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Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
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Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [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: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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Xu C, Wei W, Zuo M, Zuo W, Li K, Lian X, Wang S, Zhou X, Zhang X, Zhong S. Genetic polymorphisms and phylogenetic characteristics of Tibeto-Burman-speaking Lahu population from southwest China based on 41 Y-STR loci. Ann Hum Biol 2023; 50:75-81. [PMID: 36688851 DOI: 10.1080/03014460.2023.2171123] [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: 01/24/2023]
Abstract
BACKGROUND Male sex-linked Y-chromosome short tandem repeats (Y-STRs) have been widely used in forensic cases and population genetics research. At present, the forensic-related Y-STR data in the Chinese Lahu population are still poorly understood. AIM To enrich the available Y-STR data of this Chinese minority population and investigate its phylogenetic relationships with other reported populations. SUBJECTS AND METHODS The genetic polymorphisms of 41 Y-STR loci were analysed in 299 unrelated healthy Lahu male individuals from Southwest China. Phylogenetic analyses were performed by multidimensional scaling analysis and neighbor-joining phylogenetic tree construction. RESULTS A total of 379 alleles were observed at the 41 Y-STR loci. The allele frequencies ranged from 0.0033 to 0.9666. The genetic diversity values ranged from 0.0653 to 0.9072. A total of 254 different haplotypes of the 41 Y-STR loci were observed in 299 individuals. The values of haplotype diversity, haplotype match probability, and discrimination capacity were 0.9987, 0.0047, and 0.8495, respectively. The phylogenetic analysis indicated that the Tibeto-Burman-speaking Lahu population showed a close genetic relationship with the Yunnan Yi population. CONCLUSIONS The haplotype data of the present study can enrich the forensic databases of this Chinese minority population and will be useful for population genetics and forensic DNA application.
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Affiliation(s)
- Chongchong Xu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wei Wei
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Mingxin Zuo
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wu Zuo
- Institute of Criminal Science and Technology, Yuxi Municipal Public Security Bureau, Yuxi, China
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xinqing Lian
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Shixu Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xuemei Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
| | - Shurong Zhong
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Judicial Expertise Center of Kunming Medical University, Kunming, China
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Ikram MS, Mehmood T, Rakha A, Akhtar S, Khan MIM, Al-Qahtani WS, Safhi FA, Hadi S, Wang CC, Adnan A. Genetic diversity and forensic application of Y-filer STRs in four major ethnic groups of Pakistan. BMC Genomics 2022; 23:788. [PMID: 36451116 PMCID: PMC9714238 DOI: 10.1186/s12864-022-09028-z] [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: 06/12/2022] [Accepted: 09/14/2022] [Indexed: 12/05/2022] Open
Abstract
17 Y-chromosomal STRs which are part of the Yfiler Amplification Kit were investigated in 493 unrelated Pakistani individuals belonging to the Punjabi, Sindhi, Baloch, and Pathan ethnic groups. We have assessed the forensic parameters and population genetic structure for each group. Among the 493 unrelated individuals from four ethnic groups (128 Baloch, 122 Pathan, 108 Punjabi, and 135 Sindhi), 82 haplotypes were observed with haplotype diversity (HD) of 0.9906 in Baloch, 102 haplotypes with HD value of 0.9957 in Pathans, 80 haplotypes with HD value of 0.9924 in Punjabi, and 105 haplotypes with HD value of 0.9945 in the Sindhi population. The overall gene diversity for Baloch, Pathan, Punjabi, and Sindhi populations was 0.6367, 0.6479, 0.6657, and 0.6112, respectively. The results had shown us that Pakistani populations do not have a unique set of genes but share the genetic affinity with regional (Central Asia and Northern India) populations. The observed low gene diversity (heterozygosity) values may be because of endogamy trends and this observation is equally supported by the results of forensic parameters which are mostly static across 4 combinations (minimal STRs, extended 11 Y-STRs, Powerplex 12 Y System, and Yfiler 17 Y-STRs) of STRs in these four populations.
