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Hajjej A, Abdrakhmanova S, Turganbekova A, Almawi WY. HLA allele and haplotype frequencies in Kazakhstani Russians and their relationship with other populations. HLA 2023; 101:249-261. [PMID: 36502279 DOI: 10.1111/tan.14937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/12/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan.,Faculty of Sciences, El-Manar University, Tunis, Tunisia
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2
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Almawi WY, Hajjej A, Abdrakhmanova S, Turganbekova A. Distribution of HLA-A, -C, -B, -DRB1, and -DQB1 polymorphisms in the Korean minority in Kazakhstan, and relatedness to neighboring and distant populations. Gene 2022; 823:146386. [PMID: 35248657 DOI: 10.1016/j.gene.2022.146386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan; Faculty of Sciences, El-Manar University, Tunis, Tunisia.
| | - Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
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Ghafouri-Fard S, Hussen BM, Pashmforoush S, Akbari MT, Arsang-Jang S, Nazer N, Hamidieh AA, Hajifathali A, Dinger ME, Sayad A, Dehaghi MO. HLA alleles and haplotype frequencies in Iranian population. Hum Antibodies 2022; 30:79-96. [PMID: 35342084 DOI: 10.3233/hab-220004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND HLA genotyping is a prerequisite for selection of suitable donors in the process of bone marrow transplantation. METHODS In the current study, the frequencies of HLA-A, -B, -C and -DRB1 alleles and A-B-C-DRB1 haplotypes were assessed in 855 healthy Iranian persons using a low-resolution sequence specific primer (SSP) kit. RESULTS Frequencies were compared between 11 subpopulations including Armani, Balouch, Bandari, Turk, Turkaman, Arab, Fars, Kurd, Gilaki, Lor and Mazani. In total, 17 HLA-A alleles were detected, one of which (HLA-A*74) was present only among Lors. HLA-A*23 and -A*26 were the most frequent HLA-A alleles among Armanis. HLA-A*23 was also common among Turkamans. HLA-A*11 and -A*26 were most frequent among the Balouch subpopulation. The former allele was also frequent among Bandaris. HLA-A*02 was identified as the most common HLA-A allele among Turk, Arab and Fars subpopulations. HLA-A*30 were strongly enriched among Gilakis. A total of 31 HLA-B alleles were detected across the target population. While all alleles were present among Fars subgroup, Armanis and Turkamans had the lowest degree of diversity among the alleles examined. Moreover, HLA-B*35 and B*49 alleles were strongly enriched among Armanis and Turkamans, respectively. A total of 13 HLA-C alleles were identified across the population, all of which were present in the Fars subpopulation. HLA-C*03 and C*04 were the only HLA-C alleles identified among the Bandari subpopulation. HLA-DRB1*08 was not detected in any subpopulation other than Fars. HLA-DRB1*16 was significantly enriched among Bandaris. CONCLUSION These data have practical significance in anthropological studies, disease association investigations and bone marrow transplantation.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq.,Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | | | - Shahram Arsang-Jang
- Department of Biostatistics and Epidemiology, Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Naghme Nazer
- Department of Electrical Engineering, Sharif University of Technology, Tehran, Iran
| | - Amir Ali Hamidieh
- Department of Clinical Nutrition, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Hajifathali
- Pediatric Cell Therapy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Marcel E Dinger
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arezou Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mohammadreza Ostadali Dehaghi
- Dental Research Center, Research Institute for Dental Sciences, Dental School, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Abedini F, Rahmanian N, Heidari Z, Feizi A, Sherkat R, Rezaei M. Diversity of HLA class I and class II alleles in Iran populations: Systematic review and Meta-Analaysis. Transpl Immunol 2021; 69:101472. [PMID: 34555503 DOI: 10.1016/j.trim.2021.101472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
The human leukocyte antigen (HLA) system plays an essential role in the peptides antigen presentation and more regulation of immune responses. Regarding all HLA molecules' associations with various diseases and their clinical utilities in understanding drug reactions or prediction of transplantation outcome, there is a need for much more extensive HLA data generated from Asian countries. METHOD A comprehensive search was conducted in electronic databases between 1990 and 2021 to identify relevant articles to HLA frequency in the normal Iranian population. Two independent reviewers screened and selected the eligible studies. After data extraction, the meta-analysis was performed using STATA version 14. The overall frequencies and their 95% confidence intervals (CIs) were obtained using the random-effects model. RESULTS Among 1141 studies 78 were eligible for this study and the sample sizes varied from 14 to 15,600. The most frequent alleles of HLA class I were HLA-A*02 (22%; 95%CI: 20-24%; I2 = 88.63%), -B*35 (18%; 95%CI: 16-21%; I2 = 90.95%), -C*12 (18%; 95%CI: 13-22%; I2 = 89.51%). HLA-DQA1*01 (42%; 95%CI: 40-44%; I2 = 56.80%), -DQB1*03 (38%; 95%CI: 35-42%; I2 = 92.38%), and -DRB1*11 (24%; 95%CI: 22-26%; I2 = 90.72%) were the most frequent alleles of HLA class II in Iran. DISCUSSION Our meta-analysis results point out that the comprehensive report of HLA allele frequency in the Iranian population could be helpful as reference data for planning and managing transplantation and immune disease treatment in Iran.
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Affiliation(s)
- Fateme Abedini
- Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Narges Rahmanian
- Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Heidari
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical sciences, Isfahan, Iran
| | - Roya Sherkat
- Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marzieh Rezaei
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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Hajjej A, Abdrakhmanova S, Turganbekova A, Almawi WY. Origin of the Ukrainian minority of Kazakhstan as inferred from HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes distribution. HLA 2021; 98:525-535. [PMID: 34293241 DOI: 10.1111/tan.14377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 06/05/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, NazarbayevUniversity, Astana, Kazakhstan.,College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
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6
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Messoussi M, Hajjej A, Ammar Elgaaied AB, Almawi WY, Arnaiz-Villena A, Hmida S, Fadhlaoui-Zid K. HLA Class II Allele and Haplotype Diversity in Libyans and Their Genetic Relationships with Other Populations. Immunol Invest 2019; 48:875-892. [PMID: 31161824 DOI: 10.1080/08820139.2019.1614950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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.
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Affiliation(s)
- Monia Messoussi
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia
| | - Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center , Tunis , Tunisia
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia
| | - Wassim Y Almawi
- School of Medicine, Nazarbayev University , Astana , Kazakhstan.,Department of Biological Sciences, Faculty of Sciences, El-Manar University , Tunis , Tunisia
| | - Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center , Madrid , Spain
| | - Slama Hmida
- Department of Immunogenetics, National Blood Transfusion Center , Tunis , Tunisia
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar , Tunis , Tunisia.,Department of Biology, College of Science, Taibah University , Al Madinah Al Monawarah , Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba , Beja , Tunisia
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Burton EK. Narrating ethnicity and diversity in Middle Eastern national genome projects. SOCIAL STUDIES OF SCIENCE 2018; 48:762-786. [PMID: 30289023 DOI: 10.1177/0306312718804888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Most Middle Eastern populations outside Israel have not been represented in Western-based international human genome sequencing efforts. In response, national-level projects have emerged throughout the Middle East to decode the Arab, Turkish and Iranian genomes. The discourses surrounding the 'national genome' that shape scientists' representation of their work to local and international audiences evoke three intersecting analytics of nationalism: methodological, postcolonial and diasporic. Methodologically, ongoing human genome projects in Turkey and Iran follow the population logics of other national and international genome projects, for example justifying research with reference to projected health benefits to their fellow citizens. Meanwhile, assumptions about and representations of ethnicity and diversity are deeply inflected by local histories of scientific development and nationalist politics. While Iranian geneticists have transformed this paradigm to catalog national genetic diversity through a discourse of 'Iranian ethnicities', Turkish geneticists remain politically constrained from acknowledging ethnic diversity and struggle to distance their work from racialized narratives of Turkish national identity. Such nationally-framed narratives of genomic diversity are not confined to their original contexts, but travel abroad, as demonstrated by a US-based genome project that articulates a form of Iranian-American diasporic nationalism.
