Cancer neoantigens

TN Schumacher, W Scheper… - Annual review of …, 2019 - annualreviews.org
Malignant transformation of cells depends on accumulation of DNA damage. Over the past
years we have learned that the T cell–based immune system frequently responds to the …

Targeting neoantigens to augment antitumour immunity

M Yarchoan, BA Johnson III, ER Lutz… - Nature Reviews …, 2017 - nature.com
The past decade of cancer research has been marked by a growing appreciation of the role
of immunity in cancer. Mutations in the tumour genome can cause tumours to express …

Human leukocyte antigen susceptibility map for severe acute respiratory syndrome coronavirus 2

A Nguyen, JK David, SK Maden, MA Wood… - Journal of …, 2020 - Am Soc Microbiol
Genetic variability across the three major histocompatibility complex (MHC) class I genes
(human leukocyte antigen A [HLA-A],-B, and-C genes) may affect susceptibility to and …

[HTML][HTML] MHCflurry 2.0: improved pan-allele prediction of MHC class I-presented peptides by incorporating antigen processing

TJ O'Donnell, A Rubinsteyn, U Laserson - Cell systems, 2020 - cell.com
Computational prediction of the peptides presented on major histocompatibility complex
(MHC) class I proteins is an important tool for studying T cell immunity. The data available to …

Fundamentals and methods for T‐and B‐cell epitope prediction

JL Sanchez-Trincado… - Journal of …, 2017 - Wiley Online Library
Adaptive immunity is mediated by T‐and B‐cells, which are immune cells capable of
developing pathogen‐specific memory that confers immunological protection. Memory and …

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

M Łuksza, N Riaz, V Makarov, VP Balachandran… - Nature, 2017 - nature.com
Checkpoint blockade immunotherapies enable the host immune system to recognize and
destroy tumour cells. Their clinical activity has been correlated with activated T-cell …

[HTML][HTML] Challenges in neoantigen-directed therapeutics

L Lybaert, S Lefever, B Fant, E Smits, B De Geest… - Cancer Cell, 2023 - cell.com
A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

[HTML][HTML] Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction

M Müller, F Huber, M Arnaud, AI Kraemer, ER Altimiras… - Immunity, 2023 - cell.com
The accurate selection of neoantigens that bind to class I human leukocyte antigen (HLA)
and are recognized by autologous T cells is a crucial step in many cancer immunotherapy …

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

JD Campbell, A Alexandrov, J Kim, J Wala, AH Berger… - Nature …, 2016 - nature.com
To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to
identify new drivers of lung carcinogenesis, we examined the exome sequences and copy …

[HTML][HTML] SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors

AS Shomuradova, MS Vagida, SA Sheetikov… - Immunity, 2020 - cell.com
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting
the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID …