Journal
HUMAN IMMUNOLOGY
Volume 79, Issue 12, Pages 839-847Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.humimm.2018.09.004
Keywords
HLA; NGS; Allele frequency; Haplotype frequency; Population; Linkage disequilibrium; Genetic distance
Categories
Funding
- Sirona Genomics
- Bill and Melinda Gates Foundation [OPP1066265, 116468]
- National Institutes of Health [2U19AI057229]
- Howard Hughes Medical Institute
- Bill and Melinda Gates Foundation [OPP1066265] Funding Source: Bill and Melinda Gates Foundation
Ask authors/readers for more resources
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A,-B,-C,-DPA1,-DPB1,-DQA1, -DQB1,-DRB1,-DRB3,-DRB4, and-DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A*23:17, A*43:01, A*29:11, A*68:27:01, A*01:23, B*14:01:01, B*15:10:01, B*39:10:01, B*45:07, B*82:02:01 and C*08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class H loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DABS. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available