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Hajjej A, Almawi WY, Arnaiz-Villena A, Hattab L, Hmida S. The genetic heterogeneity of Arab populations as inferred from HLA genes. PLoS One 2018. [PMID: 29522542 PMCID: PMC5844529 DOI: 10.1371/journal.pone.0192269] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
- * E-mail:
| | - Wassim Y. Almawi
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Lasmar Hattab
- Department of Medical Analysis, Hospital of Gabes (Ghannouch), Gabes, Tunisia
| | - Slama Hmida
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
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9
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Arnaiz-Villena A, Palacio-Grüber J, Muñiz E, Campos C, Alonso-Rubio J, Gomez-Casado E, Salih SF, Martin-Villa M, Al-Qadi R. Genetic HLA Study of Kurds in Iraq, Iran and Tbilisi (Caucasus, Georgia): Relatedness and Medical Implications. PLoS One 2017; 12:e0169929. [PMID: 28114347 PMCID: PMC5256937 DOI: 10.1371/journal.pone.0169929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/22/2016] [Indexed: 11/30/2022] Open
Abstract
Kurds from Iraq (Dohuk and Erbil Area, North Iraq) have been analyzed for HLA genes. Their HLA genetic profile has been compared with that of other Kurd groups from Iran and Tbilisi (Georgia, Caucasus) and also Worldwide populations. A total of 7,746 HLA chromosomes have been used. Genetic distances, NJ dendrograms and correspondence analyses have been carried out. Haplotype HLA-B*52—DRB1*15 is present in all three analyzed Kurd populations. HLA-A*02-B*51-DRB1*11 is present in Iraq and Georgia Kurds. Haplotypes common to Iran and Iraq Kurds are HLA DRB1*11—DQB1*03, HLA DRB1*03—DQB1*02 and others in a lower frequency. Our HLA study conclusions are that Kurds most probably belong to an ancient Mediterranean / Middle East / Caucasian genetic substratum and that present results and those previously obtained by us in Kurds may be useful for Medicine in future Kurd transplantation programs, HLA Epidemiology (HLA linked diseases) and Pharmacogenomics (HLA-associated drug side effects) and also for Anthropology. It is discussed that one of the most ancient Kurd ancestor groups is in Hurrians (2,000 years BC).
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Affiliation(s)
- Antonio Arnaiz-Villena
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
- * E-mail:
| | - Jose Palacio-Grüber
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Ester Muñiz
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Cristina Campos
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Javier Alonso-Rubio
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Eduardo Gomez-Casado
- Department of Inmunología Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Autopista A6, Hipódromo, Madrid, Spain
| | | | - Manuel Martin-Villa
- Department of Immunology, University Complutense, School of Medicine, Madrid Regional Blood Center, Madrid, Spain
| | - Rawand Al-Qadi
- HLA Typing Department, Dohuk Specialized Laboratory Center, Dohuk, Iraq
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10
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Varzi AM, Shahsavar F, Tarrahi MJ. Distribution of HLA-DRB1 and HLA-DQB1 alleles in Lak population of Iran. Hum Immunol 2016; 77:580-3. [PMID: 27189628 DOI: 10.1016/j.humimm.2016.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 04/17/2016] [Accepted: 05/13/2016] [Indexed: 11/16/2022]
Abstract
Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and encode the highly polymorphic molecules critically involved in immune responses. Anthropological studies based on highly polymorphic HLA genes provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine the HLA-DRB1 and HLA-DQB1 allele frequencies in 100 unrelated Lak individuals from Lorestan province of Iran. Finally, we compared the results with those previously described in four other Iranian populations. Commercial HLA-Type kits were used for determination of the HLA-DRB1 and HLA-DQB1 allele frequencies. Differences between populations in the distribution of HLA-DRB1 and HLA-DQB1 alleles were estimated by χ2 test with Yate's correction and Fisher's exact test. The most frequent HLA-DRB1 alleles were (*)1103=4 (23%), (*)1502 (9.5%), (*)0701 (9%), (*)0301 (8.5%), (*)1101 (7.5%) and (*)1501 (6%) while HLA-DQB1(*)0301 (40%), (*)0201 (15%), (*)0502 (10.5%), (*)0303 (10%), (*)0602=3 (9.5%), and (*)0501 (7.5%) were the most frequent alleles in Lak population. HLA-DRB1(*)0409, (*)0804, (*)1102, (*)1112, (*)1405, and HLA-DQB1(*)0503, (*)0604 were the least observed frequencies in Lak population. Our results based on HLA-DRB1 and HLA-DQB1 allele frequencies showed that the Lak population possesses the previously reported general features of the Lur and Kurd populations but still with unique, decreased or increased frequencies of several alleles. In other words, the Lak population is close to Lurs Khorramabadi and Kurd but far from Lurs Kohkiloyeh/Boyerahmad and Bakhtiari.
