Genetic affinities among Mongol ethnic groups and their relationship to Turks

Sequence diversity of hepatitis D virus in Mongolia

Introduction

The Hepatitis Delta Virus (HDV) is a defective, single-stranded RNA virusoid encoding for a single protein, the Hepatitis Delta Antigen (HDAg), which requires the hepatitis B virus (HBV) envelope protein (HBsAg) for its transmission. Currently, hepatitis D is the most aggressive form of viral hepatitis and treatment options are limited. Worldwide 12 million people are chronically infected with HDV being at high risk for progression to cirrhosis and development of liver cancer.

Objectives

Although it is well established that Mongolia is the country with the highest prevalence of HDV infections, the information on the molecular epidemiology and factors contributing to HDV sequence diversity are largely unclear. The aim of the study was to characterize the sequence diversity of HDV in rural areas from Mongolia and to determine the extent of HLA class I-associated selection pressure.

Patients and methods

From the HepMongolia cohort from rural areas in Mongolia, 451 HBsAg-positive individuals were selected and anti-HDV, HDV-RNA and the sequence of the large HDAg was determined. For all individuals the HLA class I locus was genotyped. Residues under selection pressure in the presence of individual HLA class I types were identified with the recently published analysis tool HAMdetector.

Results

Of 431 HBsAg positive patients, 281 were anti-HDV positive (65%), and HDV-RNA could be detected in 207 of 281 (74%) of patients. The complete large HDAg was successfully sequenced from 131 samples. Phylogenetic analysis revealed that all Mongolian HDV isolates belong to genotype 1, however, they separate into several different clusters without clear regional association. In turn, from phylogeny there is strong evidence for recent local transmission events. Importantly, we found multiple residues with strong support for HLA class I-associated selection pressure consistent with a functional CD8⁺ T cell response directed against HDV.

Conclusion

HDV isolates from Mongolia are highly diverse. The molecular epidemiology suggests circulation of multiple subtypes and provides evidence for ongoing recent transmissions.

North Asian population relationships in a global context

Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.

Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians

Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.

HLA Profile of Kami Population Refutes the Earlier Proposition of Exclusive Closer Genetic Affinity of All the Gorkhas to Mongoloids

OBJECTIVE

Based on the HLA profile of Indian Gorkhas, Debnath and Chaudhuri (2006) proposed that Gorkhas are genetically closer to Mongoloids, and they may have originated from Mongolians or Tibetan stocks. However, the major limitation of the earlier study was that Gorkhas comprise 2 broad groups, i.e. Tibeto-Burmans and Indo-Aryans. Besides, Gorkhas have an assemblage of many sociocultural and linguistically distinct populations such as Rai, Magar, Limbu, Tamang, Newar, Bahun, Kami, and so on. Thus, the generalization of the findings on Gorkhas by considering them as a single homogenous population may not be free from biases. Therefore, the present study aims to understand the genetic affinity of a constituent population from the Gorkha community, i.e. Kami, based on HLA polymorphism.

METHODS

First field HLA typing was performed among 158 Kami individuals by PCR-SSP methods.

RESULTS

The most frequent genes observed were HLA-A*11, HLA-B*15, HLA-DRB1*15. The frequency of HLA-DRB1*15 reported here is the highest recorded among the North Indian population to date, which is a noteworthy finding of the study. The hierarchical cluster analysis and principal component analysis showed that the Kami population lies within the cluster of the Indian subcontinental population.

CONCLUSION

The study refutes the earlier proposition of exclusive belongingness of all the Gorkhas to Mongoloids.

HLA class I alleles frequencies in the Syrian population

Objective

The HLA system is known to be the most polymorphic genetic loci in humans. Distribution and frequencies of HLA alleles are highly variable among different human ethnic groups. The HLA system has an important role in disease susceptibility and resistance, especially in autoimmune diseases and cancer. This study is the first report about HLA genetic variability and haplotypes among Syrians. Frequency of the HLA class I (A, B and C) alleles was determined in 105 healthy unrelated Syrian individuals from different regions in Syria. We also studied the associated haplotypes frequencies. Alleles frequencies were compared with those reported for other populations.

Results

Fifty-eight HLA class I alleles were observed in Syrians including 15 for HLA-A, 28 for HLA-B and 15 for HLA-C. We observed 37 HLA-A/C haplotypes, 32 B/C, and 31 A/B haplotypes. The most frequent haplotypes were A*01/C*04, A*02/C*07, A*02/B*35, and B*35/C*04. In conclusions, our preliminary study suggests a high variability in HLA class I alleles in the Syrian population. This study also gives a general reference database about the genetic pool distribution of HLA class I alleles among Syrians and can be consulted for HLA related diseases.

