1
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Ashirbekov Y, Nogay A, Abaildayev A, Zhunussova A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan. Ann Hum Biol 2023; 50:48-51. [PMID: 36650935 DOI: 10.1080/03014460.2023.2170465] [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: 01/19/2023]
Abstract
BACKGROUND The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. AIM To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. SUBJECTS AND METHODS The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. RESULTS A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. CONCLUSIONS The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Anastassiya Nogay
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Aigul Zhunussova
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | - Zhaxylyk Sabitov
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan.,Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Republic of Kazakhstan
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2
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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3
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Kairov U, Molkenov A, Sharip A, Rakhimova S, Seidualy M, Rhie A, Kozhamkulov U, Zhabagin M, Kim JI, Lee JH, Terwilliger JD, Seo JS, Zhumadilov Z, Akilzhanova A. Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals. Front Genet 2022; 13:902804. [PMID: 35899193 PMCID: PMC9309552 DOI: 10.3389/fgene.2022.902804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the genomes of five ethnic Kazakhs at high coverage using the Illumina HiSeq2000 next-generation sequencing platform. The five Kazakhs yielded a total number of base pairs ranging from 87,308,581,400 to 107,526,741,301. On average, 99.06% were properly mapped. Based on the Het/Hom and Ti/Tv ratios, the quality of the genomic data ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Genetic variants were identified and annotated. Functional analysis of the genetic variants identified several variants that were associated with higher risks of metabolic and neurogenerative diseases. The present study showed high levels of genetic admixture of Kazakhs that were comparable to those of other Central Asians. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype–phenotype relations at the population level.
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Affiliation(s)
- Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- *Correspondence: Ulykbek Kairov, ; Ainur Akilzhanova,
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aigul Sharip
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Madina Seidualy
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Arang Rhie
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Maxat Zhabagin
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Jong-Il Kim
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Joseph H. Lee
- Sergievsky Center, Departments of Neurology and Epidemiology, Taub Institute, Columbia University, New York City, NY, United States
| | - Joseph D. Terwilliger
- Departments of Genetics and Development and Psychiatry, Sergievsky Center, Columbia University, New York City, NY, United States
| | - Jeong-Sun Seo
- Ilchun Genomic Medicine Institute, Seoul National University, Seoul, Korea
| | - Zhaxybay Zhumadilov
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- *Correspondence: Ulykbek Kairov, ; Ainur Akilzhanova,
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4
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Ashirbekov Y, Abaildayev A, Neupokoyeva A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Northern Kazakhstan. Ann Hum Biol 2022; 49:87-89. [PMID: 35132894 DOI: 10.1080/03014460.2022.2039292] [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: 11/01/2022]
Abstract
BACKGROUND Previous studies of the genetic polymorphism of the Y-chromosome of Kazakhs were focused on the Eastern, Central, Southern, and Western regions of Kazakhstan. In addition, many of these studies were limited to 17 Y-STR loci from the Yfiler. AIM To enrich the existing Kazakhstan Y-chromosome Haplotype Reference Database from the Northern Kazakh population data by a wide set of 27 Y-STR and investigate the population genetic relationships with previously published data. SUBJECTS AND METHODS 27 Y-STR loci from the Yfiler Plus PCR Amplification Kit were analysed in 382 healthy unrelated Kazakh males from Northern Kazakhstan. Genetic polymorphism was analysed using Arlequin software. RESULTS A total of 326 distinct haplotypes of the 27 Y-STR loci were observed in 382 individuals. The discrimination capacity (0.9982) and haplotype diversity (0.8534) were computed. A total of 168 alleles at single-copy loci were observed, and their frequencies ranged from 0.003 to 0.843. The pairwise genetic distance (RST) showed that the Northern Kazakh population is genetically distinct from the Chinese Kazakh population. CONCLUSIONS Genetic polymorphism shows that the potential value of 27 Y-STR loci for forensic casework in the Northern Kazakh population, and the current findings, might be beneficial for paternal lineages in the study of population genetics.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Republic of Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Republic of Kazakhstan
| | | | - Zhaxylyk Sabitov
- National Center for Biotechnology, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Republic of Kazakhstan.,Young Researchers Alliance, Republic of Kazakhstan
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5
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Khussainova E, Kisselev I, Iksan O, Bekmanov B, Skvortsova L, Garshin A, Kuzovleva E, Zhaniyazov Z, Zhunussova G, Musralina L, Kahbatkyzy N, Amirgaliyeva A, Begmanova M, Seisenbayeva A, Bespalova K, Perfilyeva A, Abylkassymova G, Farkhatuly A, Good SV, Djansugurova L. Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz. Front Genet 2022; 12:801295. [PMID: 35069700 PMCID: PMC8777105 DOI: 10.3389/fgene.2021.801295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.