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Affiliation(s)
- Ali Mohammad Varzi
- Department of Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Farhad Shahsavar
- Department of Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Mohammad Javad Tarrahi
- Department of Epidemiology and Biostatistics, School of Public Health, Lorestan University of Medical Sciences, Khorramabad, Iran.
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Kuranov AB, Vavilov MN, Abildinova GZ, Akilzhanova AR, Iskakova AN, Zholdybayeva EV, Boldyreva MN, Müller CA, Momynaliev KT. Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan. PLoS One 2014; 9:e115265. [PMID: 25531278 PMCID: PMC4274022 DOI: 10.1371/journal.pone.0115265] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations. METHODOLOGY/PRINCIPAL FINDINGS A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians. CONCLUSIONS/SIGNIFICANCE The HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.
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12
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Rostami-Nejad M, Romanos J, Rostami K, Ganji A, Ehsani-Ardakani MJ, Bakhshipour AR, Zojaji H, Mohebbi SR, Zali MR, Wijmenga C. Allele and haplotype frequencies for HLA-DQ in Iranian celiac disease patients. World J Gastroenterol 2014; 20:6302-6308. [PMID: 24876751 PMCID: PMC4033468 DOI: 10.3748/wjg.v20.i20.6302] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 12/31/2013] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the distribution of human leukocyte antigen (HLA)-DQ2 and -DQ8 in Iranian celiac disease (CD) patients and compare them to healthy Iranian controls.
METHODS: To predict the HLA-DQA1 and -DQB1 genes, we used six previously reported HLA-tagging single nucleotide polymorphism to determine HLA genotypes in 59 Iranian patients with ‘biopsy-confirmed’ CD and in 151 healthy Iranian individuals. To test the transferability of the method, 50 cases and controls were also typed using a commercial kit that identifies individual carriers of DQ2, DQ7 and DQ8 alleles.
RESULTS: In this pilot study 97% of CD cases (n = 57) and 58% of controls (n = 87) were carriers of HLA-DQ2 and/or HLA-DQ8 heterodimers, either in the homozygous or heterozygous state. The HLA-DQ pattern of these 57 CD patients: heterozygous DQ2.2 (n = 14) and homozygous DQ2.2 (n = 1), heterozygous DQ2.5 (n = 33) and homozygous DQ2.5 (n = 8), heterozygous DQ8 (n = 13) and homozygous DQ8 (n = 2). Two CD patients were negative for both DQ2 and DQ8 (3%).
CONCLUSION: The prevalence of DQ8 in our CD population was higher than that reported in other populations (25.4%). As reported in other populations, our results underline the primary importance of HLA-DQ alleles in the Iranian population’s susceptibility to CD.
