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Dong B, Lei F, Lin Y, Wang X, Yuan X, Cai M, Zhao M, Zhu B. Genetic profile and ancestral polymorphism research of the Guizhou Shui and Dong ethnic groups using a novel self-developed AIM-InDel panel. Forensic Sci Int 2024; 363:112171. [PMID: 39159589 DOI: 10.1016/j.forsciint.2024.112171] [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: 05/29/2023] [Revised: 07/03/2024] [Accepted: 07/26/2024] [Indexed: 08/21/2024]
Abstract
Insertion or deletion (InDel), a genetic marker with short insertion/deletion fragment length polymorphism, is widely used in the field of forensic biological research. The Guizhou Shui (Shui) ethnic group and Guizhou Dong (Dong) ethnic group are located in the southwestern region of China, with rich historical and cultural background. In this study, a self-developed panel included 56 ancestry informative marker (AIM)-InDel loci on the autosomes, three InDel loci on the Y chromosome, and one sex-determined Amelogenin locus. Firstly, we used the 56 autosomal loci to assess the forensic individual identification and paternity testing abilities in both the Shui and Dong groups. The cumulative probability of match and probability of exclusion for the Shui and Dong groups were 2.228×10-15 and 0.991518139; 7.604×10-16 and 0.992253273, respectively. In addition, we also conducted in-depth analyses for the genetic backgrounds and structures of the Shui and Dong groups based on 56 AIM-InDel loci. This research has found that the Shui and Dong groups have close genetic relationships with the East Asian populations. Meanwhile, we also found that the Shui group has a close genetic distance with Chinese Dai in Xishuangbanna (CDX). These insights provide vital information for the genetic structures of the Shui and Dong groups, as well as basic population data and molecular biological evidence support for individual identification and biogeographic ancestry inference in forensic genetic field.
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Affiliation(s)
- Bonan Dong
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
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Wang X, Zhang H, Wang Q, Yang M, Liu Y, Ran Q, Huang C, Huang J, Ren Z, Jin X. Insertion/deletion polymorphism for genetic background and forensic performance exploration of the Sui group from Guizhou. Heliyon 2023; 9:e21384. [PMID: 38027767 PMCID: PMC10643464 DOI: 10.1016/j.heliyon.2023.e21384] [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: 05/11/2023] [Revised: 09/08/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Insertion/deletion polymorphisms (InDels) as ideal genetic markers for forensic genetics are appreciated by scholars both nationally and internationally because they integrated the favorable features of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Nevertheless, with the limited identification efficiency of InDels, the multiplex amplification systems of InDels might just be applied as the supplementary methods in paternity testing with respect to commonly used STRs. In the current research, we successfully genotyped 105 unrelated individuals from the Guizhou Sui population based on a six-color fluorescence multiplex panel that could simultaneously detect 64 genetic markers (59 autosomal InDels, two autosomal miniSTRs and three Y chromosomal genetic markers). In addition, frequency distributions and forensic statistical parameters of these loci in the Sui group were assessed using the STRAF software. Phylogenetic relationships among the Sui group and other reference populations were dissected by two methods (principal component analysis and phylogenetic trees) based on 59 InDels. The combined discrimination power and probability of exclusion values of 61 autosomal genetic markers in the Sui group were nearly equal to 1-1.90063 × 10-27 and 0.999998272, respectively. Furthermore, we observed that the Sui group from Guizhou had closer genetic affinities with East Asian populations with respect to other continental populations. In summary, we stated that the multiplex amplification system might be utilized as a prospective independent tool for human individual identification and parentage testing in the Sui group residing in Guizhou.
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Affiliation(s)
- Xiaoxue Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qianchong Ran
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Chunli Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
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Ren Z, Yang M, Jin X, Wang Q, Liu Y, Zhang H, Ji J, Wang CC, Huang J. Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.995783] [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
The genome-wide characteristics and admixture history of the Tai-Kadai-speaking populations are essential for understanding the population genetic diversity in southern China. We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China. We merged the genome-wide data with available populations and ancients in East and Southeast Asia to infer Tai-Kadai-speaking populations’ admixture history and genetic structure. We observed a genetic substructure within the studied six populations in the PCA, ADMIXTURE, ChromoPainter, GLOBETROTTER, f-statistics, and qpWave analysis. The Dong, Zhuang, and Bouyei people had a strong genetic affinity with other Tai-Kadai-speaking and Austronesian groups in the surrounding area. However, Gelao showed an affinity to Sino-Tibetan groups, and Mulao people were genetically close to Hmong-Mien populations. qpAdm further illuminated that Gelao and Dong_Tongren composited more Han-related ancestry than Dong, Zhuang, Bouyei, and Mulao people. Meanwhile, we observed high frequencies of Y-chromosome haplogroup O in studied Tai-Kadai-speaking groups except for Gelao people with a high haplogroup N frequency. From the maternal side, haplogroup M7 was frequent in studied populations except for Tongren Dong, who had a high frequency of haplogroup B5. Our newly reported data are helpful for further exploring population dynamics in southern China.
