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Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles

Human molecular genetics, 2019-06, Vol.28 (12), p.2078-2092 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. ;info:eu-repo/semantics/openAccess ;The Author(s) 2018. Published by Oxford University Press. 2018 ;ISSN: 0964-6906 ;EISSN: 1460-2083 ;DOI: 10.1093/hmg/ddy443 ;PMID: 30590525

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Title:
Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles
Author: Degenhardt, Frauke ; Wendorff, Mareike ; Wittig, Michael ; Ellinghaus, Eva ; Datta, Lisa W ; Schembri, John ; Ng, Siew C ; Rosati, Elisa ; Hübenthal, Matthias ; Ellinghaus, David ; Jung, Eun Suk ; Lieb, Wolfgang ; Abedian, Shifteh ; Malekzadeh, Reza ; Cheon, Jae Hee ; Ellul, Pierre ; Sood, Ajit ; Midha, Vandana ; Thelma, B K ; Wong, Sunny H ; Schreiber, Stefan ; Yamazaki, Keiko ; Kubo, Michiaki ; Boucher, Gabrielle ; Rioux, John D ; Lenz, Tobias L ; Brant, Steven R ; Franke, Andre
Subjects: African Americans - ethnology ; African Americans - genetics ; Alleles ; Asian Continental Ancestry Group ; Benchmarking ; Bioinformatics ; Cluster Analysis ; Ethnic Groups ; European Continental Ancestry Group - ethnology ; European Continental Ancestry Group - genetics ; Gene Frequency ; Genotype ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Histocompatibility Antigens Class I - genetics ; Histocompatibility Antigens Class II - genetics ; HLA Antigens - genetics ; HLA-DRB3 Chains - genetics ; HLA-DRB4 Chains - genetics ; HLA-DRB5 Chains - genetics ; Humans ; Polymorphism, Single Nucleotide ; Retrospective Studies
Is Part Of: Human molecular genetics, 2019-06, Vol.28 (12), p.2078-2092
Description: Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina's Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.
Publisher: England: Oxford University Press
Language: English;Norwegian
Identifier: ISSN: 0964-6906
EISSN: 1460-2083
DOI: 10.1093/hmg/ddy443
PMID: 30590525
Source: GFMER Free Medical Journals
MEDLINE
NORA Norwegian Open Research Archives
Alma/SFX Local Collection

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Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles

The Author(s) 2018. Published by Oxford University Press. ;info:eu-repo/semantics/openAccess ;The Author(s) 2018. Published by Oxford University Press. 2018 ;ISSN: 0964-6906 ;EISSN: 1460-2083 ;DOI: 10.1093/hmg/ddy443 ;PMID: 30590525

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