1. Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest
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Derek J. Pappas, Jarek Meller, Pierre-Antoine Gourraud, Vanja Paunic, Antoine Lizee, Steven J. Mack, Jill A. Hollenbach, Damjan Vukcevic, Karl R. Beutner, Lue Ping Zhao, Jacek Biesiada, Xiuwen Zheng, Martin Maiers, Stephen Leslie, Allan Motyer, Kent D. Taylor, Center for Genetics [Oakland, CA, USA], Children's Hospital Oakland Research Institute, Department of Neurology [San Francisco, CA, USA], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Bioinformatics Research [Minneapolis, MN, USA] (National Marrow Donor Program), National Marrow Donor Program [Minneapolis], Centre for Systems Genomics [Melbourne, Australia] (Schools of Mathematics and Statistics, and BioSciences), University of Melbourne-Schools of Mathematics and Statistics, and BioSciences [Melbourne, Australia], Murdoch Children’s Research Institute [Melbourne, Australia], Department of Biomedical Informatics [Cincinnati, OH, USA], University of Cincinnati (UC)-Cincinnati Children's Hospital Medical Center, Los Angeles Biomedical Research Institute (LA BioMed), Department of Biostatistics [Seattle, WA, USA], University of Washington [Seattle], Fred Hutchinson Cancer Research Center [Seattle] (FHCRC), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Département de Santé Publique [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), ONR grant N00014-08-1-1207 (KB, DP, PAG, JAH, AL, SJM, MM and VP), NIH grants U01AI067068 (JAH and SJM) and U19AI067152 (ARRA administrative supplement) (PAG) awarded by the NIAID, R01GM109030 (JAH, SJM and DJP) and P01GM099568 (XZ) awarded by the NIGMS, RO1NS076492 (PAG), RO1NS046297 (PAG) and R01NS049477 (PAG) awarded by the NINDS, NMSS grant RG 2899-D11 (PAG), the Australian National Health and Medical Research Council (NHMRC) Career Development Fellowship ID 1053756 (SL), and by the Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0240 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government, Australia (SL). Research at the Murdoch Childrens Research Institute was supported by the Victorian Government’s Operational Infrastructure Support Program. PAG is a recipient of the Race to Erase MS Junior Investigator Award and the European Federation for Immunogenetics Julia Bodmer Award., Le Bihan, Sylvie, University of California [San Francisco] (UCSF), and University of California-University of California
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0301 basic medicine ,Linkage disequilibrium ,Genotype ,Genome-wide association study ,Human leukocyte antigen ,HLA-C Antigens ,Biology ,Polymorphism, Single Nucleotide ,White People ,Article ,03 medical and health sciences ,HLA Antigens ,Genetics ,HLA-B Antigens ,SNP ,Humans ,Pharmacology & Pharmacy ,Imputation (statistics) ,Polymorphism ,1000 Genomes Project ,HLA Complex ,Alleles ,Pharmacology ,Genome ,[SDV.MHEP] Life Sciences [q-bio]/Human health and pathology ,HLA-A Antigens ,Genome, Human ,Human Genome ,Genetic Variation ,Single Nucleotide ,Pharmacology and Pharmaceutical Sciences ,030104 developmental biology ,Haplotypes ,Molecular Medicine ,Generic health relevance ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology ,Human ,Genome-Wide Association Study ,HLA-DRB1 Chains - Abstract
International audience; 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
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- 2018