ArticlePloS one2013
Imputing amino acid polymorphisms in human leukocyte antigens.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 418 papers, 12 of them syntheses that pooled it.
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Who cites it
418 citing papers in PubMed, 12 syntheses or guidelines pooled it, 708 citations in OpenAlex.
- Association of genetic variation with age at diagnosis in type 1 diabetes.BMJ open diabetes research & care · 2026Pooled it
- Pooled it
- Identification of a novel genetic locus associated with immune-mediated thrombotic thrombocytopenic purpura.Haematologica · 2022Pooled it
- Determining in which pre-arthritis stage HLA-shared epitope alleles and smoking exert their effect on the development of rheumatoid arthritis.Annals of the rheumatic diseases · 2022Pooled it
- Genome-wide association study identifies susceptibility loci for acute myeloid leukemia.Nature communications · 2021Pooled it
- Genome-wide search for genes affecting the age at diagnosis of type 1 diabetes.Journal of internal medicine · 2021Pooled it
- Genetic control of CCL24, POR, and IL23R contributes to the pathogenesis of sarcoidosis.Communications biology · 2020Pooled it
- The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis.Nature communications · 2020Pooled it
- Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.Biological psychiatry · 2020Pooled it
- A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn's disease.Scientific reports · 2020Pooled it
- Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.Clinical pharmacology and therapeutics · 2019Pooled it
- Genetics of idiopathic inflammatory myopathies: insights into disease pathogenesis.Current opinion in rheumatology · 2019Pooled it
- Association of rheumatoid factor, anti-citrullinated protein antibodies and shared epitope with clinical response to initial treatment in patients with early rheumatoid arthritis: data from a randomised controlled trial.Annals of the rheumatic diseases · 2024Trial
- Genetics are not likely to offer clinically useful predictions for elevated liver enzyme levels in patients using low dose methotrexate.Seminars in arthritis and rheumatism · 2022Trial
- Genome-wide pharmacogenetics of anti-drug antibody response to bococizumab highlights key residues in HLA DRB1 and DQB1.Scientific reports · 2022Trial
- Residual β cell function in long-term type 1 diabetes associates with reduced incidence of hypoglycemia.The Journal of clinical investigation · 2021Trial
- Proteome-wide Mendelian randomization identifies APOM and TNXB as actionable mediators of steroid-sensitive nephrotic syndrome.Pediatric nephrology (Berlin, Germany) · 2026Article
- HLA-B*44 Alleles and HLA-DQA1*03:01 as Genetic Risk Factors for Drug-Induced Liver Injury due to Fluoroquinolones.Liver international : official journal of the International Association for the Study of the Liver · 2026Article
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358 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
Abstract
DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.
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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.