HLA class II diversity in HIV-1 uninfected individuals from the placebo arm of the RV144 Thai vaccine efficacy trial

The RV144 HIV vaccine trial in Thailand elicited antibody responses to the envelope of HIV-1, which correlated significantly with the risk of HIV-1 acquisition. Human leukocyte antigen (HLA) class II molecules are essential in antigen presentation to CD4 T cells for activation of B cells to produce antibodies. We genotyped the classical HLA-DRB1, DQB1, and DPB1 genes in 450 individuals from the placebo arm of the RV144 study to determine the background allele and haplotype frequencies of these genes in this cohort. High-resolution 4 and 6-digit class II HLA typing data was generated using sequencing-based methods. The observed diversity for the HLA loci was 33 HLA-DRB1, 15 HLA-DQB1, and 26 HLA-DPB1 alleles. Common alleles with frequencies greater than 10% were DRB1*07:01, DRB1*09:01, DRB1*12:02, DRB1*15:02, DQB1*02:01/02, DQB1*03:01, DQB1*03:03, DQB1*05:01, DQB1*05:02, DPB1*04:01:01, DPB1*05:01:01, and DPB1*13:01:01. We identified 28 rare alleles with frequencies of less than 1% in the Thai individuals. Ambiguity for HLA-DPB1*28:01 in exon 2 was resolved to DPB1*296:01 by next-generation sequencing of all exons. Multi-locus haplotypes including HLA class I and II loci were reported in this study. This is the first comprehensive report of allele and haplotype frequencies of all three HLA class II genes from a Thai population. A high-resolution genotyping method such as next-generation sequencing avoids missing rare alleles and resolves ambiguous calls. The HLA class II genotyping data generated in this study will be beneficial not only for future disease association/vaccine efficacy studies related to the RV144 study, but also for similar studies in other diseases in the Thai population, as well as population genetics and transplantation studies.

HLA class II alleles in the Otomi population of the Mezquital Valley: a genetic approach to the history of interethnic migrations in the Mexican Central Plateau

From a historical and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the population dynamics of the Mexican Central Plateau. Due to the antiquity of their presence in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua. In this study we analyzed the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intraregional-level historical perspective of the genetic relationships between the Otomi of the Mezquital Valley and indigenous populations from other regions of Mexico. We examined genetic variation in HLA-DRB1 and -DQB1 loci in 66 nonrelated individuals belonging to seven indigenous communities from the Ixmiquilpan municipality in the Mezquital Valley, in the State of Hidalgo, Mexico. The variability of the HLA-DRB1 gene among the Otomi of the Mezquital Valley was mainly concentrated in five alleles: -DRB1*08:02 (31.06%), -DRB1*04:07 (25.77%), -DRB1*14:06 (7.55%), -DRB1*14:02 (6.06%), and -DRB1*16:02 (4.55%); these alleles have been previously described in other indigenous populations. The most frequent alleles at the HLA-DQB1 locus were -DQB1*03:02 (34.09%), -DQB1*04:02 (31.03%), and -DQB1*03:01 (19.7%). Furthermore, the HLA-DQB1*02:02 allele was found in the Otomi group with a frequency of 2.27%; this allele has not been reported in Mexican indigenous populations. In conclusion, the genetic constitution of the Otomi population is intermediate to the northern groups and the genetic variability shared by the peoples of the central regions of Mexico. Furthermore, HLA-DRB1 and -DQB1 allelic variability among the Otomi provides insight into the historical processes implied in the biological admixture with European, Asian, and African populations as well as in the admixture with the population of Mexico City associated with long-standing migratory processes.

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.

HLA gene and haplotype frequencies in Russians, Bashkirs and Tatars, living in the Chelyabinsk Region (Russian South Urals)

