HLA-A-B-C-DRB1-DQB1 phased haplotypes in 124 Nigerian families indicate extreme HLA diversity and low linkage disequilibrium in Central-West Africa

The simultaneous typing of five‐HLA loci at high resolution and the availability of pedigree data allowed us to characterize extended five‐locus phased haplotypes in 124 Nigerian families and to compare the observed frequencies with those expected by an expectation–maximization algorithm for unphase...

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Published inTissue antigens Vol. 86; no. 4; pp. 285 - 292
Main Authors Testi, M., Battarra, M., Lucarelli, G., Isgro, A., Morrone, A., Akinyanju, O., Wakama, T., Nunes, J. M., Andreani, M., Sanchez-Mazas, A.
Format Journal Article
LanguageEnglish
Published Oxford, UK Blackwell Publishing Ltd 01.10.2015
Subjects
African peopling history
Alleles
anthropology
Family
family data
Gene Expression
Gene Frequency
Genetic Variation
Genetics, Population
Haplotypes
Histocompatibility Testing
HLA haplotypes
HLA-A Antigens - genetics
HLA-A Antigens - immunology
HLA-B Antigens - genetics
HLA-B Antigens - immunology
HLA-C Antigens - genetics
HLA-C Antigens - immunology
HLA-DQ beta-Chains - genetics
HLA-DQ beta-Chains - immunology
HLA-DRB1 Chains - genetics
HLA-DRB1 Chains - immunology
Humans
Linkage Disequilibrium
malaria resistance
Nigeria
Nigerian population
Pedigree
population genetics
Nigeria
African peopling history
population genetics
anthropology
Nigerian population
HLA haplotypes
family data
malaria resistance
linkage disequilibrium
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Summary:The simultaneous typing of five‐HLA loci at high resolution and the availability of pedigree data allowed us to characterize extended five‐locus phased haplotypes in 124 Nigerian families and to compare the observed frequencies with those expected by an expectation–maximization algorithm for unphased data. Despite the occurrence of some frequent alleles at each locus (e.g. B*53:01, which is assumed to protect against Plasmodium falciparum), as many as 82% of the sampled individuals carry two unique five‐locus haplotypes and only three extended haplotypes with frequency above 1% exhibit significant linkage disequilibrium. Although preliminary, these results reveal an extreme level of HLA diversity in the Nigerian population, which reflects both its multi‐ethnic composition and the very ancient demographic history of African populations.
Bibliography:Swiss National Foundation - No. 31003A_144180
ark:/67375/WNG-ZGQ7ZTWP-P
IME Foundation
ArticleID:TAN12642
istex:9DE609E9F22D16BB778CBBD9517B45794843BD15
Table S1. HLA first-field allele frequencies and summary statistics in Nigerians (N = 245 individuals).Table S2. HLA second-field allele frequencies and summary statistics in Nigerians (N = 97 individuals).Table S3. Matrices of FST with associated P-values (obtained by using ARLEQUIN permutation test) per HLA locus between the five Nigerian subsamples (this study) and the Yoruba sample from the 1000 genomes project .Table S4. HLA first-field five-loci haplotype frequencies in Nigerians (N = 245 individuals, phased data).Table S5. HLA second-field five-locus haplotype frequencies in Nigerians (N = 97 individuals, phased-data).Table S6. Global linkage disequilibrium among pairs of loci in the Nigerian population (N = 97 individuals tested at the second-field level of resolution).Table S7. Most frequent HLA first-field haplotype frequencies estimated both on phased data and on data considered to be unphased (N = 245 individuals).
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:0001-2815
1399-0039
DOI:10.1111/tan.12642