title: Human leukocyte antigen class I (A, B, C) and II (DRB1) diversity in the black and Caucasian South African population.
abstract: A cross-section of black and Caucasian South Africans (N = 302) were genotyped at high resolution (class I HLA-A, -B, -C and class II HLA-DRB1). Five new class I alleles (A*30:01:02, A*30:02:02, A*68:27, B*42:06, and B*45:07) and one new confirmatory allele (A*29:11) were identified in the black population. Alleles and haplotypes showed expected differences between the black and Caucasian populations, with the black population, on average, showing a broader spectrum of allele representation (less single allele dominance). The most prevalent alleles at the four loci in the black population were A*30:01, B*58:02, C*06:02, and DRB1*13:01 and in the Caucasian population were A*02:01:01, B*07:02:01, C*07:01, and DRB1*03:01. HLA-B, and HLA-C loci showed the strongest overall linkage disequilibrium (LD) and HLA-B/HLA-C two locus haplotypes also showed the strongest LD (D'(ij)) in both population groups. Bw allotype representation was similar between the two populations; however C allotypes differed significantly (C1 higher representation in Caucasians; C2 higher representation in blacks). HLA-A Supertype family phenotypic frequencies did not differ between the two populations, but four (B08, B27, B58, and B62) HLA-B Supertype families differed significantly. However, vaccine coverage estimation came close to 100% in both population groups, with inclusion of only four Supertype families (A1, A2, B7, B58).
authors.affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and the University of the Witwatersrand, Johannesburg, South Africa. paxim@nicd.ac.za
authors.forename: Maria
authors.initials: M
authors.lastname: Paximadis
authors.forename: Tiyani Y
authors.initials: TY
authors.lastname: Mathebula
authors.forename: Nikki L
authors.initials: NL
authors.lastname: Gentle
authors.forename: Eftyhia
authors.initials: E
authors.lastname: Vardas
authors.forename: Mark
authors.initials: M
authors.lastname: Colvin
authors.forename: Clive M
authors.initials: CM
authors.lastname: Gray
authors.forename: Caroline T
authors.initials: CT
authors.lastname: Tiemessen
authors.forename: Adrian
authors.initials: A
authors.lastname: Puren
mesh_terms: D000483:Alleles; D044383:Black People / Q000208:ethnology / Q000235:genetics*; D015331:Cohort Studies; D005787:Gene Frequency; D014644:Genetic Variation; D005838:Genotype; D015234:HLA-A Antigens / Q000235:genetics*; D015235:HLA-B Antigens / Q000235:genetics*; D015236:HLA-C Antigens / Q000235:genetics*; D059811:HLA-DRB1 Chains / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013019:South Africa; D044465:White People / Q000208:ethnology / Q000235:genetics*
chemical_list: D015234:HLA-A Antigens; D015235:HLA-B Antigens; D015236:HLA-C Antigens; D059811:HLA-DRB1 Chains