Neoantigen prediction from genomic and transcriptomic data Methods in Enzymology, Volume 635, 2020, pp. 267-281 Sebastiano Battaglia Most non-canonical proteins uniquely populate the proteome or immunopeptidome Cell Reports, Volume 34, Issue 10, 2021, Article 108815 Maria Virginia Ruiz Cuevas,…, Jon...
It has been shown, however, that consensus approaches combining both methods can improve the binding affinity prediction accuracy.108,111 Although ANNs have addressed the non-linear nature of the peptide-HLA binding process, there are known limitations to the methods depending on the datasets each ...
To the best of our knowledge however, none of the present MHC-II epitope prediction methods consider the corresponding DNA loci of the neoantigens in the perspective of 3D genome, which carries important additional information compared to the amino acid sequence alone [39]. In this work, we ...
In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing ...
A. et al. From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43, 11.10.1–11.10.33 (2013). Google Scholar Nielsen, M. & Andreatta, M. NetMHCpan-3.0; improved prediction of binding to MHC class I molecules ...
1 Please cite this article in press as: Wells et al., Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction, Cell (2020), https://doi.org/10.1016/j.cell.2020.09.015 ll Resource independent cohort of 310 epitopes prioritized from tumor...
Neoantigen epitope prediction algorithms have enabled the detection of neoantigens and the creation of tailored neoantigen vaccines as a result of the fast development of next‐generation sequencing and cancer bioinformatics. Here we provide an overview of the current neoantigen cancer vaccines and ...
In the identification of neoantigen, how can computer prediction be combined with mass spectro-based immunoproteome technology to achieve the best results? Furthermore, how many epitopes can achieve the best antitumor effect [80]? At the same time, what is the immune mechanism of PD-1 /PD-L1...
In certain embodiments, HLA alleles may be determined by other means (e.g. HLA-A01:01, HLA-A26:01) and the results can also be utilized by the method, thereby avoiding the need for in silico prediction. Identifying Candidate Neoantigens and Prioritizing Candidate Neoantigens ...
an epitope that binds to a protein encoded by an HLA allele of the subject can be predicted to bind to an MHC molecule encoded by the HLA allele with an affinity of 400 nM, 300 nM, 200 nM, 150 nM, 100 nM, 75 nM, 50 nM, or 25 nM or less using an MHC epitope prediction progra...