HLA-Cw*1701 is associated with two sub-Saharan African-derived HLA haplotypes: HLA-B*4201, DRB1*03 and HLA-B*4202 without DRB1*03

Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine

A significant portion of the world's population is infected with herpes simplex virus type 1 and/or type 2 (HSV-1 and/or HSV-2), that cause a wide range of diseases including genital herpes, oro-facial herpes, and the potentially blinding ocular herpes. While the global prevalence and distribution of HSV-1 and HSV-2 infections cannot be exactly established, the general trends indicate that: (i) HSV-1 infections are much more prevalent globally than HSV-2; (ii) over a half billion people worldwide are infected with HSV-2; (iii) the sub-Saharan African populations account for a disproportionate burden of genital herpes infections and diseases; (iv) the dramatic differences in the prevalence of herpes infections between regions of the world appear to be associated with differences in the frequencies of human leukocyte antigen (HLA) alleles. The present report: (i) analyzes the prevalence of HSV-1 and HSV-2 infections across various regions of the world; (ii) analyzes potential associations of common HLA-A, HLA-B and HLA-C alleles with the prevalence of HSV-1 and HSV-2 infections in the Caucasoid, Oriental, Hispanic and Black major populations; and (iii) discusses how our recently developed HLA-A, HLA-B, and HLA-C transgenic/H-2 class I null mice will help validate HLA/herpes prevalence associations. Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A(∗)24, HLA-B(∗)27, HLA-B(∗)53 and HLA-B(∗)58 alleles. In contrast, low prevalence of herpes infection and disease appears to be associated with high frequency of HLA-B(∗)44 allele. The finding will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy.

Correlation between genetic HLA class I and II polymorphisms and anthropological aspects in the Chaouya population from Morocco (Arabic speaking)

The aim of this study was to provide genetic and anthropological information on the Chaouya (CH), an Arabic-speaking population living in West Morocco, Atlantic coast (Settat). In 98 unrelated healthy CH volunteers, we first investigated the human leukocyte antigen (HLA) class I and II allele polymorphisms using a sequence-based typing method and examined haplotypes and relatedness of this group to other African and Mediterranean populations. The study showed the close relatedness with Tunisian population and other North Africans, together with a strong influence of various immigrations, mainly Spaniards, French, and Portuguese, as expected. Nevertheless, analysis of class II allele frequencies (afs) showed that Oromo and Amhara Ethiopian groups cluster together with the Berbers and other North Africans, confirming the relationship between these populations (Afro-Asiatic linguistic group, Hamites). South and sub-Saharan Africans cluster separately at a great distance from CH, except the sub-Saharan Bantu population from Congo Kinshasa, which shows a relatively close genetic relationship ascribable to the effect of a diversifying selection. On the other hand, considering HLA class I afs analyses, it was noteworthy that CH grouped together with sub-Saharans, showing a close genetic distance mainly with Ugandas and Kenians Luo.

High-resolution human leukocyte antigen (HLA) haplotypes and linkage disequilibrium of HLA-B and -C and HLA-DRB1 and -DQB1 alleles in a Taiwanese population

Using the maximum-likelihood method with the expectation-maximization (EM) algorithm of PYPOP, high-resolution human leukocyte antigen (HLA) three-locus haplotypes (HLA-A, -B, and -C; HLA-A, -B, and -DRB1) and four-locus haplotypes (HLA-A, -B, -C, and -DRB1) were determined. Linkage disequilibrium of high-resolution HLA-B and -C alleles and HLA-DRB1 and -DQB1 alleles was also calculated. Comparison of the Taiwanese haplotypes and haplotypes from donors in the Chinese Han population, the Asia Pacific Islander ethnic category of the NMDP (National Marrow Donor Program), and the Taiwanese cord blood units demonstrated similarities and dissimilarities among the four populations. HLA allele frequencies of our study suggested that the Taiwanese have a relative population relationship with the southern Han Chinese with regard to HLA. Our results also indicated that the Taiwanese population exhibits genetic proximity with Asian Americans with regard to HLA-A and -DRB1 but not HLA-B.

