High Resolution HLA â¼A, â¼B, â¼C, â¼DRB1, â¼DQA1, and â¼DQB1 Diversity in South African Populations.
Front Genet
; 13: 711944, 2022.
Article
en En
| MEDLINE
| ID: mdl-35309124
ABSTRACT
Background:
Lack of HLA data in southern African populations hampers disease association studies and our understanding of genetic diversity in these populations. We aimed to determine HLA diversity in South African populations using high resolution HLA â¼A, â¼B, â¼C, â¼DRB1, â¼DQA1 and â¼DQB1 data, from 3005 previously typed individuals.Methods:
We determined allele and haplotype frequencies, deviations from Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD) and neutrality test. South African HLA class I data was additionally compared to other global populations using non-metrical multidimensional scaling (NMDS), genetic distances and principal component analysis (PCA).Results:
All loci strongly (p < 0.0001) deviated from HWE, coupled with excessive heterozygosity in most loci. Two of the three most frequent alleles, HLA â¼DQA1*0502 (0.2584) and HLA â¼C*1701 (0.1488) were previously reported in South African populations at lower frequencies. NMDS showed genetic distinctness of South African populations. Phylogenetic analysis and PCA clustered our current dataset with previous South African studies. Additionally, South Africans seem to be related to other sub-Saharan populations using HLA class I allele frequencies. Discussion andConclusion:
Despite the retrospective nature of the study, data missingness, the imbalance of sample sizes for each locus and haplotype pairs, and induced methodological difficulties, this study provides a unique and large HLA dataset of South Africans, which might be a useful resource to support anthropological studies, disease association studies, population based vaccine development and donor recruitment programs. We additionally provide simulated high resolution HLA class I data to augment the mixed resolution typing results generated from this study.
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Colección:
01-internacional
Base de datos:
MEDLINE
Idioma:
En
Revista:
Front Genet
Año:
2022
Tipo del documento:
Article
País de afiliación:
Sudáfrica