Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest
- Pappas, Derek,
- Lizee, Antoine
- Paunic, Vanja
- Beutner, Karl,
- Motyer, Allan
- Vukcevic, Damjan
- Leslie, Stephen
- Biesiada, Jacek
- Meller, Jarek
- Taylor, Kent,
- Zheng, Xiuwen
- Zhao, Lue,
- Gourraud, Pierre-Antoine
- Hollenbach, Jill,
- Mack, Steven,
- Maiers, Martin
DOIAbstract
International audienceFour 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, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable...
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