Generation of the B*41 group of alleles as indicated by intron sequences+

The generation of the B*41 alleles has been analysed using exon 1, intron 1, exon 2, intron 2 and exon 3 sequences. Results showed that B*4102 may have been generated as the first B*41 allele by a recombination mechanism between B*400102 and B*0801 or B*4201 involving intron 2. B*4101, B*4104 and B*4107 alleles could have been generated from B*4102 by a gene conversion event taking three different fragments from sequences belonging to intron 2/exon 3 of B*45, B*50 or B*49 alleles. B*4105 and B*4106 could be generated from B*4101 allele by point mutations, and B*4103 generation is unclear due to the lack of intron 2. The importance of introns in HLA-B allele polymorphism generation is stressed.

Rapid detection of all HLA-B*27 alleles (B*2701-B*2725) by group-specific polymerase chain reaction

Human leucocyte antigen-B*27 is strongly associated with a number of rheumatic diseases, including ankylosing spondylitis and reactive arthritis. Targeted detection of the B*27 group by molecular methods is hampered by the extreme heterogeneity of the serological B*27 group. Here, we describe a simple, rapid sequence-specific primer-based method for detection of all 28 B*27 alleles defined to date. The method involves an initial screening with two sequence-specific polymerase chain reactions (PCRs), which has to be followed by two additional PCR amplifications in samples carrying a few rare subtypes of B*27, B*4202 or B*7301. The described protocol should be useful for laboratories involved in diagnostics and research of rheumatoid diseases.

Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci

The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 subjects from five sub-Saharan populations from Kenya (Nandi and Luo), Mali (Dogon), Uganda, and Zambia. Distributions of genotypes at all loci and in all populations fit Hardy-Weinberg equilibrium expectations. There was not a single allele predominant at any of the loci in these populations, with the exception of A*3002 [allele frequency (AF) = 0.233] in Zambians and Cw*1601 (AF = 0.283) in Malians. This distribution was consistent with balancing selection for all class I loci in all populations, which was evidenced by the homozygosity F statistic that was less than that expected under neutrality. Only in the A locus in Zambians and the C locus in Malians, the AF distribution was very close to neutrality expectations. There were six instances in which there were significant deviations of allele distributions from neutrality in the direction of balancing selection. All allelic lineages from each of the class I loci were found in all the African populations. Several alleles of these loci have intermediate frequencies (AF = 0.020-0.150) and seem to appear only in the African populations. Most of these alleles are widely distributed in the African continent and their origin may predate the separation of linguistic groups. In contrast to native American and other populations, the African populations do not seem to show extensive allelic diversification within lineages, with the exception of the groups of alleles A*02, A*30, B*57, and B*58. The alleles of human leukocyte antigen (HLA)-B are in strong linkage disequilibrium (LD) with alleles of the C locus, and the sets of B/C haplotypes are found in several populations. The associations between A alleles with C-blocks are weaker, and only a few A/B/C haplotypes (A*0201-B*4501-Cw*1601; A*2301-B*1503-Cw*0202; A*7401-B* 1503-Cw*0202; A*2902-B*4201-Cw*1701; A*3001-B*4201-Cw*1701; and A*3601-B*5301-Cw*0401) are found in multiple populations with intermediate frequencies [haplotype frequency (HF) = 0.010-0.100]. The strength of the LD associations between alleles of HLA-A and HLA-B loci and those of HLA-B and HLA-C loci was on average of the same or higher magnitude as those observed in other non-African populations for the same pairs of loci. Comparison of the genetic distances measured by the distribution of alleles at the HLA class I loci in the sub-Saharan populations included in this and other studies indicate that the Luo population from western Kenya has the closest distance with virtually all sub-Saharan population so far studied for HLA-A, a finding consistent with the putative origin of modern humans in East Africa. In all African populations, the genetic distances between each other are greater than those observed between European populations. The remarkable current allelic and haplotypic diversity in the HLA system as well as their variable distribution in different sub-Saharan populations is probably the result of evolutionary forces and environments that have acted on each individual population or in their ancestors. In this regard, the genetic diversity of the HLA system in African populations poses practical challenges for the design of T-cell vaccines and for the transplantation medical community to find HLA-matched unrelated donors for patients in need of an allogeneic transplant.

