ArticlePloS one2014
Construction and application of a Korean reference panel for imputing classical alleles and amino acids of human leukocyte antigen genes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Article
- Article
- Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.Nature protocols · 2023Review
- PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations.Nucleic acids research · 2023Article
- HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases.Seminars in immunopathology · 2022Review
- Accurate imputation of human leukocyte antigens with CookHLA.Nature communications · 2021Article
- Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort.NAR genomics and bioinformatics · 2020Article
- Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles.Human molecular genetics · 2019Article
- Cross-ethnicity tagging SNPs for HLA alleles associated with adverse drug reaction.The pharmacogenomics journal · 2019Article
- Review
- Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.PLoS genetics · 2019Article
- Understanding HLA associations from SNP summary association statistics.Scientific reports · 2019Article
- SNP-based HLA allele tagging, imputation and association with antiepileptic drug-induced cutaneous reactions in Hong Kong Han Chinese.The pharmacogenomics journal · 2018Article
- Population Stratification in Genetic Association Studies.Current protocols in human genetics · 2017Review
- MergeReference: A Tool for Merging Reference Panels for HLA Imputation.Genomics & informatics · 2017Article
- The MHC locus and genetic susceptibility to autoimmune and infectious diseases.Genome biology · 2017Review
- Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease.Nature genetics · 2016Article
- Article
- Association of HLA Genotype and Fulminant Type 1 Diabetes in Koreans.Genomics & informatics · 2015Article
- An HLA-C amino-acid variant in addition to HLA-B*27 confers risk for ankylosing spondylitis in the Korean population.Arthritis research & therapy · 2015Article
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic variations of human leukocyte antigen (HLA) genes within the major histocompatibility complex (MHC) locus are strongly associated with disease susceptibility and prognosis for many diseases, including many autoimmune diseases. In this study, we developed a Korean HLA reference panel for imputing classical alleles and amino acid residues of several HLA genes. An HLA reference panel has potential for use in identifying and fine-mapping disease associations with the MHC locus in East Asian populations, including Koreans. A total of 413 unrelated Korean subjects were analyzed for single nucleotide polymorphisms (SNPs) at the MHC locus and six HLA genes, including HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1. The HLA reference panel was constructed by phasing the 5,858 MHC SNPs, 233 classical HLA alleles, and 1,387 amino acid residue markers from 1,025 amino acid positions as binary variables. The imputation accuracy of the HLA reference panel was assessed by measuring concordance rates between imputed and genotyped alleles of the HLA genes from a subset of the study subjects and East Asian HapMap individuals. Average concordance rates were 95.6% and 91.1% at 2-digit and 4-digit allele resolutions, respectively. The imputation accuracy was minimally affected by SNP density of a test dataset for imputation. In conclusion, the Korean HLA reference panel we developed was highly suitable for imputing HLA alleles and amino acids from MHC SNPs in East Asians, including Koreans.
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