1. Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest
- Author
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Pappas, DJ, Lizee, A, Paunic, V, Beutner, KR, Motyer, A, Vukcevic, D, Leslie, S, Biesiada, J, Meller, J, Taylor, KD, Zheng, X, Zhao, LP, Gourraud, P-A, Hollenbach, JA, Mack, SJ, and Maiers, M
- Subjects
Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Genetics ,Human Genome ,Generic health relevance ,Alleles ,Genetic Variation ,Genome ,Human ,Genome-Wide Association Study ,Genotype ,HLA Antigens ,HLA-A Antigens ,HLA-B Antigens ,HLA-C Antigens ,HLA-DRB1 Chains ,Haplotypes ,Humans ,Polymorphism ,Single Nucleotide ,White People ,Pharmacology & Pharmacy ,Pharmacology and pharmaceutical sciences - Abstract
Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall,
- Published
- 2018