Inheritable variable sizes of DNA stretches in the human MHC: conserved extended haplotypes and their fragments or blocks

The difference in sizes of conserved stretches of DNA sequence within the major histocompatibility complex (MHC) in human individuals constitutes an underappreciated genetic diversity that has many practical implications. We developed a model to describe the variable sizes of stretches of conserved DNA in the MHC using the known frequencies of four different kinds of small (< 0.2 Mb) blocks of relatively conserved DNA sequence: HLA-Cw/B; TNF; complotype; and HLA-DR/DQ. Each of these small blocks is composed of two or more alleles of closely linked loci inherited as one genetic unit. We updated the concept of the conserved extended haplotype (CEH) using HLA allele identification and TNF microsatellites to show that specific combinations of the four blocks form single genetic units (>/= 1.5 Mb) with a total haplotype frequency in the Caucasian population of 0.30. Some CEHs extend to the HLA-A and -DPB1 loci forming fixed genetic units of up to at least 3.2 Mb of DNA. Finally, intermediate fragments of CEHs also exist, which are, nevertheless, larger than any of the four small blocks. This complexity of genetic fixity at various levels should be taken into account in studies of genetic disease association, immune response control, and human diversity. This knowledge could also be used for matching CEHs and their fragments for patients undergoing allotransplantation.

TNF-alpha promoter single nucleotide polymorphisms are markers of human ancestry

We present a map of single nucleotide polymorphisms (SNPs) in the human tumor necrosis factor (TNF)-alpha promoter based upon exploratory sequencing of 333 human TNF-alpha gene promoters from individuals of distinct ancestral backgrounds. We detect 10 TNF-alpha promoter SNPs that occur with distinct frequencies in populations of different ancestry. Consistent with these findings, we show that two TNF-alpha SNPs, the -243 SNP and the -856 SNP, are the first SNP markers of a sub-Saharan African-derived extended haplotype and an Amerindian HLA haplotype, respectively. Comparisons of TNF-alpha promoter SNP allele frequencies can thus help elucidate variation of HLA haplotypes and their distribution among existing ethnic groups and shed light into the history of human populations.

HLA class I polymorphism, as characterised by PCR-SSOP, in a Brazilian exogamic population

HLA-A, -B and -C genes were analysed in the population living in the metropolitan region of Curitiba, the main city of Parana State, southern Brazil, to provide data for studies and applications in HLA-related fields, and to contribute to the understanding of human microevolution. Heterozygosity is high (95-99%) for all three loci. Frequencies for most alleles and haplotypes of sub-Saharan African and of European ancestry presented a clear gradient between the White, Mulatto and Black subpopulations. Among Whites, the four most common haplotypes were A*01-Cw*07-B*0801, A*02-Cw*07-B*07, A*11-Cw*0401-B*35 and A*03-Cw*0401-B*35. Their frequencies ranged from 5.6% to 3.0%. In the Mulatto sub-population, six haplotypes presented very similar frequencies, close to 2.0-2.4%: A*02-Cw*03-B*15, A*02-Cw*0401-B*35, A*02-Cw*07-B*07, A*03-Cw*0401-B*35, A*30-Cw*17-B*4201, A*68-Cw*03-B*15. Haplotype A*30-Cw*17-B*4201 was found to be very common (6.6%) in the Black sub-population. Admixture estimate revealed the relative contributions of Europeans, sub-Saharan Africans and Amerindians to this populations which were, respectively, 94%, 3% and 3% for the White sub-population, 57%, 39% and 4% for the Mulatto sub-population, and 25%, 74% and 1% for the Black sub-population.