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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [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: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Song M, Zhou Y, Zhao C, Song F, Hou Y. YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs. Forensic Sci Int 2024; 361:112113. [PMID: 38936202 DOI: 10.1016/j.forsciint.2024.112113] [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: 03/18/2024] [Revised: 05/24/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope, which has been used in forensic scenarios. However, existing software aids in familial searching using Y-STRs (Y-chromosome short tandem repeats) to predict Y-SNP (Y-chromosome single nucleotide polymorphism) haplogroups, they often lack resolution. In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Leveraging existing datasets (219 haplogroups, 4064 samples in total), YHP predicts haplogroups with 0.923 accuracy under the highest haplogroup resolution, employing a random forest algorithm. YHP, available on Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-), facilitates high-resolution haplogroup prediction, haplotype mismatch analysis, and haplotype similarity comparison. Notably, it demonstrates efficacy in East Asian populations, benefiting from training data from eight distinct East Asian ethnic populations. Moreover, it enables seamless integration of additional training sets, extending its utility to diverse populations.
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Affiliation(s)
- Mengyuan Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chenxi Zhao
- College of Computer Science, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Zhang H, Yang M, Zhang H, Ren Z, Wang Q, Liu Y, Jin X, Ji J, Feng Y, Cai C, Ran Q, Li C, Huang J. Forensic features and phylogenetic structure survey of four populations from southwest China via the autosomal insertion/deletion markers. Forensic Sci Res 2024; 9:owad052. [PMID: 38765700 PMCID: PMC11102079 DOI: 10.1093/fsr/owad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/09/2023] [Indexed: 05/22/2024] Open
Abstract
Insertion/Deletion (InDel) polymorphisms, characterized by their smaller amplicons, reduced mutation rates, and compatibility with the prevalent capillary electrophoresis (CE) platforms in forensic laboratories, significantly contribute to the advancement and application of genetic analysis. Guizhou province in China serves as an important region for investigating the genetic structure, ethnic group origins, and human evolution. However, DNA data and the sampling of present-day populations are lacking, especially about the InDel markers. Here, we reported data on 47 autosomal InDels from 592 individuals from four populations in Guizhou (Han, Dong, Yi, and Chuanqing). Genotyping was performed with the AGCU InDel 50 kit to evaluate their utility for forensic purposes and to explore the population genetic structure. Our findings showed no significant deviations from Hardy-Weinberg and linkage equilibriums. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) for each population demonstrated that the kit could be applied to forensic individual identification and was an effective supplement for parentage testing. Genetic structure analyses, including principal component analysis, multidimensional scaling, genetic distance calculation, STRUCTURE, and phylogenetic analysis, highlighted that the genetic proximity of the studied populations correlates with linguistic, geographical, and cultural factors. The observed genetic variances within four research populations were less pronounced than those discerned between populations across different regions. Notably, the Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. These results underscore the potential of InDel markers in forensic science and provide insights into the genetic landscape and human evolution in multi-ethnic regions like Guizhou. Key points InDel markers show promise for forensic individual identification and parentage testing via the AGCU InDel 50 kit.Genetic analysis of Guizhou populations reveals correlations with linguistic, geographical, and cultural factors.Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi.
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Affiliation(s)
- Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Changsheng Cai
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qianchong Ran
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Jiang Huang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819. Leg Med (Tokyo) 2024; 67:102390. [PMID: 38190775 DOI: 10.1016/j.legalmed.2023.102390] [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: 09/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.
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Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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Ralf A, van Wersch B, Montiel González D, Kayser M. Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses. Genes (Basel) 2024; 15:227. [PMID: 38397216 PMCID: PMC10887500 DOI: 10.3390/genes15020227] [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: 01/19/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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Li J, Song F, Lang M, Xie M. Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230814. [PMID: 37736526 PMCID: PMC10509572 DOI: 10.1098/rsos.230814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
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Affiliation(s)
- Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Min Lang
- Sichuan University Law School, Sichuan University, Chengdu, People's Republic of China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, People's Republic of China
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Liu J, Jiang L, Zhao M, Du W, Wen Y, Li S, Zhang S, Fang F, Shen J, He G, Wang M, Dai H, Hou Y, Wang Z. Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection. Forensic Sci Int Genet 2022; 61:102786. [DOI: 10.1016/j.fsigen.2022.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/25/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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Fan GY. Assessing the factors influencing the performance of machine learning for classifying haplogroups from Y-STR haplotypes. Forensic Sci Int 2022; 340:111466. [PMID: 36150277 DOI: 10.1016/j.forsciint.2022.111466] [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: 07/28/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Two distinct genetic markers, single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs), exist simultaneously in the non-recombining portion of the Y chromosome. Because of their different rates of mutation, Y-STRs and Y-SNPs play distinct roles in forensic and evolutionary genetics. Current approaches to infer haplogroup status rely on genotyping lots of Y-SNP loci. Given the relationship between haplotype and haplogroup of a Y chromosome, a cost-effective strategy of Y-STRs typing had an advantage in haplogroup prediction. Many machine learning algorithms have sprung up for assigning a Y-STR haplotype to a haplogroup. However, a series of issues must be solved before the using of machine learning method in practice. Thus, the k-nearest neighbor (kNN) classifier was built respectively based on different situations in this study. We assessed different factors which may influence the performance of the kNN prediction model for classifying haplogroups. The training set was based on a diverse ground-truth data set comprising Y-STR haplotypes and corresponding Y-SNP haplogroups. Our results showed that combining different levels of haplogroups into the observations or transracial prediction was impractical. Moreover, using more slow mutation Y-STR loci in the category is good for promoting classification accuracy. The preconditions for an effective and accurate haplogroup assignment by the kNN classifier were revealed.
