Genetic HLA Study of Kurds in Iraq, Iran and Tbilisi (Caucasus, Georgia): Relatedness and Medical Implications

HLA allele and haplotype frequencies in Kazakhstani Russians and their relationship with other populations

HLA class I and class II genotypes from 947 Kazakhstani individuals of Russian origin were analyzed for investigating their most likely origin. The results were compared with similar data from other Russians (East and West), and also Worldwide populations, using standard genetic distances, neighbor-joining dendrograms, correspondence and haplotype analysis. Of the five HLA loci analyzed (HLA-A, HLA-C, HLA-B, HLA-DRB1, and HLA-DQB1) genotyped, 216 HLA alleles were identified. The most frequent alleles were A*02:01 (26.5%), B*07:02 (11.1%), C*04:01 (13.5%) and C*06:02 (12.1%), DRB1*07:01 (13.8%) and DRB1*15:01 (12.2%), and DQB1*03:01 (19.7%). Significant linkage disequilibrium was noted between all HLA pairs. DRB1*15:01 ~ DQB1*06:02 (10.5%), B*07:02 ~ C*07:02 (10.0%), B*07:02 ~ DRB1*15:01 (6.3%), and A*01:01 ~ B*08:01 (4.5%) were the most frequent two-locus haplotypes identified. Subsequent analyses showed that Kazakhstani Russians were closely related to West Russia-residing populations (Northwest Slavic, Vologda, Chelyabinsk, Moscow), East Europeans (Belarus Brest, Ukraine, Poland) and Scandinavians (Swedish, Finns), but distinct from East Russia-residing populations (Tuvians, Siberians from Chukotka, Kamchatka, and Ulchi) and East Mediterraneans (Levantines, Turks, North Macedonians, Albanians), and East Asians (Koreans, Japanese, Taiwanese, Mongolians). These results are in accordance with historical data indicating that the Russians of central Asia originate mainly from European Russia during the migratory flow of 18th and 19th centuries.

HLA genetic study in Iran Saqqez-Baneh Kurds: no genetic trace of Aryan invasions in Anatolian Turks and Kurds is found

Kurds are living at Middle East region comprising several countries (38 million people) and also have emigrated to Asia, Europe and America. Kurds from Iran have been HLA typed in the present work from Saqqez and Baneh towns, Kordestan province, Iran. Origin of Kurds is considered autochthonous from Anatolia and surrounding mountains :they have been referred as "the mountain people" by classic Persian, Greek and Roman authors. Present day Turks are also autochthonous from Anatolia, but they were not recognized by classical authors as living in the mountains and they speak a language of Asian origin that was imposed to Anatolia by a "elite" invasion without a noticeable high Asian gene input. Most frequent class I and class II HLA alleles found in Iranian Kurds population are: HLA-A*24:02, A*02:01 and HLA-B*35:01, and HLA-DRB1*11:01, DRB1*03:02 and HLA-DQB1*03:01; also, most frequent HLA extended haplotypes from this Iran Kurdish sample are not shared with Iranians but with Mediterranean, Turkish and Caucasus people. This is confirmed by Neighbour-Joining and correspondence analysis studied together with the corresponding populations. Finally, our studies show that both Kurds and Turks are genetically original from Anatolian Peninsula and surrounding countries and that an apparent Asian genetic or Aryan invasion does not exist in the area.

Distribution of HLA-A, -C, -B, -DRB1, and -DQB1 polymorphisms in the Korean minority in Kazakhstan, and relatedness to neighboring and distant populations

BACKGROUND

Among the 125 ethnicities and linguistic groups in Kazakhstan, Koreans represent the eighth minority numerically. HLA class I and class II allele frequencies and extended haplotypes were studied for the first time and were compared to related and distant populations worldwide.

METHODS

HLA class I (A, B, C) and class II (DRB1, DQB1) profile was investigated in Kazakhstani Koreans, and were compared to other populations using standard genetic distances (SGD), neighbor-joining dendrograms, correspondence, and haplotype analysis.

RESULTS

One hundred and thirty-one HLA alleles were identified in Koreans living in Kazakhstan, with A*02:01 (23.08%), B*35:01 (8.24%), C*01:02 (15.38%), DRB1*08:03 (9.89%), and DQB1*03:01 (21.98%) being the most frequent alleles. A*03:01 ∼ B*07:02 (3.85%), B*08:01 ∼ DRB1*03:01 (3.85%), B*07:02 ∼ C*07:02 (7.14%), and DRB1*08:03 ∼ DQB1*06:01 (9.34%) were the most frequent two-locus haplotypes, while A*02:01 ∼ B*18:01 ∼ C*07:01 ∼ DRB1*11:04 ∼ DQB1*03:01 and A*33:03 ∼ B*44:03 ∼ C*14:03 ∼ DRB1*13:02 ∼ DQB1*06:04 (2.2% each) were the most frequent five-locus haplotypes.