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Affiliation(s)
- Muhammad Salman Ikram
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China ,grid.412782.a0000 0004 0609 4693Institute of Chemistry, University of Sargodha, Sargodha, 40100 Punjab Pakistan
| | - Tahir Mehmood
- grid.412782.a0000 0004 0609 4693Institute of Chemistry, University of Sargodha, Sargodha, 40100 Punjab Pakistan ,grid.11173.350000 0001 0670 519XCentre for Applied and Molecular Biology (CAMB), University of the Punjab, Lahore, 53700 Punjab Pakistan
| | - Allah Rakha
- grid.412956.d0000 0004 0609 0537Department of Forensic Sciences, University of Health Sciences, Lahore, 54600 Pakistan
| | - Sareen Akhtar
- grid.412956.d0000 0004 0609 0537Department of Forensic Sciences, University of Health Sciences, Lahore, 54600 Pakistan
| | | | - Wedad Saeed Al-Qahtani
- grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
| | - Fatmah Ahmed Safhi
- grid.449346.80000 0004 0501 7602Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671 Saudi Arabia
| | - Sibte Hadi
- grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
| | - Chuan-Chao Wang
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Atif Adnan
- grid.12955.3a0000 0001 2264 7233Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China ,grid.472319.a0000 0001 0708 9739Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh, 11452 Kingdom of Saudi Arabia
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He G, Adnan A, Al-Qahtani WS, Safhi FA, Yeh HY, Hadi S, Wang CC, Wang M, Liu C, Yao J. Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.939659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.
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Genetic Polymorphism of 27 Y-STR Loci in the Western Kazakh Tribes from Kazakhstan and Karakalpakstan, Uzbekistan. Genes (Basel) 2022; 13:genes13101826. [PMID: 36292713 PMCID: PMC9601638 DOI: 10.3390/genes13101826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
Abstract
Data on the genetic polymorphism of 27 Y-STR in Kazakhs of the Junior Zhuz has been presented and analyzed in relation to forensic features. A total of 464 representatives of the Western Kazakh tribes of Kazakhstan (Western Kazakhs, n = 405) and Uzbekistan (Karakalpakstan Kazakhs, n = 59) were examined by the Yfiler Plus set. The data are available in the YHRD under accession numbers YA006010 and YA006009. Genetic analysis (AMOVA and MDS) did not show significant differences between the two groups (Kazakhstan and Karakalpakstan Kazakhs) in terms of Y-chromosome diversity. Both groups are characterized by haplogroup C2a1a2 as a founder effect, which dominated two of the three tribes: Alimuly (67%), Baiuly (74.6%), and Zhetiru (25.8%). At the same time, the phylogenetic network for each tribe found its own clusters within C2a1a2. Western Kazakhs and Karakalpakstan Kazakhs present high values of unique haplotypes (84.44% and 96.61%), discrimination capacity (90.37% and 98.30%), and haplotype diversity (0.9991 and 0.9994). A set of 27 Y-STR loci distinguishes closely related individuals within the Western Kazakh tribes quite well. It is suitable for forensic application, and is also optimal for population genetics studies.
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Nazir S, Adnan A, Rehman RA, Al-Qahtani WS, Alsaleh AB, Al-Harthi HS, Safhi FA, Almheiri R, Lootah R, Alreyami A, Almarri I, Wang CC, Rakha A, Hadi S. Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan. Genes (Basel) 2022; 13:genes13081403. [PMID: 36011314 PMCID: PMC9407599 DOI: 10.3390/genes13081403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1−20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father−son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.
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Affiliation(s)
- Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Abrar B. Alsaleh
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
| | - Hussam S. Al-Harthi
- Prince Sultan Military Medical City, Makkah Al Mukarramah Road, Al-Sulimaniyah, Riyadh 12233, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Reem Almheiri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Reem Lootah
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Afra Alreyami
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Imran Almarri
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naïf Arab University of Security Sciences, Riyadh 11452, Saudi Arabia
- Correspondence: (A.A.); (C.-C.W.); (A.R.); (S.H.)
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Ran P, Ou S, Hadi S, Safhi FA, Al-Qahtani WS, Xuan JF, Adnan A, Pei B. Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs. Ann Hum Biol 2022; 49:204-209. [PMID: 35815603 DOI: 10.1080/03014460.2022.2100478] [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 Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%). AIM To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs. SUBJECTS & METHODS In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci. RESULTS All haplotypes generated for 406 Xibe samples using Goldeneye® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers. CONCLUSION According to pairwise RST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.
