ArticleBMC genetics2014
Performance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, -DQB1, and -DPB1.
Article in BMC genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Imputation-Based HLA Typing with GWAS SNPs.Methods in molecular biology (Clifton, N.J.) · 2024Article
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- Assessing HLA imputation accuracy in a West African population.bioRxiv : the preprint server for biology · 2023Article
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- Novel HLA associations with outcomes of Mycobacterium tuberculosis exposure and sarcoidosis in individuals of African ancestry using nearest-neighbor feature selection.Genetic epidemiology · 2022Article
- 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
- An immunogenetic view of COVID-19.Genetics and molecular biology · 2021Article
- A high-resolution HLA imputation system for the Taiwanese population: a study of the Taiwan Biobank.The pharmacogenomics journal · 2020Article
- How Ancestry Influences the Chances of Finding Unrelated Donors: An Investigation in Admixed Brazilians.Frontiers in immunology · 2020Article
- Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.The pharmacogenomics journal · 2018Article
- A genomic perspective on HLA evolution.Immunogenetics · 2018Review
- Comparison of HLA allelic imputation programs.PloS one · 2017Article
- Human leucocyte antigen class I and II imputation in a multiracial population.International journal of immunogenetics · 2016Article
- Differential frequency of NKG2C/KLRC2 deletion in distinct African populations and susceptibility to Trachoma: a new method for imputation of KLRC2 genotypes from SNP genotyping data.Human genetics · 2016Article
- HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set.Human immunology · 2016Article
- Advances in the Pharmacogenomics of Adverse Drug Reactions.Drug safety · 2016Review
- Fine mapping of chromosome 15q25 implicates ZNF592 in neurosarcoidosis patients.Annals of clinical and translational neurology · 2015Article
- Association of HLA-DRB1 with Sarcoidosis Susceptibility and Progression in African Americans.American journal of respiratory cell and molecular biology · 2015Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region's haplotype structure, but the performance of these methods in admixed populations (such as African Americans) has not been adequately evaluated. We compared genotype-based-derived from both genome-wide genotyping and targeted sequencing-imputation results to existing allele data for HLA-DRB1, -DQB1, and -DPB1.
resultsIn European Americans, the newly-developed HLA Genotype Imputation with Attribute Bagging (HIBAG) method outperformed HLA*IMP:02. In African Americans, HLA*IMP:02 performed marginally better than HIBAG pre-built models, but HIBAG models constructed using a portion of our African American sample with both SNP genotyping and four-digit HLA class II allele typing had consistently higher accuracy than HLA*IMP:02. However, HIBAG was significantly less accurate in individuals heterozygous for local ancestry (p ≤0.04). Accuracy improved in models with equal numbers of African and European chromosomes. Variants added by targeted sequencing and SNP imputation further improved both imputation accuracy and the proportion of high quality calls.
conclusionCombining the HIBAG approach with local ancestry and dense variant data can produce highly-accurate HLA class II allele imputation in African Americans.
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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.