CONCLUSION

Korean minority in Kazakhstan was closely related to East Asians, including Mongolians (SGD, 0.044), Tuvans (East Siberia; SGD, 0.081), Burayts (Siberia; SGD, 0.094), but distant from East Mediterranean such as Lebanese (SGD, 0.367), Greek (SGD, 0.377), and Saudi (SGD, 0.414), and most Siberians (SGD, 0.473-0.699). This relatedness could be mainly attributed to massive migration of Koryo Saram to Kazakhstan in the 20th century.

HLA alleles and haplotypes in Iran Tabriz Azeris population: genes and languages do not correlate

Azeri people are at present day mainly living in an area which comprises North (Azerbaijan) and South (Azeri Iran provinces) parts, living the biggest population in Azeri Iran provinces with about 17-20 million people. They were studied HLA-A, -B, -DRB1 and -DQB1 allele and extended haplotype frequencies in unrelated Iranian Tabriz Azeris from a rural area close to Tabriz City. The HLA extended haplotypes with highest frequencies are: 1) HLA- A*24:02-B*35:01-DRB1*11:01-DQB1*03:01, shared with Mediterraneans and southern Russians (Chuvash, which also show Mediterranean characters); and 2) HLA-A*01:02-B*08:01-DRB1*03:01-DQB1*02:01, found also in Chuvash and other Azeri samples from Tabriz. Neí's DA HLA-DRB1 genetic distances, HLA-DRB1 Neighbour-Joining dendrogram and Vista analyses show that population with closest distance is Kurdish, followed by Iranian Gorgan and Southern Russia/ North Caucasus Chuvash; probably these latter groups and Azeris were populating North Mesopotamia/ Caucasus Mts. since prehistoric times. Kurds (in Iraq and Iran) do not speak Turk while Azeris do: they are both genetically close, but they are not genetically close to present day Anatolia (Turkey) Turks who also speak Turk language and show a typical Mediterranean HLA profile. In summary, Azeri population studies show examples that genes and languages do not correlate, contradicting the postulate asserted by others.

Origin of the Ukrainian minority of Kazakhstan as inferred from HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes distribution

The present-day population of Kazakhstan comprises more than a hundred ethnic and linguistic groups, of which Ukrainians rates numerically as the fourth, following native Kazakhs, Russians, and Uzbeks. We investigated the HLA profile of Kazakhstani Ukrainians and compared them with those of other populations by applying genetic distances, correspondence analysis, admixture, and haplotype examination. Of the 128 HLA alleles identified, A*02:01 (28.64%), B*07:02 (9.71%), B*13:02 (9.71%), C*06:02 (15.05%), DRB1*07:01 (15.20%), and DQB1*03:01 (24.76%) were the utmost common alleles. The most common 2-locus haplotypes identified were A*02:01 ~ B*13:02 (6.66%), B*13:02 ~ DRB1*07:01 (6.57%), B*13:02 ~ C*06:02 (10.10%), and DRB1*01:01 ~ DQB1*05:01 (12.12%), while A*02:01 ~ B*13:02 ~ C*06:02 ~ DRB1*07:01 ~ DQB1*02:01 were the most frequent five-locus haplotype (4.04%) in Kazakhstani Ukrainians. Comparative analysis revealed that Ukrainians of Kazakhstan are closely related to Eastern Europeans (included Ukrainians), and European Russians, but distant from Asian populations. This supports the historical notion that Kazakhstani Ukrainians originated from Ukraine, following their massive migrations to central Asia in the 18th-20th centuries. This article is protected by copyright. All rights reserved.

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-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies and phylogenetic analysis of Bahraini population

The origin of Arab-speaking population is classified according to their geographical location, ethnic background, and historical influx of nearby and distant populations. Data on HLA class I and class II loci in (Arabian Peninsula) Bahraini population are lacking. We analyzed HLA genetic profile of Bahrainis with neighboring communities, and with Levantines, North Africans, Sub-Saharans, Europeans, and Asians, using genetic distances, neighbor-joining dendrograms, correspondence and haplotype analysis. HLA class I and class II genotyping were done by high resolution PCR-SSP in 175 Bahraini subjects. In total, 19 HLA-A, 33 HLA-B, 15 HLA-C, 14 DRB1 and 7 DQB1 alleles were identified. The most common class I alleles were A*02:01:01 (18.3%), A*01:01:01(15.4%), B*35:01:02 (12.9%), C*12:01:01 (15.1%), and C*04:01:01 (14.9%), while DRB1*03:01:01 (18.0%), DQB1*02:01:01 (29.1%), and DQB1*05:01:01 (24.9%) were the most frequent class II alleles. Significant linkage disequilibrium was seen between all HLA loci pairs. DRB1*03:01:01-DQB1*02:01:01 (15.18%) was the most frequent two-locus haplotype. Significant negative Fnd values were observed, indicating balancing selection at studied loci. Bahrainis appear to be related to Western Mediterranean (North Africans, Iberians and French), but relatively distinct from Levantines (Palestinians, Lebanese, and Jordanians) and Sub-Saharans. This indicates limited genetic contribution of Levantine Arabs and Sub-Saharans to the Bahraini gene pool.

