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

Tissue Antigens. 2015 Oct;86(4):285-92. doi: 10.1111/tan.12642. Epub 2015 Aug 24.


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.

Keywords: African peopling history; HLA haplotypes; Nigerian population; anthropology; family data; linkage disequilibrium; malaria resistance; population genetics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Family
  • Gene Expression
  • Gene Frequency
  • Genetic Variation
  • Genetics, Population
  • 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
  • Haplotypes*
  • Histocompatibility Testing
  • Humans
  • Linkage Disequilibrium*
  • Nigeria
  • Pedigree


  • HLA-A Antigens
  • HLA-B Antigens
  • HLA-C Antigens
  • HLA-DQ beta-Chains
  • HLA-DQB1 antigen
  • HLA-DRB1 Chains