ArticleNucleic acids research2015
Development of a high-resolution NGS-based HLA-typing and analysis pipeline.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Analytical and Clinical Validation of Action PharmaKitDx: A Comprehensive NGS Panel for the Identification of Pharmacogenetic Variants in Diverse Populations.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Ancient DNA study provides clues to leprosy susceptibility in medieval Europe.Genome biology · 2026Article
- Advancing human leukocyte antigen-based cancer immunotherapy: from personalized to broad-spectrum strategies for genetically heterogeneous populations.Trends in cancer · 2025Review
- Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).International journal of oncology · 2025Review
- Admixture as a source for HLA variation in Neolithic European farming communities.Genome biology · 2025Article
- Article
- 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
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- 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
- High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing.NAR genomics and bioinformatics · 2022Article
- Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide.HGG advances · 2022Article
- Distribution ofFrontiers in pharmacology · 2022Article
- SARS-CoV-2 Host Immunogenetic Biomarkers.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational cancer neoantigen prediction: current status and recent advances.Immuno-oncology technology · 2021Review
- Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence.Signal transduction and targeted therapy · 2021Review
- SMOX expression predicts the prognosis of non-small cell lung cancer.Annals of translational medicine · 2021Article
- Neoantigen Quantity and Quality in Relation to Pancreatic Cancer Survival.Frontiers in medicine · 2021Article
- Approaches for Controlling Antibody-Mediated Allograft Rejection Through Targeting B Cells.Frontiers in immunology · 2021Review
- Review
- Whole-exome and HLA sequencing in Febrile infection-related epilepsy syndrome.Annals of clinical and translational neurology · 2020Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.
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