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13
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Farjadian S, Safi S. Genetic connections among Turkic-speaking Iranian ethnic groups based on HLA class II gene diversity. Int J Immunogenet 2013; 40:509-14. [DOI: 10.1111/iji.12066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/22/2013] [Accepted: 05/15/2013] [Indexed: 11/26/2022]
Affiliation(s)
- S. Farjadian
- Department of Immunology; Shiraz University of Medical Sciences; Shiraz Iran
| | - S. Safi
- Department of Immunology; Shiraz University of Medical Sciences; Shiraz Iran
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Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N, Achilli A, Olivieri A, Gandini F, Houshmand M, Sanati MH, Torroni A, Semino O. Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One 2012; 7:e41252. [PMID: 22815981 PMCID: PMC3399854 DOI: 10.1371/journal.pone.0041252] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Silvia Parolo
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
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15
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The investigation of allele and genotype frequencies of human C3 (rs2230199) in south Iranian population. Mol Biol Rep 2012; 39:8919-24. [DOI: 10.1007/s11033-012-1759-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
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16
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Ioana M, Ferwerda B, Farjadian S, Ioana L, Ghaderi A, Oosting M, Joosten LAB, van der Meer JWM, Romeo G, Luiselli D, Dediu D, Netea MG. High variability of TLR4 gene in different ethnic groups in Iran. Innate Immun 2011; 18:492-502. [DOI: 10.1177/1753425911423043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Infectious diseases exert a constant evolutionary pressure on the innate immunity genes. TLR4, an important member of the TLR family, specifically recognizes conserved structures of various infectious pathogens. Two functional TLR4 polymorphisms, Asp299Gly and Thr399Ile, modulate innate host defense against infections, and their prevalence between various populations has been proposed to be influenced by local infectious pressures. If this assumption is true, strong local infectious pressures would lead to a homogeneous pattern of these ancient TLR4 polymorphisms in geographically-close populations, while a weak selection or genetic drift may result in a diverse pattern. We evaluated TLR4 polymorphisms in 15 ethnic groups in Iran, to assess whether infections exerted selective pressures on different haplotypes containing these variants. The Iranian subpopulations displayed a heterogeneous pattern of TLR4 polymorphisms, comprising various percentages of Asp299Gly and Thr399Ile, alone or in combination. The Iranian sample, as a whole, showed an intermediate mixed pattern when compared with commonly-found patterns in Africa, Europe, Eastern Asia and the Americas. These findings suggest a weak, or absent, selection pressure on TLR4 polymorphisms in the Middle-East that does not support the assumption of an important role of these polymorphisms in the host defense against local pathogens.
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Affiliation(s)
- Mihai Ioana
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
- Department of Molecular and Cellular Biology, University of Medicine and Pharmacy of Craiova, Romania
- University of Medicine and Pharmacy ‘Carol Davila’ Bucharest, Romania
| | - Bart Ferwerda
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shirin Farjadian
- Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran
- Allergy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Luiza Ioana
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marije Oosting
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
| | - Leo AB Joosten
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
| | - Jos WM van der Meer
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
| | - Giovanni Romeo
- Unità di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi, Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Biologia Evoluzionistica Sperimentale, Fisiche e Naturali, Università di Bologna, Italy
| | - Dan Dediu
- Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Mihai G Netea
- Radboud University Nijmegen Medical Centre, and Nijmegen Institute for Infection, Inflammation and Immunity (N4i), Department of Medicine, Nijmegen, The Netherlands
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17
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Farjadian S, Sazzini M, Tofanelli S, Castrì L, Taglioli L, Pettener D, Ghaderi A, Romeo G, Luiselli D. Discordant patterns of mtDNA and ethno-linguistic variation in 14 Iranian Ethnic groups. Hum Hered 2011; 72:73-84. [PMID: 21912140 DOI: 10.1159/000330166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 06/09/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND/AIMS Present-day Iran has long represented a natural hub for the expansion of human genes and cultures. That being so, the overlapping of prehistoric and more recent demographic events interacting at different time scales with geographical and cultural barriers has yielded a tangled patchwork of anthropological types within this narrow area. This study aims to comprehensively evaluate this ethnic mosaic by depicting a fine-grained picture of the Iranian mitochondrial landscape. METHODS mtDNA variability at both HVS-I and coding regions was surveyed in 718 unrelated individuals belonging to 14 Iranian ethnic groups characterized by different languages, religions and patterns of subsistence. RESULTS A discordant pattern of high ethno-linguistic and low mtDNA heterogeneity was observed for the whole examined Iranian sample. Geographical factors and cultural/linguistic differences actually represented barriers to matrilineal gene flow only for the Baloch, Lur from Yasouj, Zoroastrian and Jewish groups, for which unusual reduced levels of mtDNA variability and high inter-population distances were found. CONCLUSION Deep rooting genealogies and endogamy in a few of the examined ethnic groups might have preserved ancestral lineages that can be representative of Proto-Indo-Iranian or prehistoric mitochondrial profiles which survived relatively recent external contributions to the Iranian gene pool.