We have characterized the HLA-A, -B, -DRB1, -DQA1 and -DQB1 profiles of three major ethnic groups living in Chelyabinsk Region of Russian South Urals, viz., Russians (n = 207), Bashkirs (n = 146) and Tatars (n = 135). First field level typing was performed by PCR using sequence-specific primers. Estimates included carriage and gene frequencies, linkage disequilibrium and its significance and related values. Population comparisons were made between the allele family frequencies of the three populations and between these populations and 20 others using a dendrogram. Chelyabinsk Region Russians demonstrate all the features typical of a Caucasoid population, but also have some peculiarities. Together with Tatars, Russians have high frequencies of allele families and haplotypes characteristic of Finno-Ugric populations. This presupposes a Finno-Ugric impact on Russian and Tatar ethnogenesis. However, this was not apparent in Bashkirs, the first of the three populations to live in this territory, and implies admixture with populations of a Finno-Ugric origin with precursors of Russians and Tatars before they came to the South Urals. The Bashkirs appear close to Mongoloids in allele and haplotype distribution. However, Bashkirs cannot be labelled either as typical Mongoloids or as Caucasoids. Thus, Bashkirs possess some alleles and haplotypes frequent in Mongoloids, which supports the Turkic impact on Bashkir ethnogenesis, but also possess the AH 8.1 haplotype, which could evidence an ancient Caucasoid population that took part in their ethnic formation or of recent admixture with adjacent populations (Russians and Tatars). Bashkirs showed no features of populations with a substantial Finno-Ugric component, for example Chuvashes or Russian Saami. This disputes the commonly held belief of a Finno-Ugric origin for Bashkirs. Tatars appeared close to many European populations. However, they possessed some characteristics of Asiatic populations possibly reflecting a Mongoloid influence on Tatar ethnogenesis. Some aspects of HLA in Tatars appeared close to Chuvashes and Bulgarians, thus supporting the view that Tatars may be descendents of ancient Bulgars.

Distribution of human leukocyte antigen alleles and haplotypes in Oroqen and Ewenki nationality minority in Inner Mongolia Autonomous Region of China

The frequencies of the human leukocyte antigen alleles HLA-A,-B, DRB1 and the A-B, A-DRB1, B-DRB1, A-B-DRB1 haplotypes were investigated through means of PCR-based reverse line-strip sequence specific oligonucleotide hybridization on 108 Oroqen and 104 Ewenki nationality unrelated healthy individuals from the Inner Mongolia Autonomous Region of China. A total of thirteen different HLA-A alleles, 21 different HLA-B alleles and 13 different HLA-DRB1 alleles were detected in the Oroqen ethnic group and the most frequent HLA alleles found were A*24(35.65%), B*15(17.92%), and DRB1*09(17.59%), respectively. The common HLA-A-B-DRB1 haplotypes were A*24-B*40-DRB1*09(5.09%), A*24-B*48-DRB1*12(2.78%) and A*24-B*51-DRB1*04(2.78%); and the HLA-A*33-B*58, A*30-B*13, A*01-B*37, A*33-DRB1*03, A*01-DRB1*10, A*30-DRB1*07, B*37-DRB1*10, B*58-DRB1*03, B*38-DRB1*08, B*13-DRB1*07 were significant positive linkage disequilibrium in the Oroqen nationality group. In total, 14 different HLA-A alleles, 27 B alleles and 12 DRB1 alleles were found in Ewenki nationality group, and the most frequent HLA alleles found were A*24(24.49%), B*40(17.35%), and DRB1*04(14.80%), respectively. The common HLA-A-B-DRB1 haplotypes were A*33-B*58-DRB1*03(6.25%), A*01-B*51-DRB1*11(2.88%) and A*24-B*40-DRB1*09(2.88%); the HLA-A*33-B*58, A*29-B*44, A*03-B*52, A*33-DRB1*03, A*29-DRB1*07, A*24-DRB1*09, B*58-DRB1*03, B*08-DRB1*03, B*46-DRB1*09 were significant positive linkage disequilibrium in Ewenki nationality group. The distribution of HLA A,-B, DRB1, alleles haplotypes frequencies and phylogenetic tree indicated that the Oroqen and Ewenki population groups belongs to northern group of China, together as a group cluster.

Genetic affinities of north and northeastern populations of India: inference from HLA-based study

India is like a microcosm of the world in terms of its diversity; religion, climate and ethnicity which leads to genetic variations in the populations. As a highly polymorphic marker, the human leukocyte antigen (HLA) system plays an important role in the genetic differentiation studies. To assess the genetic diversity of HLA class II loci, we studied a total of 1336 individuals from north India using DNA-based techniques. The study included four endogamous castes (Kayastha, Mathurs, Rastogies and Vaishyas), two inbreeding Muslim populations (Shias and Sunnis) from north India and three northeast Indian populations (Lachung, Mech and Rajbanshi). A total of 36 alleles were observed at DRB1 locus in both Hindu castes and Muslims from north, while 21 alleles were seen in northeast Indians. At the DQA1 locus, the number of alleles ranged from 11 to 17 in the studied populations. The total number of alleles at DQB1 was 19, 12 and 20 in the studied castes, Muslims and northeastern populations, respectively. The most frequent haplotypes observed in all the studied populations were DRB1*0701-DQA1*0201-DQB1*0201 and DRB1*1501-DQA1*0103-DQB1*0601. Upon comparing our results with other world populations, we observed the presence of Caucasoid element in north Indian population. However, differential admixturing among Sunnis and Shias with the other north Indians was evident. Northeastern populations showed genetic affinity with Mongoloids from southeast Asia. When genetic distances were calculated, we found the north Indians and northeastern populations to be markedly unrelated.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