HLA Class II Allele and Haplotype Diversity in Libyans and Their Genetic Relationships with Other Populations

Background: Libya witnessed the succession of many civilizations and ethnic groups throughout history, thereby questioning the origin of present-day Libyans. Indeed, they were considered Africans given the geographical position of the country, Arabs at the cultural level, and Berbers because of the notable presence of Berber tribes. Genetic anthropology studies investigating the origin of Libyans were rarely reported, and thus little was known about the population structure of current Libyans, particularly at autosomic markers level. Methods: We examined HLA class II (DRB1, DQB1) gene profiles of 101 unrelated Libyans, and compared them with Arab-speaking communities and with Sub-Saharan and Mediterranean populations using Neighbour-Joining dendrograms, genetic distances, correspondence, and haplotype analysis. Results: Of the 42 DRB1 alleles identified, DRB1*07:01 (14.36%), DRB1*03:01 (12.38%) were the most frequent, while DQB1*02:01 (24.17%), DQB1*02:02 (13.86%), and DQB1*03:01 (12.38%) were the most frequent of the 17 DQB1 alleles detected. DRB1*03:01-DQB1*02:01 (6.93%), DRB1*07:01-DQB1*02:02 (4.45%), and DRB1*04:03-DQB1*03:02 (3.46%) were the most frequent DRB1-DQB1 haplotypes. Conclusion: Libyans appear to be closely related to North Africans, Saudis, and Iberians, but distinct from Levantine Arabs, East Mediterraneans, and Sub-Saharan Africans. This indicates limited genetic contribution of Levantine Arabs and Sub-Saharans on the makeup of Libyan gene pool. Our study confirmed genetic heterogeneity among Arab populations, with three identified groups. The first comprises North Africans, Saudis, and Kuwaitis who were related to Iberians and West Mediterraneans, while the second consists of Levantine Arabs who were close to East Mediterraneans, and the third contained Sudanese and Comorians, with a close relatedness to Sub-Saharans.

Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry

Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.

The genetic heterogeneity of Arab populations as inferred from HLA genes

This is the first genetic anthropology study on Arabs in MENA (Middle East and North Africa) region. The present meta-analysis included 100 populations from 36 Arab and non-Arab communities, comprising 16,006 individuals, and evaluates the genetic profile of Arabs using HLA class I (A, B) and class II (DRB1, DQB1) genes. A total of 56 Arab populations comprising 10,283 individuals were selected from several databases, and were compared with 44 Mediterranean, Asian, and sub-Saharan populations. The most frequent alleles in Arabs are A*01, A*02, B*35, B*51, DRB1*03:01, DRB1*07:01, DQB1*02:01, and DQB1*03:01, while DRB1*03:01-DQB1*02:01 and DRB1*07:01-DQB1*02:02 are the most frequent class II haplotypes. Dendrograms, correspondence analyses, genetic distances, and haplotype analysis indicate that Arabs could be stratified into four groups. The first consists of North Africans (Algerians, Tunisians, Moroccans, and Libyans), and the first Arabian Peninsula cluster (Saudis, Kuwaitis, and Yemenis), who appear to be related to Western Mediterraneans, including Iberians; this might be explained for a massive migration into these areas when Sahara underwent a relatively rapid desiccation, starting about 10,000 years BC. The second includes Levantine Arabs (Palestinians, Jordanians, Lebanese, and Syrians), along with Iraqi and Egyptians, who are related to Eastern Mediterraneans. The third comprises Sudanese and Comorians, who tend to cluster with Sub-Saharans. The fourth comprises the second Arabian Peninsula cluster, made up of Omanis, Emiratis, and Bahrainis. It is noteworthy that the two large minorities (Berbers and Kurds) are indigenous (autochthonous), and are not genetically different from "host" and neighboring populations. In conclusion, this study confirmed high genetic heterogeneity among present-day Arabs, and especially those of the Arabian Peninsula.

Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan

To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.