ArticleFrontiers in immunology2021
Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms.
Article in Frontiers in immunology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 31 citations in OpenAlex.
- Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer.Nature cancer · 2026Trial
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- Computational methods and data resources for predicting tumor neoantigens.Briefings in 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
- A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis.Computational and structural biotechnology journal · 2024Article
- Full-resolution HLA and KIR gene annotations for human genome assemblies.Genome research · 2024Article
- Article
- Tumor-Derived Antigenic Peptides as Potential Cancer Vaccines.International journal of molecular sciences · 2024Review
- Full resolution HLA and KIR genes annotation for human genome assemblies.bioRxiv : the preprint server for biology · 2024Article
- 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
- The HLA-DRB1*09:01-DQB1*03:03 haplotype is associated with the risk for late-onset Alzheimer's disease in APOEnpj aging · 2024Article
- Evaluation of HLA typing content of next-generation sequencing datasets from family trios and individuals of arab ethnicity.Frontiers in genetics · 2024Article
- Benchmarking NGS-Based HLA Typing Algorithms.Methods in molecular biology (Clifton, N.J.) · 2024Article
- HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases.Communications biology · 2023Article
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- HLA Variation and SARS-CoV-2 Specific Antibody Response.Viruses · 2023Review
- Designing neoantigen cancer vaccines, trials, and outcomes.Frontiers in immunology · 2023Review
- Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing.Frontiers in immunology · 2023Article
- Toxin exposure and HLA alleles determine serum antibody binding to toxic shock syndrome toxin 1 (TSST-1) ofFrontiers in immunology · 2023Article
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the great progress made recently in next generation sequencing (NGS) technology, sequencing accuracy and throughput have increased, while the cost for data has decreased. Various human leukocyte antigen (HLA) typing algorithms and assays have been developed and have begun to be used in clinical practice. In this study, we compared the HLA typing performance of three HLA assays and seven NGS-based HLA algorithms and assessed the impact of sequencing depth and length on HLA typing accuracy based on 24 benchmarked samples. The algorithms HISAT-genotype and HLA-HD showed the highest accuracy at both the first field and the second field resolution, followed by HLAscan. Our internal capture-based HLA assay showed comparable performance with whole exome sequencing (WES). We found that the minimal depth was 100X for HISAT-genotype and HLA-HD to obtain more than 90% accuracy at the third field level. The top three algorithms were quite robust to the change of read length. Thus, we recommend using HISAT-genotype and HLA-HD for NGS-based HLA genotyping because of their higher accuracy and robustness to read length. We propose that a minimal sequence depth for obtaining more than 90% HLA typing accuracy at the third field level is 100X. Besides, targeting capture-based NGS HLA typing may be more suitable than WES in clinical practice due to its lower sequencing cost and higher HLA sequencing depth.
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