ArticleCell reports methods2023
SpecHLA enables full-resolution HLA typing from sequencing data.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comprehensive detection of genetic and epigenetic alterations in cancer using long reads with TumorLens.medRxiv : the preprint server for health sciences · 2026Article
- Association between Human Leukocyte Antigen Alleles and Neuropathological Outcomes in Lewy Body Disease.Annals of neurology · 2026Article
- Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms.Briefings in bioinformatics · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- FuFiHLA: A tool for Full-Field HLA typing from long reads data.bioRxiv : the preprint server for biology · 2025Article
- HLA variation associated with peanut allergy and anaphylaxis among non-Hispanic Black individuals.The journal of allergy and clinical immunology. Global · 2025Article
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- 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
- Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and Tumor Immune Microenvironment.Cancer discovery · 2025Article
- Neoantigen-based immunotherapy: advancing precision medicine in cancer and glioblastoma treatment through discovery and innovation.Exploration of targeted anti-tumor therapy · 2025Review
- 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
- MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.Genome biology · 2024Article
- A comprehensive analysis of germline predisposition to early-onset ovarian cancer.Scientific reports · 2024Article
- DNA structural features and variability of complete MHC locus sequences.Frontiers in bioinformatics · 2024Review
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconstructing diploid sequences of human leukocyte antigen (HLA) genes, i.e., full-resolution HLA typing, from sequencing data is challenging. The high homogeneity across HLA genes and the high heterogeneity within HLA alleles complicate the identification of genomic source loci for sequencing reads. Here, we present SpecHLA, which utilizes fine-tuned reads binning and local assembly to achieve accurate full-resolution HLA typing. SpecHLA accepts sequencing data from paired-end, 10×-linked-reads, high-throughput chromosome conformation capture (Hi-C), Pacific Biosciences (PacBio), and Oxford Nanopore Technology (ONT). It can also incorporate pedigree data and genotype frequency to refine typing. In 32 Human Genome Structural Variation Consortium, Phase 2 (HGSVC2) samples, SpecHLA achieved 98.6% accuracy for G-group-resolution HLA typing, inferring entire HLA alleles with an average of three mismatches fewer, ten gaps fewer, and 590 bp less edit distance than HISAT-genotype per allele. Additionally, SpecHLA exhibited a 2-field typing accuracy of 98.6% in 875 real samples. Finally, SpecHLA detected HLA loss of heterozygosity with 99.7% specificity and 96.8% sensitivity in simulated samples of cancer cell lines.
Indexed as
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.