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Feng Y, Zhang H, Wang Q, Jin X, Le C, Liu Y, Wang X, Jiang H, Ren Z. Whole mitochondrial genome analysis of Tai-Kadai-speaking populations in Southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1000493] [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
As a single matrilineal gene, human mitochondrial DNA plays a very important role in the study of population genetics. The whole mitogenome sequences of 287 individuals of the Tai-Kadai-speaking population in Guizhou were obtained. It was discovered that there were 82, 104, and 94 haplotypes in 83 Bouyei individuals, 107 Dong individuals, and 97 Sui individuals, respectively; and the haplotype diversity in Bouyei, Dong, and Sui groups was 1.000 ± 0.02, 0.9993 ± 0.0015, and 0.999 ± 0.002, respectively. The result of neutrality tests of the Tai-Kadai-speaking population in Guizhou showed significant negative values, and the analysis of mismatch distribution showed an obvious unimodal distribution. The results implied that Guizhou Tai-Kadai-speaking populations had high genetic diversities and may have experienced recent population expansion. In addition, the primary haplogroups of studied populations were M*, F, B, D, and R*, implying that they may origin from Southern China. The matrilineal genetic structure of the Tai-Kadai-speaking populations in Guizhou was analyzed by merging the mitogenome data of 79 worldwide populations as reference data. The results showed that there were close relationships between studied populations and other Tai-Kadai as well as some Austronesian populations in East and Southeast Asia. Overall, the mitogenome data generated in this study will provide important data for the study of genetic structure of Tai-Kadai speaking populations.
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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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Yang M, Yang X, Ren Z, He G, Zhang H, Wang Q, Liu Y, Zhang H, Ji J, Chen J, Guo J, Huang J, Wang CC. Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844761] [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
Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
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Bin X, Wang R, Huang Y, Wei R, Zhu K, Yang X, Ma H, He G, Guo J, Zhao J, Yang M, Chen J, Zhang X, Tao L, Liu Y, Huang X, Wang CC. Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China. Front Genet 2021; 12:735084. [PMID: 34616433 PMCID: PMC8489805 DOI: 10.3389/fgene.2021.735084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2-54.7%) and ancient coastal Southeast Asian-related ancestry (45.3-63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.
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Affiliation(s)
- Xiaoyun Bin
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youyi Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rongyao Wei
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | | | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiufeng Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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Luo C, Duan L, Li Y, Xie Q, Wang L, Ru K, Nazir S, Jawad M, Zhao Y, Wang F, Du Z, Peng D, Wen SQ, Qiu P, Fan H. Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups. Front Genet 2021; 12:676917. [PMID: 34108995 PMCID: PMC8181459 DOI: 10.3389/fgene.2021.676917] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Guangdong province is situated in the south of China with a population size of 113.46 million. Hakka is officially recognized as a branch of Han Chinese, and She is the official minority group in mainland China. There are approximately 25 million Hakka people who mainly live in the East and North regions of China, while there are only 0.7 million She people. The genetic characterization and forensic parameters of these two groups are poorly defined (She) or still need to be explored (Hakka). In this study, we have genotyped 475 unrelated Guangdong males (260 Hakka and 215 She) with Promega PowerPlex® Y23 System. A total of 176 and 155 different alleles were observed across all 23 Y-STRs for Guangdong Hakka (with a range of allele frequencies from 0.0038 to 0.7423) and Guangdong She (0.0047–0.8605), respectively. The gene diversity ranged from 0.4877 to 0.9671 (Guangdong Hakka) and 0.3277–0.9526 (Guangdong She), while the haplotype diversities were 0.9994 and 0.9939 for Guangdong Hakka and Guangdong She, with discrimination capacity values of 0.8885 and 0.5674, respectively. With reference to geographical and linguistic scales, the phylogenetic analyses showed us that Guangdong Hakka has a close relationship with Southern Han, and the genetic pool of Guangdong Hakka was influenced by surrounding Han populations. The predominant haplogroups of the Guangdong She group were O2-M122 and O2a2a1a2-M7, while Guangdong She clustered with other Tibeto-Burman language-speaking populations (Guizhou Tujia and Hunan Tujia), which shows us that the Guangdong She group is one of the branches of Tibeto-Burman populations and the Huonie dialect of She languages may be a branch of Tibeto-Burman language families.
