ReviewNature protocols2023
Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 2 of them syntheses that pooled it.
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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.
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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.
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Who cites it
36 citing papers in PubMed, 2 syntheses or guidelines pooled it, 43 citations in OpenAlex.
- Human leukocyte antigen (HLA) class I and II genetic relationships with brain imaging measures: A systematic review and meta-analysis.Brain, behavior, and immunity · 2025Pooled it
- Pooled it
- Genetic Risk in Multiple Sclerosis: Susceptibility, Modifiers and Unresolved Questions.Neurology and therapy · 2026Review
- Development and application of type 1 diabetes polygenic scores across diverse populations.Diabetologia · 2026Review
- Polygenic risk scores and HLA class II variants are biomarkers of corticosteroid response in childhood nephrotic syndrome.Kidney international · 2026Article
- Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood.Science advances · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- HLA-DQB1*03:01 and risk of HBV-related HCC.Hepatology (Baltimore, Md.) · 2026Article
- Article
- Preliminary population genetic analysis of 12 X-STR loci in a sample from Türkiye: allele frequencies, haplotype diversity, and linkage disequilibrium.Turkish journal of medical sciences · 2026Article
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Host Genetic Architecture between Epstein-Barr Virus Activity and Multiple Sclerosis Reveals Shared Pathways.medRxiv : the preprint server for health sciences · 2025Article
- Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing.Nature communications · 2025Article
- HLA loci heterozygosity modulates genetic risk in idiopathic inflammatory myopathies.Annals of the rheumatic diseases · 2025Article
- Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- Neoantigen-driven personalized tumor therapy: An update from discovery to clinical application.Chinese medical journal · 2025Review
- Article
- Polygenic Risk Scores and HLA Class II Variants are Biomarkers of Corticosteroid Response in Childhood Nephrotic Syndrome.medRxiv : the preprint server for health sciences · 2025Article
- Uncovering genetic diversity and admixture of British Africans with HLA alleles inferred from whole genome sequencing.European journal of human genetics : EJHG · 2025Article
Corrections and comments
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Authors and funding
19 authors at 8 institutions in 7 countries.
Funding
Abstract
The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software ( https://github.com/immunogenomics/HLA_analyses_tutorial ). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.
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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 Socratic graph.