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Alinaghi S, Mohseni M, Fattahi Z, Beheshtian M, Ghodratpour F, Zare Ashrafi F, Arzhangi S, Jalalvand K, Najafipour R, Khorram Khorshid HR, Kahrizi K, Najmabadi H. Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups. ARCHIVES OF IRANIAN MEDICINE 2024; 27:79-88. [PMID: 38619031 PMCID: PMC11017261 DOI: 10.34172/aim.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity. RESULTS Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples. CONCLUSION The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.
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Affiliation(s)
- Somayeh Alinaghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs. Mol Genet Genomics 2020; 295:1315-1324. [PMID: 32588126 PMCID: PMC7524810 DOI: 10.1007/s00438-020-01696-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022]
Abstract
We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, Abdullah MT, Chambers GK, Edinur HA. Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia. Int J Legal Med 2020; 134:1335-1337. [PMID: 31897667 DOI: 10.1007/s00414-019-02237-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia.
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia.
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia
| | - Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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Haplotype diversity of 17 Y-STRs in Sheikh population of Punjab. Int J Legal Med 2019; 134:1325-1326. [PMID: 31709479 DOI: 10.1007/s00414-019-02202-1] [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: 09/23/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Y chromosomal short tandem repeat (Y-STR) haplotype diversity of 180 genetically unrelated male individuals from Sheikh population of Punjab Pakistan was studied by amplifying 17 Y-STR markers through the AmpFISTR®Yfiler™ PCR amplification kit. The analysis of data revealed mean discrimination capacity of 0.6438 and matching probability of 0.3561. Sheikh population was also compared with 11 other populations in order to determine its population relationships which indicated that Punjabi Sheikhs have low genetic resemblance with Indian-Balmiki, UAE [Arab], Yousafzai Pathan from Pakistan, and Pathans from Afghanistan. The data of this study could have valuable application in forensic cases, in population genetics studies, and in strengthening the Y-STR database.
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Khubrani YM, Wetton JH, Jobling MA. Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs. Forensic Sci Int Genet 2017; 33:98-105. [PMID: 29220824 DOI: 10.1016/j.fsigen.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 10/18/2022]
Abstract
Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.
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Affiliation(s)
- Yahya M Khubrani
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK; Forensic Genetics Laboratory, General Administration of Criminal Evidence, Public Security, Ministry of Interior, Saudi Arabia
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
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Jones RJ, Tay GK, Mawart A, Alsafar H. Y-Chromosome haplotypes reveal relationships between populations of the Arabian Peninsula, North Africa and South Asia. Ann Hum Biol 2017; 44:738-746. [PMID: 28948851 DOI: 10.1080/03014460.2017.1384508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The United Arab Emirates (UAE) is positioned at the crossroads of human migration out of Africa and through to Asia and Europe. AIM To compare the degree of genetic diversity of the Arabian UAE population with populations in other countries from the Middle East, South Asia and North Africa. SUBJECTS AND METHODS Twenty-seven Y-STR were analysed in 217 individuals. Y-STR haplotypes from this study were compared to population data stored in YHRD, using MDS and AMOVA. RESULTS Two hundred and twelve haplotypes were observed in the 217 individuals studied. Although the reduction in Y-STR loci from 27 to 17 resulted in a decrease in discriminatory power, comparisons of populations were possible. The UAE population clustered closer with other populations of the Middle East. The South Asian and North African populations were separated by Middle Eastern populations in between both clusters. CONCLUSION This is the first study to report the diversity of a population of the Arabian Peninsula using 27 Y-STR. MDS plots show that Middle Eastern populations are positioned in the centre, with African, Asian and European populations around the Arab population cluster. The findings of this study are consistent with this region being at the epicentre of human migration between continents.
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Affiliation(s)
- Rebecca J Jones
- a School of Anatomy, Physiology and Human Biology , University of Western Australia , Crawley , WA , Australia
| | - Guan K Tay
- b School of Psychiatry and Clinical Neurosciences , University of Western Australia , Crawley , WA , Australia.,c School of Medical and Health Sciences , Edith Cowan University , Joondalup , WA , Australia.,d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
| | - Aurélie Mawart
- d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
| | - Habiba Alsafar
- d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates.,e Faculty of Biomedical Engineering , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
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Population genetics for 17 Y-STR loci in Hui ethnic minority from Liaoning Province, Northeast China. Forensic Sci Int Genet 2017; 28:e36-e37. [DOI: 10.1016/j.fsigen.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 02/05/2017] [Accepted: 02/19/2017] [Indexed: 11/20/2022]
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