ArticlePloS one2013
An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial.Nature medicine · 2021Trial
- Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma.Cell reports. Medicine · 2020Trial
- The clinical utility of exome sequencing for risk stratification in celiac disease.Journal of human immunity · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Clinical applications and methodology updates in HLA typing.BMC immunology · 2026Review
- Analytical and clinical validation of CancerMaster, an automated targeted NGS panel, for tumor-only precision oncology.Scientific reports · 2026Article
- NGSMHC: a simple bioinformatics tool for comprehensively typing major histocompatibility complex genes in non-human species using next-generation sequencing data.Animal bioscience · 2026Article
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- Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline.Nucleic acids research · 2025Article
- Long-read sequencing reveals novel genetic polymorphisms in the major histocompatibility complex region and their impacts on the Han Chinese population.Science China. Life sciences · 2025Article
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- Article
- Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis of immunopeptidomic data.Computational and structural biotechnology journal · 2025Article
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy.Frontiers in immunology · 2024Review
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
- Article
- Allelic imbalance of HLA-B expression in human lung cells infected with coronavirus and other respiratory viruses.European journal of human genetics : EJHG · 2022Article
- HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade.Annals of oncology : official journal of the European Society for Medical Oncology · 2022Article
Corrections and comments
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Authors and funding
23 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.
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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.