ArticlePloS one2017
Comparison of HLA allelic imputation programs.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 67 citations in OpenAlex.
- Association Between Single-Nucleotide Polymorphisms in HLA Alleles and Human Immunodeficiency Virus Type 1 Viral Load in Demographically Diverse, Antiretroviral Therapy-Naive Participants From the Strategic Timing of AntiRetroviral Treatment Trial.The Journal of infectious diseases · 2019Trial
- HLA-A*32:01 and Lamotrigine-Induced Drug Reaction With Eosinophilia and Systemic Symptoms.JAMA network open · 2026Article
- Genomic landscape of cancer in racially and ethnically diverse populations.Nature reviews. Genetics · 2025Review
- Genotype imputation methods for whole and complex genomic regions utilizing deep learning technology.Journal of human genetics · 2024Review
- Association of Human Leukocyte Antigen Alleles with COVID-19 Severity and Mortality in a Spanish Population.Medicina (Kaunas, Lithuania) · 2024Article
- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
- Article
- Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes.Journal of translational medicine · 2022Article
- Novel Analysis Methods to Mine Immune-Mediated Phenotypes and Find Genetic Variation Within the Electronic Health Record (Roadmap for Phenotype to Genotype: Immunogenomics).The journal of allergy and clinical immunology. In practice · 2022Review
- HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases.Seminars in immunopathology · 2022Review
- A comparison of genotyping arrays.European journal of human genetics : EJHG · 2021Article
- Fine mapping of the HLA locus in Parkinson's disease in Europeans.NPJ Parkinson's disease · 2021Article
- Class II Human Leukocyte Antigen Variants Associate With Risk of Pegaspargase Hypersensitivity.Clinical pharmacology and therapeutics · 2021Article
- Genetic susceptibility to multiple sclerosis: interactions between conserved extended haplotypes of the MHC and other susceptibility regions.BMC medical genomics · 2021Article
- Rapid genotype imputation from sequence with reference panels.Nature genetics · 2021Article
- MiDAS-Meaningful Immunogenetic Data at Scale.PLoS computational biology · 2021Article
- In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales.Briefings in bioinformatics · 2021Article
- Accurate imputation of human leukocyte antigens with CookHLA.Nature communications · 2021Article
- Associations between human leukocyte antigens and renal function.Scientific reports · 2021Article
- Human Leukocyte Antigen B*14:01 and B*35:01 Are Associated With Trimethoprim-Sulfamethoxazole Induced Liver Injury.Hepatology (Baltimore, Md.) · 2021Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.
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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.