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Affiliation(s)
| | - Ilya Kisselev
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- The University of Winnipeg, Winnipeg, MB, Canada
| | - Olzhas Iksan
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Alexander Garshin
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | - Lyazzat Musralina
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | | | - Kira Bespalova
- Institute of Genetics and Physiology, Almaty, Kazakhstan
| | | | | | | | - Sara V. Good
- The University of Winnipeg, Winnipeg, MB, Canada
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6
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Adnan A, Rakha A, Nazir S, Alghafri R, Hassan Q, Wang CC, Lu J. Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs. Int J Legal Med 2021; 135:1777-1784. [PMID: 33818632 DOI: 10.1007/s00414-021-02591-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/26/2021] [Indexed: 11/27/2022]
Abstract
The Hazara population across Durand line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan's army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. In the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1), and haplotype diversity was 0.9992. For the Baloch population, every individual was unique at 27 Y-STR loci; gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes were shared between 178 individuals, while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling plot, neighbor-joining tree, linear discriminatory analysis, and median-joining network were performed, which shed light on the history of Hazara and Baloch populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand line.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates
| | - Qudsia Hassan
- Department of Forensic Medicine & Toxicology, Ziauddin Medical College Clifton, Karachi, Pakistan
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
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7
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Kulmambetova G, Shtefanov I, Aitkulova A, Imanbekova M, Iskakova A, Makishev A, Ramankulov Y. Association of polymorphisms in TP53 and the promoter region of IL10 with gastric cancer in a Kazakh population. Bosn J Basic Med Sci 2020; 20:539-546. [PMID: 32651972 PMCID: PMC7664782 DOI: 10.17305/bjbms.2020.4761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
The emerging evidence indicates that single nucleotide polymorphisms (SNPs) of the tumor necrosis factor (TNF), interleukin 10 (IL10), tumor protein p53 (TP53), and cluster of differentiation 14 (CD14) genes may determine individual susceptibility to gastric cancer (GC). We aimed to investigate the associations for polymorphisms of the TNF, IL10, TP53, and CD14 genes in a population of Kazakhs, to identify potential risk or protective associations of the SNPs with GC. A case group of 143 patients hospitalized for GC was enrolled. Controls were 355 volunteers with no history of any cancer and frequency matched with cases by age. Differences in proportions for categorical variables and the assessment of genotypic frequencies conforming to the Hardy-Weinberg equilibrium law were evaluated by the Chi-square test. Associations between genetic polymorphisms and the risk of GC were estimated by regression analysis. For genetic analysis, three genetic models (additive, dominant, and recessive) were used. Four significant associations were found. The SNPs rs1042522 of TP53 and rs1800896 of IL10 were risk factors for GC by the additive model. Two polymorphisms of IL10 were protective of GC, namely, rs1800872 by additive model and rs1800871 by recessive model. No significant associations were observed between the TNF and CD14 polymorphisms and GC. The polymorphisms TP53 rs1042522 and IL10 rs1800896 are associated with GC risk, while the polymorphisms IL10 rs1800872 and rs1800871 are protective of GC in the population of Kazakhs.
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Affiliation(s)
- Gulmira Kulmambetova
- Biotechnology Core Facility, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Ivan Shtefanov
- Department of Oncology, City Oncology Center, Nur-Sultan, Kazakhstan
| | - Akbota Aitkulova
- Biotechnology Core Facility, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Meruyert Imanbekova
- Biotechnology Core Facility, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Aisha Iskakova
- Biotechnology Core Facility, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Abay Makishev
- Department of Oncology, City Oncology Center, Nur-Sultan, Kazakhstan
| | - Yerlan Ramankulov
- Biotechnology Core Facility, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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8
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Liu B, Ma P, Wang C, Yan S, Yao H, Li Y, Xie Y, Meng S, Sun J, Cai Y, Sarengaowa S, Li H, Cheng H, Wei L. Paternal origin of Tungusic‐speaking populations: Insights from the updated phylogenetic tree of Y‐chromosome haplogroup
C2a‐M86. Am J Hum Biol 2020; 33:e23462. [DOI: 10.1002/ajhb.23462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Bing‐Li Liu
- Institute of Chinese and Culture Education Studies Huaqiao University Xiamen China
| | - Peng‐Cheng Ma
- School of Life Sciences Jilin University Changchun China
| | - Chi‐Zao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
| | - Shi Yan
- Human Phenome Institute Fudan University Shanghai China
| | - Hong‐Bing Yao
- Key Laboratory of Evidence Science of Gansu Province Gansu University of Political Science and Law Lanzhou China
| | - Yong‐Lan Li
- Laboratory for Human Biology and Human Genetics Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University Hohhot China
| | - Yong‐Mei Xie
- Laboratory for Human Biology and Human Genetics Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University Hohhot China
| | - Song‐Lin Meng
