ArticleGenome research2023
Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 49 citations in OpenAlex.
- A Phase Ib/II Study of Atezolizumab in Combination with Thiopurine Therapy in Patients with Metastatic Solid Tumors and Intermediate Tumor Mutational Burden.Cancer research communications · 2026Trial
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Aristolochic Acid and Alternative Lengthening of Telomeres Mechanisms Underlie Liver Angiosarcoma Pathogenesis.Liver cancer · 2026Article
- Graph-KIR: graph-based KIR copy number estimation and allele calling using short-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- HLA Alleles and Haplotype Distribution Across Russian Population Groups.International journal of molecular sciences · 2026Article
- Aberrant CD4bioRxiv : the preprint server for biology · 2026Article
- FuFiHLA: a tool for full-field HLA typing from long-read data.Bioinformatics (Oxford, England) · 2026Article
- A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genetically predicted KIR2DS4 mediate the association between gut microbe K10 and osteoporosis fractures: A mediation Mendelian randomization study.PM & R : the journal of injury, function, and rehabilitation · 2026Article
- ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.Genome biology · 2026Article
- Article
- JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes.Nucleic acids research · 2026Article
- Japanese genomes for pharmacogenomics: primary and secondary pipelines for population-specific insights.Frontiers in bioinformatics · 2026Article
- T Cell Receptor Sharing in Hypersensitivity Pneumonitis.Computational and structural biotechnology journal · 2026Article
- Development and validation of a pipeline for the systematic search for new HLA alleles in WGS data.Frontiers in bioinformatics · 2026Article
- Immunogenetics and TCR expression patterns together predict future T1D onset from multi-omic datasets.Frontiers in genetics · 2026Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
- Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.Nature genetics · 2025Article
- FuFiHLA: A tool for Full-Field HLA typing from long reads data.bioRxiv : the preprint server for biology · 2025Article
- Efficient and effective identification of cancer neoantigens from tumor only RNA-seq.NAR genomics and bioinformatics · 2025Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Killer cell immunoglobulin like receptor (KIR) genes and human leukocyte antigen (HLA) genes play important roles in innate and adaptive immunity. They are highly polymorphic and cannot be genotyped with standard variant calling pipelines. Compared with HLA genes, many KIR genes are similar to each other in sequences and may be absent in the chromosomes. Therefore, although many tools have been developed to genotype HLA genes using common sequencing data, none of them work for KIR genes. Even specialized KIR genotypers could not resolve all the KIR genes. Here we describe T1K, a novel computational method for the efficient and accurate inference of KIR or HLA alleles from RNA-seq, whole-genome sequencing, or whole-exome sequencing data. T1K jointly considers alleles across all genotyped genes, so it can reliably identify present genes and distinguish homologous genes, including the challenging
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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.