ArticleProceedings of the National Academy of Sciences of the United States of America2017
Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
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- Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase II Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2020Trial
- Cancers modulate processing and presentation of p53 neoantigens to evade T cell detection.Immunity · 2026Article
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- VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population.Nature communications · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Machine learning-based model for prediction of carbamazepine- and allopurinol-induced severe cutaneous adverse reactions in Vietnamese.The World Allergy Organization journal · 2026Article
- Pharmacogenomic landscape of a Moroccan cohort: enhancing global diversity and addressing the North African gap.Scientific reports · 2026Article
- The digital keystone: how artificial intelligence is reshaping HLA research and clinical practice.Immunogenetics · 2026Review
- ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.Genome biology · 2026Article
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 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
- Large-Scale T-cell Receptor Repertoire Profiling Unveils Tumor-Specific Signals for Diagnosing Indeterminate Pulmonary Nodules.Cancer research · 2025Article
- Article
- Human Genome REWRITE for Off-the-Shelf Stem Cells Reveals an "Epigenetic Ghost".bioRxiv : the preprint server for biology · 2025Article
- Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- 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
31 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer.
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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.