- School of History and Ethnic Culture Hulunbuir University Hulunbuir China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Yan‐Huan Cai
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Sarengaowa Sarengaowa
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
- Human Phenome Institute Fudan University Shanghai China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
| | - Hui‐Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Lan‐Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
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9
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Y-chromosome evidence confirmed the Kerei-Abakh origin of Aksay Kazakhs. J Hum Genet 2020; 65:797-803. [PMID: 32313196 DOI: 10.1038/s10038-020-0759-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/14/2020] [Accepted: 04/02/2020] [Indexed: 11/08/2022]
Abstract
Aksay Kazakhs are the easternmost branch of Kazakhs, residing in Jiuquan city, the forefront of the ancient Silk Road. However, the genetic diversity of Aksay Kazakhs and its relationships with other Kazakhs still lack attention. To clarify this issue, we analyzed the non-recombining portion of the Y-chromosome from 93 Aksay Kazakhs samples, using a high-resolution analysis of 106 biallelic markers and 17 STRs. The lowest haplogroup diversity (0.38) was observed in Aksay Kazakhs among all studied Kazakh populations. The social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation. Aksay Kazakhs tended to migrate with clans and had limited paternal admixture with neighboring populations. Aksay Kazakhs had the highest frequency (80%) of haplogroup C2b1a3a1-F3796 (previous C3*-Star Cluster) among the investigated Eurasian steppe populations, which was now seen as the genetic marker of Kerei clan. Furthermore, NETWORK analysis indicated that Aksay Kazakhs originated from sub-clan Kerei-Abakh in Kazakhstan with DYS448 = 23. TMRCA estimates of three recent descent clusters detected in C2*-M217 (xM48) network, one of which incorporate nearly all of the C2b1a3a1-F3796 Aksay Kazakhs samples, gave the age range of 976-1405 YA for DC1, 1059-1314 YA for DC2, and 1139-1317 YA for DC3, respectively; this is coherent with the 7th to the 11th centuries Altaic-speaking pastoral nomadic population expansion.
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10
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Seidualy M, Blazyte A, Jeon S, Bhak Y, Jeon Y, Kim J, Eriksson A, Bolser D, Yoon C, Manica A, Lee S, Bhak J. Decoding a highly mixed Kazakh genome. Hum Genet 2020; 139:557-568. [PMID: 32076829 PMCID: PMC7170836 DOI: 10.1007/s00439-020-02132-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/05/2020] [Indexed: 01/22/2023]
Abstract
We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.
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Affiliation(s)
- Madina Seidualy
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, 28160 Republic of Korea
| | - Anders Eriksson
- Department of Medical and Molecular Genetics, King’s College London, London, SE1 9RT UK
- cGEM, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Dan Bolser
- Geromics Ltd, Office 261, 23 Kings Street, Cambridge, CB1 1AH UK
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, 28160 Republic of Korea
- Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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Khaibullin TN, Kirillova EV, Bikbaev RM, Boyko AN. Clinical-epidemiological characteristics of multiple sclerosis and neuroopticomyelitis in the Central Asia. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:12-17. [DOI: 10.17116/jnevro20191192212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Genetic characterization of Y-chromosomal STRs in Hazara ethnic group of Pakistan and confirmation of DYS448 null allele. Int J Legal Med 2018; 133:789-793. [DOI: 10.1007/s00414-018-1962-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 10/28/2022]
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13
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Zhabagin M, Sarkytbayeva A, Tazhigulova I, Yerezhepov D, Li S, Akilzhanov R, Yeralinov A, Sabitov Z, Akilzhanova A. Development of the Kazakhstan Y-chromosome haplotype reference database: analysis of 27 Y-STR in Kazakh population. Int J Legal Med 2018; 133:1029-1032. [DOI: 10.1007/s00414-018-1859-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/11/2018] [Indexed: 10/16/2022]
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14
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Sikhayeva N, Talzhanov Y, Iskakova A, Dzharmukhanov J, Nugmanova R, Zholdybaeva E, Ramanculov E. Type 2 diabetes mellitus: distribution of genetic markers in Kazakh population. Clin Interv Aging 2018; 13:377-388. [PMID: 29551892 PMCID: PMC5842777 DOI: 10.2147/cia.s156044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy–Weinberg equilibrium. The obtained allele frequencies were further compared to publicly available data from other ethnic populations. Allele frequencies for other (compared) populations were pooled from the haplotype map (HapMap) database. Principal component analysis (PCA), cluster analysis, and multidimensional scaling (MDS) were used for the analysis of genetic relationship between the populations. Results Comparative analysis of allele frequencies of the studied SNPs showed significant differentiation among the studied populations. The Kazakh population was grouped with Asian populations according to the cluster analysis and with the Caucasian populations according to PCA. According to MDS, results of the current study show that the Kazakh population holds an intermediate position between Caucasian and Asian populations. Conclusion A high percentage of population differentiation was observed between Kazakh and world populations. The Kazakh population was clustered with Caucasian populations, and this result may indicate a significant Caucasian component in the Kazakh gene pool.
