Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

[HTML][HTML] 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] The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer

WA Freed-Pastor, LJ Lambert, ZA Ely, NB Pattada… - Cancer cell, 2021 - cell.com
The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections
and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune …

[HTML][HTML] A genomic perspective on HLA evolution

D Meyer, VR C. Aguiar, BD Bitarello, DY C. Brandt… - Immunogenetics, 2018 - Springer
Several decades of research have convincingly shown that classical human leukocyte
antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many …

NovAT tool—Reliable novel HLA alleles identification from next‐generation sequencing data

T Simakova, A Suvorova, K Krivonosova, A Abramova… - Hla, 2022 - Wiley Online Library
HLA molecules are expressed in almost all nucleated cells of the body. These molecules are
extremely variable and responsible for tissue specificity recognition. Precise HLA typing is …

[HTML][HTML] Current understanding of an emerging role of HLA-DRB1 gene in rheumatoid arthritis–from research to clinical practice

T Wysocki, M Olesińska, A Paradowska-Gorycka - Cells, 2020 - mdpi.com
Rheumatoid arthritis (RA) is an autoimmune disease with an unclear pathogenic
mechanism. However, it has been proven that the key underlying risk factor is a genetic …

[HTML][HTML] HLA variation and SARS-CoV-2 specific antibody response

D Wolday, CYJ Fung, G Morgan, S Casalino… - Viruses, 2023 - mdpi.com
Differences in SARS-CoV-2-specific immune responses have been observed between
individuals following natural infection or vaccination. In addition to already known factors …

Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population

J Hirata, K Hosomichi, S Sakaue, M Kanai… - Nature …, 2019 - nature.com
To perform detailed fine-mapping of the major-histocompatibility-complex region, we
conducted next-generation sequencing (NGS)-based typing of the 33 human leukocyte …

[HTML][HTML] Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy

Y Cai, R Chen, S Gao, W Li, Y Liu, G Su, M Song… - Frontiers in …, 2023 - frontiersin.org
The field of cancer neoantigen investigation has developed swiftly in the past decade.
Predicting novel and true neoantigens derived from large multi-omics data became difficult …

[HTML][HTML] The role of neoantigens in tumor immunotherapy

S Shang, Y Zhao, K Qian, Y Qin, X Zhang, T Li… - Biomedicine & …, 2022 - Elsevier
Tumor neoantigens are aberrant polypeptides produced by tumor cells as a result of
genomic mutations. They are also tumor-specific antigens (TSA). Neoantigens are more …