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Affiliation(s)
- Peng Ran
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
| | - Shanhai Ou
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Jin-Feng Xuan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, Liaoning, P.R. China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Bin Pei
- Xiamen Blood Center, Xiamen, Fujian province 361004, P.R. China
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Hadi S, Yao J, Adnan A. Editorial: Role of Y Chromosome in Molecular Anthropology, Forensics, and Genetic Genealogy. Front Genet 2022; 13:863455. [PMID: 35754810 PMCID: PMC9218708 DOI: 10.3389/fgene.2022.863455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/09/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
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Farhat Ullah M, Ali A, Majeed A, Ijaz A, Albastaki A, Ijaz Khan M, Ramzan Khan M, Ahmed Alghamdi H, Abdulrahman Alshahrani M. Population and Mutational Assessment of Novel Repeats in 13RM Y-STRs in Unrelated Males Born in Gilgit, Pakistan. Saudi J Biol Sci 2022; 29:3177-3183. [PMID: 35844379 PMCID: PMC9280172 DOI: 10.1016/j.sjbs.2022.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
Because they are totally transferred to the future generations until mutations occur, Y chromosome genetic markers are commonly utilised in forensics for the classification of male lineages for criminal justice purposes. The mutation rate of Rapidly Mutating Y-STRs (RM Y-STRs) markers is high. That is not seen in other Y-STRs markers, and they appear to be effective in distinguishing paternally related men. This study aimed to estimate the population and mutational parameters of 13 RM Y-STRs in 13 unrelated males born in Gilgit, Pakistan. Repeat there was no population substructure and strong discriminating capacity in the counts. In this population, there were higher mutation rates with the unusual structure of repeats. More research is needed to better characterize these loci in diverse Pakistani groups.
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Adnan A, Anwar A, Simayijiang H, Farrukh N, Hadi S, Wang CC, Xuan JF. The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs. Front Genet 2021; 12:760760. [PMID: 34976009 PMCID: PMC8719170 DOI: 10.3389/fgene.2021.760760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.
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Affiliation(s)
- Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Adeel Anwar
- Department of Orthopedic Surgery, The 3rd Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Halimureti Simayijiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Noor Farrukh
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jin-Feng Xuan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, China
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12
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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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13
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Shrivastava P, Kushwaha K, Kumawat R, Chauhan T, Saiz M, Lorente JA, Batham MS, Singh SS, Chaubey G. Untangled the genetic structure of Kahar and Tharu, using 23 Y chromosomal paternal lineage markers. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Tang J, Yang M, Wang X, Wang Q, Wang Q, Zhang H, Qian E, Zhang H, Ji J, Ren Z, Wu Y, Huang J. Genetic structure and forensic characterisation of 36 Y-chromosomal STR loci in Hmong-Mien-speaking Miao population. Ann Hum Biol 2020; 47:541-548. [PMID: 32597239 DOI: 10.1080/03014460.2020.1788159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Y-chromosomal short tandem repeats (Y-STRs) are widely used in paternity identification, pedigree investigation, and human population genetic history. AIM To investigate the Y-STR polymorphisms in a typical Miao population, and explore the genetic differentiation between the Miao population and reference groups. SUBJECTS AND METHODS We detected 36 Y-STRs genotyping in 455 unrelated Miao individuals from Guizhou province, and analysed genetic differentiation between the Miao population and 76 reference groups. RESULTS A total of 369 alleles were obtained, and the allele frequencies ranged from 0.0022 to 0.9802. In addition, the haplotype diversity, random match probability, and discrimination capacity values were 0.99997, 0.0022, and 0.9934, respectively. Moreover, the genetic relationships between Guizhou Miao and 76 ethnic populations showed that the population stratification was almost consistent with geographic distribution and language-family. CONCLUSIONS The 36 Y-STR loci in this study have good polymorphism distributions in the Guizhou Miao population, and therefore would be a useful tool in forensic identification and male parentage testing and even pedigree investigation.