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Affiliation(s)
- Guang-Yao Fan
- Forensic Center, College of Medicine, Shaoxing University, Shaoxing 312000, China.
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Song M, Wang Z, Lyu Q, Ying J, Wu Q, Jiang L, Wang F, Zhou Y, Song F, Luo H, Hou Y, Song X, Ying B. Paternal genetic structure of the Qiang ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs. Forensic Sci Int Genet 2022; 61:102774. [PMID: 36156385 DOI: 10.1016/j.fsigen.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/02/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022]
Abstract
The Qiang population mainly lived in Beichuan Qiang Autonomous County of Sichuan Province. It is one of the nomads in China, distributed along the Minjiang River. The Qiang population was assumed to have great affinity with the Han, the largest ethnic group in China, when it refers to the genetic origin. Whereas, it is deeply understudied, especially from the Y chromosome. Here in this study, we used validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) panels to study the Qiang ethnic group to unravel their paternal genetic, forensic and phylogenetic characteristics. A total of 422 male samples of the Qiang ethnic group were genotyped by 233 Y-SNPs and 29 Y-STRs. Haplogroup O-M175 (N = 312) was the most predominant haplogroup in the Qiang ethnic group, followed by D-M174 (N = 32) and C-M130 (N = 32), N-M231 (N = 27), and Q-M242 (N = 15). After further subdivision, O2a-M324 (N = 213) accounted for the majority of haplogroup O. Haplogroup C2b-Z1338 (N = 29), D1a-CTS11577 (N = 30). O2a2b1a1a1-F42 (N = 48), O2a1b1a1a1a-F11 (N = 35), and O2a2b1a1-M117 (N = 21) represented other large terminal haplogroups. The results unveiled that Qiang ethnic group was a population with a high percentage of haplogroup O2a2b1a1a1-F42 (48/422) and O2a1b1a1a1a-F11 (35/422), and O2a2b1a1-M117 (21/422), which has never been reported. Its haplogroup distribution pattern was different from any of the Han populations, implying that the Qiang ethnic group had its unique genetic pattern. Mismatch analysis indicated that the biggest mismatch number in haplogroup O2a2b1a1a1-F42 was 21, while that of haplogroup O2a1b1a1a1a-F11 was 20. The haplotype diversity of the Qiang ethnic group equaled 0.999788, with 392 haplotypes observed, of which 367 haplotypes were unique. The haplogroup diversity of the Qiang ethnic group reached 0.9767, and 53 terminal haplogroups were observed (The haplogroup diversity of the Qiang ethnic group was the highest among Qiang and all Han subgroups, indicating the larger genetic diversity of the Qiang ethnic group.). Haplogroup O2a2b1a1a1-F42 was the most predominant haplogroup, including 11.37 % of the Qiang individuals. Median-joining trees showed gene flow between the Qiang and Han individuals. Our results indicated that 1) the highest genetic diversity was observed in the Qiang ethnic group compared to any of the former studied Chinese population, suggesting that the Qiang might be an older paternal branch; 2) the haplogroup D-M174 individuals of Qiang, Tibetans and Japanese distributed in three different subclades, which was unable to identify through low-resolution Y-SNP panel; and 3) the Qiang had lower proportion of haplogroup D compared to Yi and Tibetan ethnic groups, showing that the Qiang had less genetic communication with them than with Han Chinese.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Lyu
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan 622750, Sichuan, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai 621100, Sichuan, China
| | - Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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Hu L, Zhu W, Yu J, Chen Y, Yan J, Liao Q, Zhang T. Family-based improvement for health literacy among the Yi nationality (FAMILY) in Liangshan: protocol of an open cohort stepped wedge cluster randomized controlled trial. BMC Public Health 2022; 22:1543. [PMID: 35964063 PMCID: PMC9375317 DOI: 10.1186/s12889-022-13782-w] [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: 07/03/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Improvement of health literacy constitutes a cornerstone to improving public health. However, the overall health literacy of Liangshan Yi Autonomous Prefecture (Liangshan Prefecture) in the southwest Sichuan Province of China has kept extremely low for a long time. How to improve health literacy of the Yi nationality residents is key to be urgently solved. Notably, Family Branch System is a distinctive patrilineal bloodline organization of Yi nationality, which plays an important role in the daily life of Yi nationality. Meanwhile, Contracted Family Doctor Services is conducted in Liangshan Prefecture. Therefore, this study proposes an intervention model of health education based on Family Branch System and