ArticleGenome research2024
Full-resolution HLA and KIR gene annotations for human genome assemblies.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Classical HLA allele and haplotype frequency estimates in US populations.Human immunology · 2026Article
- Complex structural variation, phylogeny, and disease associations of the mucin pangenome.medRxiv : the preprint server for health sciences · 2026Article
- Graph-KIR: graph-based KIR copy number estimation and allele calling using short-read sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- FuFiHLA: a tool for full-field HLA typing from long-read data.Bioinformatics (Oxford, England) · 2026Article
- Classical HLA Allele and Haplotype Frequency Estimates in US Populations.bioRxiv : the preprint server for biology · 2026Article
- Article
- Efficient near telomere-to-telomere assembly of Nanopore Simplex reads.bioRxiv : the preprint server for biology · 2025Article
- 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
- The Primate Major Histocompatibility Complex: A Case Study of Gene Family Evolution.bioRxiv : the preprint server for biology · 2025Article
- Haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines.Genes & diseases · 2025Article
- Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline.Nucleic acids research · 2025Article
- Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery.Nature genetics · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool.Bioinformatics (Oxford, England) · 2024Article
- Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples.Genome research · 2024Article
- Biologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool.bioRxiv : the preprint server for biology · 2024Article
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Abstract
The human leukocyte antigen (HLA) genes and the killer cell immunoglobulin-like receptor (KIR) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, it is difficult to study them with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a nontrivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotate 9931 HLA and KIR genes and found that almost half of these genes, 4068, have novel sequences compared with the current Immuno Polymorphism Database (IPD). These novel gene sequences are represented by 2664 distinct alleles, some of which contained nonsynonymous variations, resulting in 92 novel protein sequences. We demonstrate the complex haplotype structures at the two loci and report the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.
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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.