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Affiliation(s)
- Jing Tang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaojuan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Enfang Qian
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yan Wu
- Guiyang Judicial Expertise Center of Public Security, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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15
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Adnan A, Kasimu K, Rakha A, He G, Yang T, Wang C, Lu J, Xuan J. Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs. Mol Genet Genomic Med 2020; 8:e1149. [PMID: 31989793 PMCID: PMC7057124 DOI: 10.1002/mgg3.1149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/15/2019] [Accepted: 01/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Dalian is a city formed in the 1880s in Liaoning province, Northeastern China with a population of 6.69 million now. Han is the largest ethnic group not only across Mainland China (92%) and Taiwan (97%) but also considered to be the largest ethnic group of the world contributing to above 18% of world's population. METHODS In the current study, we genotyped Goldeneye® 20Y System loci in 879 unrelated male individuals from the Han ethnic group in Dalian city and calculated the forensic parameters of the 20 Y-STR loci. RESULTS In total, we observed 855 haplotypes, among which 835 (94.99%) were unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is 97.27% and it slightly reduces to 96.93% when only Y-filer® set of 17 Y-STRs were used, which mitigates using the extended set of markers in this population. We found DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed the highest gene diversity (0.7621) in single copy Y-STR, and DYS385 showed the highest gene diversity (0.9683) among all. CONCLUSION Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic distance showed difference among Han population from the east to the west and from the north to the south. We also predicted haplogroups using Y-STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a null allele at the DYS448 in our samples. We also performed linear discriminatory analysis (LDA) between Han and other prominent Chinese minority ethnic groups. We presented Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for the future forensic and other usage.
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Affiliation(s)
- Atif Adnan
- Department of Forensic Genetics and BiologySchool of Forensic MedicineChina Medical UniversityShenyangP.R. China
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Kaidirina Kasimu
- School of Clinical MedicineChina Medical UniversityShenyangP.R. China
| | - Allah Rakha
- Department of Forensic SciencesUniversity of Health Sciences LahoreLahorePakistan
| | - Guanglin He
- Department of Anthropology and EthnologyXiamen UniversityXiamenChina
| | - Tongya Yang
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Chuan‐Chao Wang
- Department of Anthropology and EthnologyXiamen UniversityXiamenChina
| | - Jie Lu
- Department of Human AnatomyCollege of Basic Medical ScienceChina Medical UniversityShenyangP.R. China
| | - Jin‐feng Xuan
- Department of Forensic Genetics and BiologySchool of Forensic MedicineChina Medical UniversityShenyangP.R. China
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16
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Adnan A, He G, Rakha A, Kasimu K, Guo J, Hassan SE, Hadi S, Wang CC, Xuan JF. Phylogenetic relationship and genetic history of Central Asian Kazakhs inferred from Y-chromosome and autosomal variations. Mol Genet Genomics 2019; 295:221-231. [PMID: 31641857 DOI: 10.1007/s00438-019-01617-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 10/04/2019] [Indexed: 02/04/2023]
Abstract
The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a very colorful ethnic region of China, harboring abundant genetic and cultural diversity. The Kazakhs are the third largest ethnic group (7.02%) after Uyghur (46.42%) and Han (38.99%) in Xinjiang, but their genetic diversity and forensic characterization are poorly understood. In the current study, we genotyped 15 autosomal short tandem repeat (STR) loci and ten Y-STRs in 889 individuals (659 male and 230 female) collected from Kazak population of the Ili Kazak Autonomous Prefecture using AGCU Expressmarker 16 and 10Y-STR Kit (EX16 + 10Y). For autosomal STRs, we observed a total of 174 different alleles ranging from 6 to 34.2 repeat units and FGA showed the greatest power of discrimination (20 alleles) in Ili Kazakh population. We have not observed departures from Hardy-Weinberg equilibrium (HWE) after sequential Bonferroni correction and only found a minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The combined power of exclusion (CPE) was 0.99999998395 and combined power of discrimination (CPD) was 99.999999999999999798%. For Y-STRs, we observed a total of 496 different haplotypes in these ten Y-STR loci. The gene diversities ranged from 0.5023 (DYS391) to 0.8357 (DYS385a/b). The overall haplotype diversity (GD) was 0.9985 with random matching probability (RMP) of 0.0015. The results of population genetic analysis based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations is generally consistent with ethnic, linguistic, and continental geographical classifications.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China. .,Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, Shenyang, 110122, China.