Contracted Family Doctor Services, which is a Family-based Improvement for Health Literacy among the Yi nationality (FAMILY) in Liangshan, when improving traditional Innovative Care for Chronic Conditions Framework (ICCC) framework. METHODS An open cohort stepped wedge cluster randomized trial design is used to implement health literacy education interventions including project preparation, core group building, promotion within family branch and competition between family branches while using Contracted Family Doctor Services as control measure. The study will be conducted among Yi nationality residents in Meigu County and Yanyuan County, with health literacy level of residents as the primary outcome. Finally, mixed-effects model and causal inference method will be used to evaluate intervention effect. DISCUSSION This study highlights family, using the unique Family Branch System and Contracted Family Doctor Services in Liangshan Prefecture to design intervention among improved ICCC framework, and combines the mixed-effects model with complier average causal effects (CACE) to estimate the intervention effect under non-compliance for the first time. Besides, other key technologies to be adopted include construction of electronic questionnaire quality control system, with quality control based on artificial intelligence. This trial contributes to exploring an effective way to improve health literacy of Yi nationality residents in Liangshan Prefecture, which will provide reference for other areas, especially poor areas, to improve residents' health literacy. TRIAL REGISTRATION ISRCTN11299863 on June 1, 2022; https://www.isrctn.com/ .
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Affiliation(s)
- Lin Hu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China
| | - Wenhui Zhu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China
| | - Jie Yu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China
| | - Ying Chen
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China
| | - Jingmin Yan
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China
| | - Qiang Liao
- Liangshan Prefecture Center for Disease Control and Prevention, Xichang, 615000, Sichuan Province, China
| | - Tao Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Renmin South Road 3rd Section NO.16, Chengdu, 610041, Sichuan Province, China.
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Wang F, Song F, Song M, Luo H, Hou Y. Genetic structure and paternal admixture of the modern Chinese Zhuang population based on 37 Y-STRs and 233 Y-SNPs. Forensic Sci Int Genet 2022; 58:102681. [DOI: 10.1016/j.fsigen.2022.102681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/05/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022]
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Cheng J, Song B, Fu J, Zheng X, He T, Fu J. Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China. Sci Rep 2021; 11:16327. [PMID: 34381158 PMCID: PMC8357927 DOI: 10.1038/s41598-021-95883-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
The Yi is one of fifty-six ethnic populations and one of the most ancient ethnic groups in China. The Liangshan Yi Autonomous Prefecture (LYAP) in Sichuan Province has the single largest Yi community in China. To establish a Yi population database in the LYAP of Sichuan in China, a Goldeneye™ DNA Identification System 20A Kit with 19 autosomal STRs (short tandem repeats) was used. As a result, the total discrimination power (TDP) and the cumulative probability of exclusion (CPE) for these STRs in 1016 unrelated individuals were 0.999999999999999999999897 and 0.9999999597, respectively. Totals of 273 alleles for 19 STRs and 8-22 alleles for each locus were found. The allelic frequencies ranged from 0.0005 to 0.5084. The forensic parameter averages of these STRs were as follows: observed heterozygosity (Hobs) of 78.44%, expected heterozygosity (Hexp) of 79.89%, discrimination power (DP) of 92.66%, and probability of exclusion (PE) of 57.68%. Penta E presented the highest levels of Hobs and DP, whereas TPOX showed the lowest Hobs and DP values. Nei's standard genetic distance matrix among 31 populations found that the nearest genetic distance to the Yi population was the Sichuan Han (0.0056). Altogether, we first reported the forensic parameters and allele frequencies of 19 autosomal STRs of the Yi group in Liangshan. These 19 STR makers could provide highly informative polymorphisms for individual identification, paternity testing and genetic population analyses.
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Affiliation(s)
- Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Binghui Song
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiaoli Zheng
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Tao He
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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