Abstract
HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.
Highlights
The human leukocyte antigen (HLA) loci, located in the major histocompatibility complex (MHC), encode cell-surface molecules that present peptides sampled from the proteome, mediating key immunological events: defining self-antigen tolerance and cellular immune responses to tumors and pathogens
One of the strongest forces molding HLA complexity has been the selective pressure exerted by numerous pathogens [8,11] which is most evident in populations that have maintained larger effective population sizes for longer periods of time [12], as is the case for East African populations [13]
Assay scope and principle To date, 36, 55, and 24 HLA-A, -B and -C alleles have been reported in East African populations [32,33], respectively
Summary
The human leukocyte antigen (HLA) loci, located in the major histocompatibility complex (MHC), encode cell-surface molecules that present peptides sampled from the proteome, mediating key immunological events: defining self-antigen tolerance and cellular immune responses to tumors and pathogens. Class I HLA-A, -B, and -C loci are essential for both innate and adaptive cellular immune responses. When solely enumerated by variants that differ at the amino acid level (i.e., ‘‘4-digit’’ resolution level) the number of currently published class I HLA alleles amounts to 700 in the HLA-A locus, 1084 in the HLA-B locus, and 371 in the HLA-C locus [5]. While these counts reflect worldwide surveys, only a subset of these alleles is usually found in any given global indigenous population [6]. One of the strongest forces molding HLA complexity has been the selective pressure exerted by numerous pathogens [8,11] which is most evident in populations that have maintained larger effective population sizes for longer periods of time [12], as is the case for East African populations [13]
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