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China.,West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, 54000, Pakistan
| | - Kaidirina Kasimu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China
| | - Sibt E Hassan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China
| | - Sibte Hadi
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China.
| | - Jin-Feng Xuan
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, Shenyang, 110122, China.
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17
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Chen P, Adnan A, Rakha A, Wang M, Zou X, Mo X, He G. Population background exploration and genetic distribution analysis of Pakistan Hazara via 23 autosomal STRs. Ann Hum Biol 2019; 46:514-518. [PMID: 31559868 DOI: 10.1080/03014460.2019.1673483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background: Short tandem repeats (STRs) have gained considerable attention in family search (Y-chromosomal STRs), complex paternity identification (X-chromosomal STRs), routine forensic personal identification (autosomal STRs) and population genetics.Aim: To explore the forensic characteristics of 23 autosomal STRs included in the Huaxia Platinum system in the South Pakistan Hazara population and investigate the genetic similarities and differences between Hazara and 54 worldwide reference populations.Subjects and methods: Variation of the 23 autosomal STRs included in the Huaxia Platinum system was first investigated and reported in a sample of 261 Quetta Hazara in Balochistan Province, Southwest Pakistan.Results: The combined power of discrimination is 0.999999999999999999999999999 and combined power of exclusion is 0.99999999989596 in Quetta Hazara. Comprehensive population comparisons between Hazara and another 13 Eurasian populations based on genotype data, as well as between Hazara and 54 worldwide populations based on the allele frequency distribution, were conducted. Multidimensional scaling plots, principal component analysis, and neighbour-joining phylogenetic trees consistently demonstrated that Pakistan Hazara harbours close affinities with neighbouring Turkic-speaking populations. Model-based genetic structure analysis further suggests that Quetta Hazara derives about half its ancestry directly from the East Asians.Conclusion: Twenty-five forensic-related markers included in the Huaxia Platinum system can be used for forensic practice in the Central Asia Hazara population. Quetta Hazara has a close genetic relationship with the Turkic-speaking populations of Uyghur and Kazakh. Further whole-genome sequencing of Hazara needs to be conducted to validate the observed genetic structure and reconstruct the fine-scale population history of Hazara.
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Affiliation(s)
- Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Science, China Medical University, Shenyang, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Mengge Wang
- Institute of Forensic medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaodan Mo
- Department of Anatomy, Medical College of Northwest University for Nationalities, Lanzhou, China
| | - Guanglin He
- Institute of Forensic medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
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18
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Adnan A, Rakha A, Ameen F, Alarfaj AA, Almansob A, Wang CC, Lu J, Xing J. Genetic structure and forensic characteristics of Saraiki population from Southern Punjab, Pakistan, revealed by 20 Y-chromosomal STRs. Int J Legal Med 2019; 134:977-979. [PMID: 31392415 DOI: 10.1007/s00414-019-02138-6] [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: 05/30/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
Pakistan harbors more than 18 major ethnic groups which speak 60 different languages. People speaking Saraiki languages are known as Saraiki or Multani. They are mainly residents of Southern Punjab including Multan, Dear Ghazi Khan, Rajanpur, and Rahim Yar khan. Here, we reported the data of 20 Y-chromosomal short tandem repeats (Y-STRs) genotyped with the Goldeneye® 20Y kit in 154 unrelated Saraiki individuals. We observed 141 different haplotypes on 20 Y-STR loci and the gene diversity (GD) ranged from 0.6566 (DYS448) to 0.9538 (DYS385a, b). The overall haplotype diversity was 0.9989 at 20 Y-STRs loci. Furthermore, we performed population genetic analyses by including data from 26 other South Asian populations. The presented haplotype data was recently included in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, 54000, Pakistan
| | - Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdullah A Alarfaj
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - A Almansob
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, 110122, China.
| | - Jiaxin Xing
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, Shenyang, 110122, China.
