Francis
Introduction The field of cancer therapy has undergone a major transformation in less than a
decade due to the introduction of checkpoint inhibitors, the advent of next generation …

The changing landscape of therapeutic cancer vaccines—novel platforms and neoantigen identification

J Jou, KJ Harrington, MB Zocca, E Ehrnrooth… - Clinical Cancer …, 2021 - AACR
Therapeutic cancer vaccines, an exciting development in cancer immunotherapy, share the
goal of creating and amplifying tumor-specific T-cell responses, but significant obstacles still …

Cancer neoantigens and applications for immunotherapy

A Desrichard, A Snyder, TA Chan - Clinical Cancer Research, 2016 - AACR
Recent advances in immune checkpoint blockade therapy have revolutionized the treatment
of cancer. Tumor-specific antigens that are generated by somatic mutation, neoantigens, can …