ArticleHuman molecular genetics2019
Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles.
Article in Human molecular genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it, 62 citations in OpenAlex.
- Detailed stratified GWAS analysis for severe COVID-19 in four European populations.Human molecular genetics · 2022Pooled it
- T cell receptor clonotypes predict human leukocyte antigen allele carriage and antigen exposure history.Communications biology · 2026Article
- T and B cell responses against Epstein-Barr virus in primary sclerosing cholangitis.Nature medicine · 2025Article
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- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.PLoS computational biology · 2024Article
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- HLA Genes: A Hallmark of Functional Genetic Variation and Complex Evolution.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.Nature protocols · 2023Review
- Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility.American journal of human genetics · 2023Article
- Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response.Nature communications · 2023Article
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- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
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- Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and commonFrontiers in immunology · 2023Article
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- How genetic risk contributes to autoimmune liver disease.Seminars in immunopathology · 2022Review
- Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1.American journal of human genetics · 2022Article
- Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1.PLoS computational biology · 2022Article
- Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide.HGG advances · 2022Article
- Analysis ofFrontiers in endocrinology · 2022Article
Corrections and comments
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Authors and funding
28 authors at 15 institutions in 11 countries.
Funding
Abstract
Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina's Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.
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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.