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Zhang D, Cao G, Xie M, Cui X, Xiao L, Tian C, Ye Y. RETRACTED ARTICLE: Y Chromosomal STR haplotypes in Chinese Uyghur, Kazakh and Hui ethnic groups and genetic features of DYS448 null allele and DYS19 duplicated allele. Int J Legal Med 2019; 135:1119. [PMID: 30923909 DOI: 10.1007/s00414-019-02049-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/20/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Danyan Zhang
- Chongqing Population and Family Planning Science and Technology Research Institute, Key Laboratory of Birth Defects and Reproductive Health, Chongqing, 400020, China
| | - Gang Cao
- Criminal Policeman Detachment, Karamay Municipal Public Security Bureau, Karamay, 834000, Xinjiang, China
| | - Mingkun Xie
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 8th Floor, Fa Yi Building, No.16, Section 3, Renmin Nan Road, Chengdu, 610016, Sichuan, China
| | - Xuejun Cui
- Criminal Policeman Detachment, Karamay Municipal Public Security Bureau, Karamay, 834000, Xinjiang, China
| | - Li Xiao
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 8th Floor, Fa Yi Building, No.16, Section 3, Renmin Nan Road, Chengdu, 610016, Sichuan, China
| | - Chenchen Tian
- Criminal Policeman Detachment, Karamay Municipal Public Security Bureau, Karamay, 834000, Xinjiang, China
| | - Yi Ye
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 8th Floor, Fa Yi Building, No.16, Section 3, Renmin Nan Road, Chengdu, 610016, Sichuan, China.
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20
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Zhao ZL, Xia L, Zhao C, Ameen F, Alyahya S, Yao J. Population genetics of 15 autosomal STR loci in the Han population of Ili Kazakh Autonomous Prefecture, Northwestern China. Ann Hum Genet 2019; 83:318-324. [PMID: 30895616 DOI: 10.1111/ahg.12314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/20/2019] [Accepted: 03/05/2019] [Indexed: 01/26/2023]
Abstract
PURPOSE China harbors 56 ethnic groups and Han accounts for >92% of the total Chinese population. We investigated the frequencies of 15 autosomal short tandem repeat (STR) loci in the Han population of the Ili Kazakh Autonomous Prefecture with the aim of expanding the available population information in human genetics databases and for forensic DNA analysis. SUBJECTS AND METHODS We explored the genetic characteristics of 15 autosomal STR loci in 552 unrelated Chinese Han individuals from Ili Kazakh Autonomous Prefecture, Northwestern China using the AmpFISTR Identifiler PCR Amplification Kit. Moreover, phylogenetic analysis was performed between the Han population and other relevant populations based on the autosomal STR genotyping. The neighbor-joining tree and principle component analysis were generated based on the Nei's standard genetic distance and allelic frequencies, respectively. RESULTS A total of 171 alleles were observed among 552 unrelated individuals and allelic frequencies ranged from 0.5145 to 0.0009. The combined power of discrimination and combined power of exclusion of the 15 autosomal STR loci were 0.9999999999999999964 and 0.999998243616671, respectively. CONCLUSIONS Population comparison revealed that the Ili Han population were lining up together with other Han populations in China while showing significant differences from other Chinese and worldwide populations.
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Affiliation(s)
- Zhi-Liang Zhao
- Hospital Office, Chengdu First People's Hospital, Chengdu, Sichuan Province, China.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Lu Xia
- Department of Rehabilitation, Chengdu First People's Hospital, Chengdu, Sichuan Province, China
| | - Cong Zhao
- Department of Gastroenterology, Chengdu First People's Hospital, Chengdu, Sichuan Province, China
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sami Alyahya
- National Center for Biotechnology, King Abdul Aziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenbei New District, Shenyang, China
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21
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Adnan A, Rakha A, Nazir S, Khan MF, Hadi S, Xuan J. Evaluation of 13 rapidly mutating Y-STRs in endogamous Punjabi and Sindhi ethnic groups from Pakistan. Int J Legal Med 2019; 133:799-802. [DOI: 10.1007/s00414-018-01997-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
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