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Affiliation(s)
- Nurgul Sikhayeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan.,Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Yerkebulan Talzhanov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Aisha Iskakova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Jarkyn Dzharmukhanov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Raushan Nugmanova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Elena Zholdybaeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Erlan Ramanculov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan.,Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.,School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
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The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
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Analysis of genetic admixture in Uyghur using the 26 Y-STR loci system. Sci Rep 2016; 6:19998. [PMID: 26842947 PMCID: PMC4740765 DOI: 10.1038/srep19998] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/22/2015] [Indexed: 11/24/2022] Open
Abstract
The Uyghur population has experienced extensive interaction with European and Eastern Asian populations historically. A set of high-resolution genetic markers could be useful to infer the genetic relationships between the Uyghur population and European and Asian populations. In this study we typed 100 unrelated Uyghur males living in southern Xinjiang at 26 Y-STR loci. Using the high-resolution 26 Y-STR loci system, we investigated genetic and phylogenetic relationship between the Uyghur population and 23 reference European or Asian populations. We found that the Uyghur population exhibited a genetic admixture of Eastern Asian and European populations, and had a slightly closer relationship with the selected European populations than the Eastern Asian populations. We also demonstrated that the 26 Y-STR loci system was potentially useful in forensic sciences because it has a large power of discrimination and rarely exhibits common haplotypes. However, ancestry inference of Uyghur samples could be challenging due to the admixed nature of the population.
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Iskakova AN, Romanova AA, Aitkulova AM, Sikhayeva NS, Zholdybayeva EV, Ramanculov EM. Polymorphisms in genes involved in the absorption, distribution, metabolism, and excretion of drugs in the Kazakhs of Kazakhstan. BMC Genet 2016; 17:23. [PMID: 26785747 PMCID: PMC4717528 DOI: 10.1186/s12863-016-0329-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/13/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Studies of genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are crucial to the development of therapeutics in clinical medicine. Such data provide information that may improve our understanding of individual differences in sensitivity or resistance to certain drugs, thereby helping to avoid adverse drug reactions (ADRs) in patients and improve the quality of therapies. Here, we aimed to analyse single nucleotide polymorphisms (SNPs) involved in the ADME of multiple drugs in Kazakhs from Kazakhstan. RESULTS A total of 158 SNPs involved in the ADME of various drugs were studied. We analysed 320 Kazakh DNA samples using OpenArray genotyping. Of the 158 SNPs, 75 were not found in heterozygous or homozygous variants. Comparative analysis among Kazakhs and world populations showed a fairly high percentage of population differentiation. CONCLUSION These results provide further information for pharmacogenetic databases and may contribute to the development of personalized approaches and safer therapies for the Kazakh population. Moreover, these data provide insights into the different racial groups that may have contributed to the Kazakh population.
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Affiliation(s)
- Aisha N Iskakova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
- Biology and Biotechnology Department, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
| | - Aliya A Romanova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
| | - Akbota M Aitkulova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
| | - Nurgul S Sikhayeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
- Faculty of Natural Sciences, L.N, Gumilyov Eurasian National University, Astana, Kazakhstan.
| | - Elena V Zholdybayeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
| | - Erlan M Ramanculov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Almaty, Kazakhstan.
- School of Science and Technology Nazarbayev University, Astana, Kazakhstan.
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Polašek O. Global mobility and the break-up of human population isolates - neglected mechanisms in health, demographics, and anthropology. Croat Med J 2015; 56:324-5. [PMID: 26321024 PMCID: PMC4576745 DOI: 10.3325/cmj.2015.56.324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ozren Polašek
- Ozren Polašek, Medical School, University of Split, Split, Croatia,
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Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction. J Genet Genomics 2015; 42:403-7. [DOI: 10.1016/j.jgg.2015.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/21/2015] [Accepted: 03/24/2015] [Indexed: 11/20/2022]
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Shan W, Ren Z, Wu W, Hao H, Abulimiti A, Chen K, Zhang F, Ma Z, Zheng X. Maternal and paternal diversity in Xinjiang Kazakh population from China. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414110143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Genetic polymorphism of 17 Y chromosomal STRs in Kazakh and Uighur populations from Xinjiang, China. Int J Legal Med 2014; 128:743-4. [DOI: 10.1007/s00414-013-0948-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
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22
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Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 2013; 58:804-11. [DOI: 10.1038/jhg.2013.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/16/2013] [Accepted: 09/27/2013] [Indexed: 01/15/2023]
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