Abstract
Human Leukocyte Antigens (HLAs) play an important role in host immune responses to infectious pathogens, and influence organ transplantation, cancer and autoimmune diseases. In this study we conducted a high resolution, sequence-based genotyping of HLA class I and class II genes of more than 2000 women from Kenya, eastern Tanzania and southern Uganda around Lake Victoria and analyzed their allele, phenotype and haplotype frequencies. A considerable genetic diversity was observed at both class I and II loci. A total of 79 HLA-A, 113 HLA-B, 53 HLA-C, 25 HLA-DPA1, 60 HLA-DPB1, 15 HLA-DQA1, 44 HLA-DQB1 and 38 HLA-DRB1 alleles have been identified. The most common class I alleles were A * 02:01:01 (10.90%), B * 58:02 (8.79%), and C * 06:02:01 (16.98%). The most common class II alleles were DPA1*01:03:01 (40.60%), DPB1 * 01:01:01 (23.45%), DQA1 * 01:02:01 (31.03%), DQB1 * 03:01:01 (21.79%), DRB1 * 11:01:02 (11.65%), DRB3 * 02:02:01 (31.65%), DRB4 * 01:01:01 (10.50%), and DRB5 * 01:01:01 (10.50%). Higher than expected homozygosity was observed at HLA-B (P = 0.022), DQA1 (P = 0.004), DQB1 (P = 0.023), and DRB1 (P = 0.0006) loci. The allele frequency distribution of this population is very similar to the ones observed in other sub-Saharan populations with the exception of lower frequencies of A * 23 (5.55% versus 11.21%) and DQA1 * 03 (4.79% versus 11.72%), and higher frequencies of DPB1 * 30 (2.26% versus 0.37%) and DRB1 * 11 (21.51% versus 15.89%). The knowledge of the diversity and allele/ phenotype frequencies of the HLA alleles of this east African population, can contribute to the understanding of how host genetic factors influence disease susceptibility and effective anti-retroviral treatment of HIV infections and future vaccine trials.
Highlights
The Human Leukocyte Antigen (HLA) genes are the most polymorphic genes within the human genome and play an important role in initiating the immune response to invading pathogens
Extensive diversity has been observed at each HLA class I locus in this East African population
Similar to other populations the greater allele diversity is observed in HLA-B, followed by HLA-A, and HLA-C
Summary
The Human Leukocyte Antigen (HLA) genes are the most polymorphic genes within the human genome and play an important role in initiating the immune response to invading pathogens. Associations between specific HLA alleles and increased/decreased risk of autoimmunity diseases [1] [2] as well as resistance and susceptibility to pathogenic infections have been reported in many studies [3]. The information related to the HLA allele frequencies and their compositions in a given population can contribute to the anthropological and transplantation studies, and to the understanding of disease epidemiology. It can provide valuable information for designing effective vaccine and clinical trials. As a founder population under the extensive selective pressure exerted by many infectious diseases, East African populations are expected to have a very diverse HLA class I and II allele composition. Comparison of HLA composition of Kenya and Cameroon populations showed various similarities and differences for specific frequencies of HLA-A and -B alleles [5] and similar genetic distance in HLA-C has been observed between the Caucasian and African population and between the African and Asian populations [6]
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