ArticleGenome medicine2012
HLA typing from RNA-Seq sequence reads.
Article in Genome medicine, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 3 of them syntheses that pooled it.
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The trial behind it
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
168 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group.Annals of oncology : official journal of the European Society for Medical Oncology · 2020Pooled it
- Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review.BMC infectious diseases · 2016Pooled it
- Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.Nature genetics · 2016Pooled it
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Large-Scale Assessment ofbioRxiv : the preprint server for biology · 2026Article
- The sequence alignment problem: boundary conditions as the unifying principle.Briefings in bioinformatics · 2026Review
- Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV.PLoS pathogens · 2026Article
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- ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.Genome biology · 2026Article
- Comprehensive detection of genetic and epigenetic alterations in cancer using long reads with TumorLens.medRxiv : the preprint server for health sciences · 2026Article
- Transcriptomic landscape of transposable elements revealsGenome research · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- Article
- Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.NAR genomics and bioinformatics · 2025Article
- Personalizing DNA Cancer Vaccines.Journal of personalized medicine · 2025Review
- Current progress in neoantigen-based dendritic cell vaccines for solid tumors.Cancer biology & medicine · 2025Review
- Article
- Genomic landscape and immunological profile of glioblastoma in East Asian patients.Cell reports. Medicine · 2025Article
- Loss of SMARCA4 Leads to Intron Retention and Generation of Tumor-Associated Antigens in Small Cell Carcinoma of the Ovary, Hypercalcemic Type.Cancer research · 2025Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
108 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and locus-specific expression level are determined. We successfully applied seq2HLA to 50 individuals included in the HapMap project, yielding 100% specificity and 94% sensitivity at a P-value of 0.1 for two-digit HLA types. We determined HLA type and expression for previously un-typed Illumina Body Map tissues and a cohort of Korean patients with lung cancer. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.
Identifiers
What OpenQuestion holds
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.