ArticleNature communications2021
Accurate imputation of human leukocyte antigens with CookHLA.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 3 of them syntheses that pooled it.
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Who cites it
31 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Genome-wide meta-analysis of myasthenia gravis uncovers new loci and provides insights into polygenic prediction.Nature communications · 2024Pooled it
- Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis.Nature communications · 2024Pooled it
- GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture.Nature genetics · 2023Pooled it
- Genome-Wide Risk Assessment and Clinical Prediction of Iodinated Contrast Media-Induced Anaphylaxis.Allergy, asthma & immunology research · 2026Article
- Novel immune-related susceptibility loci associated with pediatric steroid-sensitive nephrotic syndrome identified by a transethnic genome-wide association study.Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association · 2026Article
- The digital keystone: how artificial intelligence is reshaping HLA research and clinical practice.Immunogenetics · 2026Review
- Anti-HLA antibodies in lung transplantation: diagnostic pitfalls and future directions.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Computational identification of B- and T-cell epitopes: a unified task taxonomy and review of databases, datasets, predictive pipelines, and gaps.Frontiers in immunology · 2026Review
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Article
- Fine-mapping genomic loci refines bipolar disorder risk genes.Nature neuroscience · 2025Article
- Impact of HLA evolutionary divergence and donor-recipient molecular mismatches on antibody-mediated rejection of kidney allografts.Nature communications · 2025Article
- Population screening of adults identifies novel genetic variants associated with celiac disease.Scientific reports · 2025Article
- Smoking as a risk factor for rheumatoid arthritis: predominant association with IgA autoantibodies - comprehensive analysis of anti-modified protein antibodies with smoking and genetic risk factors in rheumatoid arthritis.Arthritis research & therapy · 2025Article
- Article
- 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
- Efficient HLA imputation from sequential SNPs data by transformer.Journal of human genetics · 2024Review
- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.PLoS computational biology · 2024Article
- Whole-genome sequencing analysis reveals new susceptibility loci and structural variants associated with progressive supranuclear palsy.Molecular neurodegeneration · 2024Article
- HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases.Communications biology · 2023Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development of imputation methods enabled the prediction of human leukocyte antigen (HLA) alleles from intergenic SNP data, allowing studies to fine-map HLA for immune phenotypes. Here we report an accurate HLA imputation method, CookHLA, which has superior imputation accuracy compared to previous methods. CookHLA differs from other approaches in that it locally embeds prediction markers into highly polymorphic exons to account for exonic variability, and in that it adaptively learns the genetic map within MHC from the data to facilitate imputation. Our benchmarking with real datasets shows that our method achieves high imputation accuracy in a wide range of scenarios, including situations where the reference panel is small or ethnically unmatched.
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