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Affiliation(s)
- S Farjadian
- Department of Immunology, Shiraz University of Medical Sciences, Iran
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18
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Terreros MC, Rowold DJ, Mirabal S, Herrera RJ. Mitochondrial DNA and Y-chromosomal stratification in Iran: relationship between Iran and the Arabian Peninsula. J Hum Genet 2011; 56:235-46. [PMID: 21326310 DOI: 10.1038/jhg.2010.174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Modern day Iran is strategically located in the tri-continental corridor uniting Africa, Europe and Asia. Several ethnic groups belonging to distinct religions, speaking different languages and claiming divergent ancestries inhabit the region, generating a potentially diverse genetic reservoir. In addition, past pre-historical and historical events such as the out-of-Africa migrations, the Neolithic expansion from the Fertile Crescent, the Indo-Aryan treks from the Central Asian steppes, the westward Mongol expansions and the Muslim invasions may have chiseled their genetic fingerprints within the genealogical substrata of the Persians. On the other hand, the Iranian perimeter is bounded by the Zagros and Albrez mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts, which may have restricted gene flow from neighboring regions. By utilizing high-resolution mitochondrial DNA (mtDNA) markers and reanalyzing our previously published Y-chromosomal data, we have found a previously unexplored, genetic connection between Iranian populations and the Arabian Peninsula, likely the result of both ancient and recent gene flow. Furthermore, the regional distribution of mtDNA haplogroups J, I, U2 and U7 also provides evidence of barriers to gene flow posed by the two major Iranian deserts and the Zagros mountain range.
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Affiliation(s)
- Maria C Terreros
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL FL 33199, USA
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The investigation of allele and genotype frequencies of CYP3A5 (1*/3*) and P2Y12 (T744C) in Iran. Mol Biol Rep 2010; 38:4873-7. [DOI: 10.1007/s11033-010-0628-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
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20
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Moosavi F, Mohabatkar H, Mohsenzadeh S. Computer-aided analysis of structural properties and epitopes of Iranian HPV-16 E7 oncoprotein. Interdiscip Sci 2010; 2:367-72. [PMID: 21153780 DOI: 10.1007/s12539-010-0040-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 01/16/2010] [Accepted: 01/18/2010] [Indexed: 11/30/2022]
Abstract
Infection by human papillomavirus type 16 (HPV-16) is the cause of 50% or more of cervical cancers in women. The E7 oncoprotein of HPV-16 has long been known as a potent immortalizing and transforming agent. We used different servers like PseAAC, MHC_binding, MHC_II_binding and Expasy for the present computational prediction. The results for T cell epitopes showed that B1501, A0203, A0201, A0202, A6801 and DRB0405 alleles had lower IC50 than other alleles. We also predicted several peptides with the best binding affinities for alleles of the most frequent MHC class I and II alleles of the various ethnic groups living in the different region of Iran. Two peptides (26-35) and (44-52) were predicted as B-cell epitopes. According to this analysis 1 N-glycosylation site, 2 PKC sites, 4 CK2 sites and 3 disulfide sites were predicted. Our computational study predicted that B cell epitope 1 was Casein kinase II phosphorylated (site No. 31) and glycosylated (site No. 29). Putative MHC-I epitopes 3 and 5 and MHC-II epitopes 19, 21 and 26 were predicted to be casein kinase II phosphorylated. MHC-II epitopes 19 and 21 was predicted to be glycosylated. T cell epitopes 1, 13, 16 and 24 were demonstrated to be kinase C phosphorylated. The result of this analysis for Iranian HPV-16 E7 also indicated that 21.43%, 18.37% and 60.20% of the protein were in the α-helix, extended strand and random coil respectively.
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Affiliation(s)
- Fatemeh Moosavi
- Department of Biology, College of Sciences, Shiraz University, Iran
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Investigation of allele and genotype frequencies of CYP2C9, CYP2C19 and VKORC1 in Iran. Pharmacol Rep 2010; 62:740-6. [DOI: 10.1016/s1734-1140(10)70332-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 11/25/2009] [Indexed: 11/22/2022]
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22
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Farjadian S, Ota M, Inoko H, Ghaderi A. The genetic relationship among Iranian ethnic groups: an anthropological view based on HLA class II gene polymorphism. Mol Biol Rep 2008; 36:1943-50. [DOI: 10.1007/s11033-008-9403-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022]
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