ArticleBioinformatics (Oxford, England)2014
OptiType: precision HLA typing from next-generation sequencing data.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04273061 (Canadian Atezolizumab Precision Targeting for Immunotherapy Intervention), which is not on this map. Cited by 495 papers, 3 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Canadian Atezolizumab Precision Targeting for Immunotherapy Intervention
Who cites it
495 citing papers in PubMed, 3 syntheses or guidelines pooled it, 818 citations in OpenAlex.
- Predicting immunotherapy response of advanced bladder cancer through a meta-analysis of six independent cohorts.Nature communications · 2025Pooled it
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- HLA-B*27 is associated with CNO in a European cohort.Pediatric rheumatology online journal · 2023Pooled it
- Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition in metastatic TNBC.Nature cancer · 2026Trial
- Impact of the tumor immune contexture in microsatellite-stable metastatic colorectal cancer treated with avelumab, cetuximab, and irinotecan.Cell reports. Medicine · 2025Trial
- Duvelisib plus romidepsin in relapsed/refractory T cell lymphomas: a phase 1b/2a trial.Nature medicine · 2024Trial
- Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).Cell reports. Medicine · 2024Trial
- Pucotenlimab in patients with advanced mismatch repair-deficient or microsatellite instability-high solid tumors: A multicenter phase 2 study.Cell reports. Medicine · 2023Trial
- Cancers modulate processing and presentation of p53 neoantigens to evade T cell detection.Immunity · 2026Article
- Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting.npj drug discovery · 2026Review
- Long-read sequencing reveals widespread novel splicing and neojunction-derived neoantigens in nasopharyngeal carcinoma.Genome research · 2026Article
- Article
- Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026Review
- Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers.Genome biology · 2026Article
- Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer.Nature communications · 2026Article
- Transcriptomic analysis of tissue-resident memory T cells of the fallopian tube reveals a precursor immune surveillance network for ovarian cancer prevention.Nature communications · 2026Article
- Invas: an inversion-aware method for transcriptome assembly.Nature communications · 2026Article
- Equal in death: Ancient genomic analysis of children's early Christian burials.Science advances · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- Assessment of tumor mutation burden based on whole-exome sequencing of extracellular vesicle-derived DNA from bronchoalveolar lavage fluid in advanced non-small cell lung cancer treated with pembrolizumab: a prospective, multicenter, observational study.Translational lung cancer research · 2026Article
435 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
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci. Established approaches, therefore, rely on specific HLA enrichment and sequencing techniques, coming at an additional cost and extra turnaround time.
resultWe present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. We also present a comprehensive benchmark dataset consisting of RNA, exome and whole-genome sequencing data. OptiType significantly outperformed previously published in silico approaches with an overall accuracy of 97% enabling its use in a broad range of applications.
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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.