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Affiliation(s)
- Chunfang Luo
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Lizhong Duan
- Beijing Municipal Public Security Bureau, Beijing, China
| | - Yanning Li
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,School of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Lingxiang Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Yifeng Zhao
- Nanjing Zhenghong Judicial Identification Institute, Nanjing, China
| | - Fenfen Wang
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Zhengming Du
- First Clinical Medical College, Hainan Medical University, Haikou, China
| | - Dehua Peng
- Heyuan Municipal Public Security Bureau, Heyuan, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Institute of Archaeological Science, Fudan University, Shanghai, China.,School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
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9
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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Song Z, Wang Q, Zhang H, Tang J, Wang Q, Zhang H, Yang M, Ji J, Ren Z, Wu Y, Huang J. Genetic structure and forensic characterization of 36 Y-chromosomal STR loci in Tibeto-Burman-speaking Yi population. Mol Genet Genomic Med 2021; 9:e1572. [PMID: 33448700 PMCID: PMC8077142 DOI: 10.1002/mgg3.1572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Male-specifically inherited Y-STRs have been widely used in population genetics and forensic investigations. METHODS We genotyped and analyzed Y chromosome haplotypes of 408 unrelated Tibeto-Burman-speaking Yi male individuals from Guizhou using Goldeneye® Y-PLUS kit. Population comparisons between the Guizhou Yi and 67 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. RESULTS A total of 389 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability, and discrimination capacity values were 0.9999, 0.0026, and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Our newly genotyped Yi samples show a close affinity with other Tibeto-Burman speaking groups in China and Southeast Asia. CONCLUSIONS The population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.
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Affiliation(s)
- Zhengyang Song
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Qian Wang
- Guiyang Judicial Expertise Center of Public SecurityGuiyangChina
| | - Han Zhang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jing Tang
- Guiyang Judicial Expertise Center of Public SecurityGuiyangChina
| | - Qiyan Wang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Hongling Zhang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Meiqing Yang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jingyan Ji
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Zheng Ren
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Yan Wu
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
| | - Jiang Huang
- Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina
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11
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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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12
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Guo J, Ji J, He G, Ren Z, Zhang H, Wang Q, Yang M, Nabijiang Y, Zhang Z, Zhang J, Huang J, Wang CC. Genetic structure and forensic characterisation of 19 X-chromosomal STR loci in Guizhou Sui population. Ann Hum Biol 2019; 46:246-253. [PMID: 31179782 DOI: 10.1080/03014460.2019.1623911] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background: Guizhou Sui people are an officially recognised ethnic group living in southwest China, but have seldom been studied genetically.Aim: To investigate the polymorphisms of 19 X-chromosome STR loci in a typical Sui population and enrich the East Asian X-STR reference database for forensic DNA analysis.Subjects and methods: A total of 400 Sui individuals (195 males and 205 females) were genotyped at 19 X-STR loci using the AGCU X19 STR Kit. The allele frequencies and forensic parameters were calculated and illustrated and the data of Guizhou Sui were merged with 18 other nationwide populations to explore genetic polymorphisms and population relationships.Results: A total of 215 alleles were observed with corresponding frequencies ranging from 0.0017-0.6512 in Sui using male and female pooled allele frequencies. Large values were observed, at least 0.9999999933, in combined powers of discrimination of Sui males and females, as well as the four mean paternity exclusion chances (MECs). The phylogenetic analysis among 19 populations showed that Sui have close genetic affinities with other Tai-Kadai populations, as well as the Sinitic populations living in southern China.Conclusions: The AGCU X-19 STRs are highly polymorphic and informative in Guizhou Sui people. The genetic relationships between Sui and other populations in China are generally consistent with the language classification and geographical distance.
