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This study aimed to establish the occurrence and frequency of HLA alleles and haplotypes for a healthy British Caucasian population bioresource from Oxfordshire. We present the results of imputation from HLA SNP genotyping data using SNP2HLA for 5553 individuals from Oxford Biobank, defining one- and two-field alleles together with amino acid polymorphisms. We show that this achieves a high level of accuracy with validation using sequence-specific primer amplification PCR. We define six- and eight-locus HLA haplotypes for this population by Bayesian methods implemented using PHASE. We determine patterns of linkage disequilibrium and recombination for these individuals involving classical HLA loci and show how analysis within a haplotype block structure may be more tractable for imputed data. Our findings contribute to knowledge of HLA diversity in healthy populations and further validate future large-scale use of HLA imputation as an informative approach in population bioresources.

Original publication

DOI

10.1016/j.humimm.2017.01.006

Type

Journal article

Journal

Hum Immunol

Publication Date

03/2017

Volume

78

Pages

242 - 251

Keywords

Allele, Genotype, HLA, Imputation, Single nucleotide polymorphism, Adult, Alleles, Bayes Theorem, England, European Continental Ancestry Group, Female, Gene Frequency, Genetics, Population, Genotype, Genotyping Techniques, HLA Antigens, Haplotypes, Humans, Linkage Disequilibrium, Male, Middle Aged, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Principal Component Analysis