ArticleGenome medicine2015
HLAreporter: a tool for HLA typing from next generation sequencing data.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.Genome biology · 2026Article
- consHLA: a next generation sequencing consensus-based HLA typing workflow.BMC bioinformatics · 2025Article
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).International journal of oncology · 2025Review
- Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.Scientific reports · 2025Article
- Article
- A walk through the development of human leukocyte antigen typing: from serologic techniques to next-generation sequencing.Clinical transplantation and research · 2024Review
- 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
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing.BMC bioinformatics · 2024Article
- Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response.BMC medical genomics · 2024Article
- A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data.bioRxiv : the preprint server for biology · 2024Article
- Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy.Frontiers in immunology · 2024Review
- Comprehensive HLA Typing from a Current Allele Database Using Next-Generation Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data.BMC genomics · 2023Article
- A Kmer-based paired-end readiScience · 2023Article
- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
- Neoantigens: promising targets for cancer therapy.Signal transduction and targeted therapy · 2023Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly developed tools such as HLAminer and PHLAT. HLAreporter can be downloaded from http://paed.hku.hk/genome/.
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Registered trials
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.