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Affiliation(s)
- Jianxin Guo
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Guanglin He
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China.,Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, PR China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Yilizhati Nabijiang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Ziqian Zhang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Jing Zhang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Chuan-Chao Wang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
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Chen P, He G, Xing H, Gao H, Wang M, Zhao M, Luo L, Wu J, Yu J, Han Y. Forensic characteristics and phylogenetic analysis of 23 Y-STR loci in the Miao population from Guizhou province, southwest China. Ann Hum Biol 2019; 46:84-87. [PMID: 30782017 DOI: 10.1080/03014460.2019.1583374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND Investigation of haplotype/allele frequency data of Y-STR loci in ethnically diverse populations is essential for forensic reference database construction and genetic application. However, the population genetic characteristics of the Chinese Miao minority from Guizhou Province remain uncharacterised. AIM To assess forensic characteristics for 23 Y-Chromosomal STR loci in Guizhou Miao and explore population genetic relationships with geographically neighbouring populations. SUBJECTS AND METHODS Twenty-three Y-Chromosomal STRs were genotyped using the Powerplex® Y23 system in 103 unrelated Chinese Miao males from Guizhou Province, southwest China. Haplotypes and forensic parameters were obtained. Population relationships of Guizhou Miao with others were revealed using AMOVA and an MDS plot. RESULTS A total of 96 haplotypes were identified with overall haplotype diversity (HD) and discrimination capacity (DC) of 0.9985 and 0.9320, respectively. Genetic differentiation was observed with most of the comparison populations, prominently for Guizhou Shui. CONCLUSION The 23 Y-STR loci were highly polymorphic and discriminating in the Guizhou Miao population and could be used for forensic practice and population genetic studies. Population relationship analysis revealed Guizhou Miao had a close genetic relationship with geographically close Guizhou Gelao, as well as Han majorities derived from different regions.
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Affiliation(s)
- Pengyu Chen
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Guanglin He
- c Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine , Sichuan University , Sichuan , China
| | - Hao Xing
- b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Hongyan Gao
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Menge Wang
- c Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine , Sichuan University , Sichuan , China
| | - Min Zhao
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Li Luo
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Jian Wu
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Jian Yu
- a Center of Forensic Expertise , Affiliated Hospital of Zunyi Medical University , Zunyi , China.,b Department of Forensic Medicine , Zunyi Medical University , Zunyi , China
| | - Yanyan Han
- d Department of Nutrition and Food Hygiene, School of Public Health , Zunyi Medical University , Zunyi , China
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14
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Y-STRs’ genetic profiling of 1953 individuals from two Chinese Han populations (Guizhou and Shanxi). Forensic Sci Int Genet 2019; 38:e8-e10. [DOI: 10.1016/j.fsigen.2018.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/20/2018] [Accepted: 10/19/2018] [Indexed: 01/07/2023]
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15
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Fan H, Wang X, Chen H, Long R, Liang A, Li W, Chen J, Wang W, Qu Y, Song T, Zhang P, Deng J. The evaluation of forensic characteristics and the phylogenetic analysis of the Ong Be language-speaking population based on Y-STR. Forensic Sci Int Genet 2018; 37:e6-e11. [DOI: 10.1016/j.fsigen.2018.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/24/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
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Park HC, Lee EJ, Nam YH, Cho NS, Lim SK, Kim W. Genetic variation for three Y-STR loci: DYS390, DYS518, and DYS643. Int J Legal Med 2018; 133:1007-1013. [PMID: 30334084 DOI: 10.1007/s00414-018-1947-9] [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: 05/02/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022]
Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to analyze male-specific DNA. Although biallelic patterns due to duplication events have been detected at some loci, Y-STRs generally appear as a single peak except for DYS385 because the Y chromosome is haploid. STR loci in regions of segmental duplication by homologous recombination on the Y chromosome exhibit double allelic peaks, rather than single peaks. In this study, we report a bi- and triallelic pattern observed simultaneously in DYS390, DYS518, and DYS643. A bi- and triallelic pattern has not previously been observed simultaneously for these three loci. We also identified the copy number variation in the region including these loci by the microarray-based analysis. Given the peak balance pattern, the copy number variation, and the close position of these three loci on the Y chromosome, we consider that this phenomenon is caused by a segmental duplication in the euchromatin region. By ruling out mixed samples, a common interpretation of multiple peaks, these results have practical implications for the interpretation of Y-STR results in forensics analyses.
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Affiliation(s)
- Hyun-Chul Park
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Jung Lee
- Forensic Medicine Division, National Forensic Service Gwangju Institute, Gwangju, 57248, Republic of Korea
| | - Youn-Hyung Nam
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Nam-Soo Cho
- Forensic Medicine Division, National Forensic Service Daejeon Institute, Daejeon, 34054, Republic of Korea
| | - Si-Keun Lim
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea.
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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