CYP1A2 polymorphism (C > A at position −163) in Ovambos, Koreans and Mongolians

Cytochrome P450 1A2 (CYP1A2) plays an important role in metabolizing drugs and xenobiotics, and is a possible participant in the development of several human diseases. Recent studies have shown that genetic polymorphism of -163 C > A single nucleotide mutation of CYP1A2 increases the risk of myocardial infarction and modulates CYP1A2 activity. In this study, we investigated the frequency of the -163 C > A mutation in Ovambos (n = 177), Koreans (n = 250) and Mongolians (n = 153) and compared our results with other studies. Detection of this single nucleotide polymorphism was by polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP). The frequencies of mutation (CYP1A2*-163A) in the Ovambos, Koreans and Mongolians were 0.46, 0.32 and 0.21, respectively. Ovambos showed a relatively higher frequency of mutation, similar to that of Tanzanians, while the Mongolians showed the lowest frequency of all study groups, including those from previous studies. This study is the first to investigate the distribution of the CYP1A2 (-163 C > A single nucleotide polymorphism) mutant allele in Ovambo, Korean and Mongolian populations.

A crypto-Dravidian origin for the nontribal communities of South India based on human leukocyte antigen class I diversity

The Dravidian communities are considered to be the original inhabitants of India, now restricted to South India. The southern most state, Kerala, is socio-culturally stratified into Hindus, Muslims and Christians on the basis of religion. The origin of these religious communities in Kerala is considered to be unique in comparison with that in other parts of the country. These communities were later influenced by the hierarchical caste structure established by the Hindu Brahmins. In the present study, we compared six nontribal (Namboothiri, Nair, Ezhava, Pulaya, Malabar Muslim and Syrian Christian) communities belonging to the major religious groups in Kerala (Hindu, Muslim and Christian) based on the human leukocyte antigen (HLA)-A, -B and -C diversity. Our aim was to understand the genomic substructuring associated with the changing social scenario in various caste and religious groups and compare it with the Dravidian tribal and other world populations. The present study reveals that the HLA diversity of the Dravidian communities is very distinct from that in the other world populations. It is obvious that the nontribal communities of Kerala display a greater Dravidian influence, but traces of genetic admixture with the Mediterranean, western European, central Asian and East Asian populations can be observed. This characterizes the crypto-Dravidian features of the nontribal communities of Kerala. Demic diffusion of the local progressive communities with the migrant communities may have given rise to crypto-Dravidian features among the nontribal communities of Kerala.

HLA class II gene polymorphism in Parsees and Zoroastrians of Iran

Extensive polymorphism of the HLA genes in different ethnic groups has been used as an invaluable tool for anthropological studies. In this study, HLA-DRB1, DQA1 and DQB1 allele frequencies and haplotypes were determined in 72 Parsees and 65 Zoroastrians living in Iran. The predominant DRB1 allele was *1103 = 4 in Parsees and *0701 in Zoroastrians. DQA1*0501 was the most common alleles in both spopulations. The most frequent DQB1 allele was *0301 in Parsees and *0201 in Zoroastrians. DRB1*1103 = 4-DQA1*0501-DQB1*0301 and DRB1*0701-DQA1*0201-DQB1*0201 were the most prevalent haplotypes in Parsees and Zoroastrians, respectively. Significant deviation from Hardy-Weinberg equilibrium was observed in DQA1 and DQB1 loci of Zoroastrians. The former locus also departed from neutrality due to balancing selection. All pairs of the studied loci in this study showed significant linkage disequilibrium. Analysis of molecular variance indicated that the main variation was confined to individuals within the studied populations. Neighbour-joining tree based on Nei's genetic distances according to DRB1 and DQB1 allele frequencies showed that Parsees and Zoroastrians of Iran were located in the same cluster of the phylogenetic tree. Furthermore, Zoroastrians of Iran and Pakistan are very close to each other. This study will serve as a reference for further anthropological studies when the HLA profile of all ethnic groups of Iran is investigated.

