ArticleBriefings in bioinformatics2021
Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
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- Advancing human leukocyte antigen-based cancer immunotherapy: from personalized to broad-spectrum strategies for genetically heterogeneous populations.Trends in cancer · 2025Review
- Immuno-epidemiologic mapping of human leukocyte antigen diversity across glioma patient cohorts.Neuro-oncology · 2025Article
- OmniNeo: a multi-omics pipeline incorporating proteomics and AI selection for neoantigen optimization in tumor immunotherapy.Frontiers in immunology · 2025Article
- Historical perspective and future directions: computational science in immuno-oncology.Journal for immunotherapy of cancer · 2024Review
- Computational immunogenomic approaches to predict response to cancer immunotherapies.Nature reviews. Clinical oncology · 2024Review
- The Mutational, Prognostic, and Therapeutic Landscape of Neuroendocrine Neoplasms.The oncologist · 2023Article
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
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- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
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- Benchmarking of 5 algorithms for high-resolution genotyping of human leukocyte antigen class I genes from blood and tissue samples.Annals of translational medicine · 2022Article
- Integrated investigation of the prognostic role of HLA LOH in advanced lung cancer patients with immunotherapy.Frontiers in genetics · 2022Article
- Identification of APC Mutation as a Potential Predictor for Immunotherapy in Colorectal Cancer.Journal of oncology · 2022Article
- Predicting Durable Responses to Immune Checkpoint Inhibitors in Non-Small-Cell Lung Cancer Using a Multi-Feature Model.Frontiers in immunology · 2022Article
- Durable Response to Immunotherapy With Antiangiogenic Drug in Large-Cell Lung Carcinoma With Multiple Fulminant Postoperative Metastases: A Case Report.Frontiers in oncology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human leukocyte antigen (HLA) can encode the human major histocompatibility complex (MHC) proteins and play a key role in adaptive and innate immunity. Emerging clinical evidences suggest that the presentation of tumor neoantigens and neoantigen-specific T cell response associated with MHC class I molecules are of key importance to activate the adaptive immune systemin cancer immunotherapy. Therefore, accurate HLA typing is very essential for the clinical application of immunotherapy. In this study, we conducted performance evaluations of 4 widely used HLA typing tools (OptiType, Phlat, Polysolver and seq2hla) for predicting HLA class Ia genes from WES and RNA-seq data of 28 cancer patients. HLA genotyping data using PCR-SBT method was firstly obtained as the golden standard and was subsequently compared with HLA typing data by using NGS techniques. For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions can present a probably superior performance for HLA-Ia typing, enabling its application in cancer immunotherapy.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.