ArticleBMC bioinformatics2018
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- High Response Rate and Durability Driven by HLA Genetic Diversity in Patients with Kidney Cancer Treated with Lenvatinib and Pembrolizumab.Molecular cancer research : MCR · 2021Trial
- Personalized neoantigen pulsed dendritic cell vaccine for advanced lung cancer.Signal transduction and targeted therapy · 2021Trial
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- Whole-Exome Sequencing to Screen Personal Neoantigens With High Immunogenicity in Patients With Microsatellite Stability (MSS)-Advanced Colorectal Cancer.Human mutation · 2026Article
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- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- Assessment of Functional Status of Human Leukocyte Antigen Class I Genes in Cancer Tissues in the Context of Personalized Neoantigen Peptide Vaccine Immunotherapy.JCO clinical cancer informatics · 2025Article
- Advances in Therapeutic Cancer Vaccines, Their Obstacles, and Prospects Toward Tumor Immunotherapy.Molecular biotechnology · 2025Review
- Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey.Briefings in bioinformatics · 2025Review
- Cancer vaccines: current status and future directions.Journal of hematology & oncology · 2025Review
- Optimized multiplex PCR-NGS for comprehensive HLA genotyping in Chinese populations: resolving ambiguities at high resolution.Frontiers in immunology · 2025Article
- Neoantigen-based immunotherapy: advancing precision medicine in cancer and glioblastoma treatment through discovery and innovation.Exploration of targeted anti-tumor therapy · 2025Review
- A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data.bioRxiv : the preprint server for biology · 2024Article
- Historical perspective and future directions: computational science in immuno-oncology.Journal for immunotherapy of cancer · 2024Review
- Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy.Frontiers in immunology · 2024Review
- Evaluation of HLA typing content of next-generation sequencing datasets from family trios and individuals of arab ethnicity.Frontiers in genetics · 2024Article
- Therapeutic cancer vaccines: advancements, challenges, and prospects.Signal transduction and targeted therapy · 2023Review
- SpecHLA enables full-resolution HLA typing from sequencing data.Cell reports methods · 2023Article
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- 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
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods.
resultsWe tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles.
conclusionsAlthough current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.
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