Conserved extended haplotypes of the major histocompatibility complex: further characterization

Since the complete sequencing of a human major histocompatibility complex (MHC) haplotype, interest in non-human leucocyte antigen (HLA) genes encoded in the MHC has been growing. Non-HLA genes, which outnumber the HLA genes, may contribute to or account for HLA and disease associations. Most information on non-HLA genes has been obtained in separate studies of individual loci. To comprehensively address polymorphisms of relevant non-HLA genes in 'conserved extended haplotypes' (CEH), we investigated 101 International Histocompatibility Workshop reference cell lines and nine additional anonymous samples representing all 37 unambiguously characterized CEHs at MICA, NFKBIL1, LTA, NCR3, AIF1, HSPA1A, HSPA1B, BF, NOTCH4 and a single nucleotide polymorphism (SNP) at HLA-DQA1 as well as MICA, NOTCH4, HSPA1B and all five tumour necrosis factor short tandem repeat (STR) polymorphisms. This work (1) provides an extensive catalogue of MHC polymorphisms in all CEHs, (2) unravels interrelationships between HLA and non-HLA haplotypical lineages, (3) resolves reported typing ambiguities and (4) describes haplospecific markers for a number of CEHs. Analysis also identified a DQA1 SNP and segments containing MHC class III polymorphisms that corresponded with class II (DRB3 and DRB4) lineages. These results portray the MHC where lineages containing non-HLA and HLA variants in linkage disequilibrium may operate in concert and can guide more thorough design and interpretation of HLA-disease relationships.

HLA-A, -B, and -DRB1 polymorphism defined by sequence-based typing of the Han population in Northern China

DNA typing for human leukocyte antigen (HLA)-A, -B and -DRB1 was performed using polymerase chain reaction-sequence-based typing method on 618 randomly selected healthy individuals of the Han population in Northern China. Allele frequencies and haplotypes were statistically analyzed. A total of 84 HLA-A alleles, 143 B alleles, and 122 DRB1 alleles were detected, and 853 A-B-DRB1 haplotypes, 473 A-B haplotypes, and 551 B-DRB1 haplotypes were statistically inferred. Statistical analysis of three-locus haplotypes showed that A*0207-B*4601-DRB1*0901 (3.06%) was the most predominant. Gene frequencies and haplotypic associations within HLA-A, -B, and -DRB1 loci were determined at a high-resolution (four digit) allelic level and should provide useful information in anthropology, bone marrow donor registry, legal medicine, and disease association studies.

HLA-B27 polymorphism in Turkish patients with ankylosing spondylitis

The aim of this study was to determine the distribution of human leukocyte antigen (HLA)-B27 subtypes in serologically HLA-B27-positive ankylosing spondylitis (AS) patients and healthy controls from the Turkish population and to compare this with other reports from other populations. We subtyped HLA-B27 in 38 HLA-B27-positive Turkish patients with AS and 47 HLA-B27-positive healthy controls without AS by polymerase chain reaction with specific sequence primers (PCR-SSP). The results demonstrated that: B*2705 was the predominant subtype among both of the patients (71.1%) and controls (68.0%). B*2702 was observed in 26.3% and 32.0% of the patients and controls, respectively. B*2708 subtype was found in 2.6% of the patients but not among the control group. When the distribution of B27 subtypes in Turkish populations was compared with that in other populations, similar frequencies with the Caucasian-Europe groups were noted. However, this should be interpreted carefully because of the small number of individuals in our study.

Human leukocyte antigen-A, -B and -C alleles and human leukocyte antigen haplotypes in Turkey: relationship to other populations

In this study, we present, for the first time, human leukocyte antigen (HLA) class I allele and haplotype frequencies at the DNA level in a sample of 142 donors from Turkey. HLA typing was performed by medium-to-high resolution polymerase chain reaction sequence-specific oligonucleotide probes method. The most frequent HLA alleles at class I locus were A*0201(0.257), -B*35(0.204) and -Cw*04(0.173). A*0201-B*35-Cw*04(0.056) was the most common three-locus haplotype. Allele and haplotype frequency comparisons and neighbour-joining dendrograms, constructed using DA genetic distances and correspondence analysis using HLA-A, -B and -C, and -DRB1 allele frequencies, revealed similarities with other Mediterranean and European populations, but not with Mongol populations. These results agree with previous studies and confirm that the present day Turkish population is genetically more similar to its geographic neighbours than its historical neighbours in central Asia. The comprehensive HLA data on the Turkish population at the DNA level including up to six-locus putative haplotypes generated in this study will be useful for further studies.