YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database
Abstract Background The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challeng...
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BMC
2025-01-01
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| Online Access: | https://doi.org/10.1186/s12915-025-02122-0 |
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| author | Mengge Wang Shuhan Duan Qiuxia Sun Kaijun Liu Yan Liu Zhiyong Wang Xiangping Li Lanhai Wei Yunhui Liu Shengjie Nie Kun Zhou 10K_CPGDP consortium Yongxin Ma Huijun Yuan Bing Liu Lan Hu Chao Liu Guanglin He |
| author_facet | Mengge Wang Shuhan Duan Qiuxia Sun Kaijun Liu Yan Liu Zhiyong Wang Xiangping Li Lanhai Wei Yunhui Liu Shengjie Nie Kun Zhou 10K_CPGDP consortium Yongxin Ma Huijun Yuan Bing Liu Lan Hu Chao Liu Guanglin He |
| author_sort | Mengge Wang |
| collection | DOAJ |
| description | Abstract Background The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challenges posed by the lack of population-scale genomic databases, have the potential to revolutionize our approach to high-resolution, population-specific Y-chromosome panels and databases for anthropological and forensic applications. Objectives This study aimed to develop the highest-resolution Y-targeted sequencing panel, utilizing time-stamped, core phylogenetic informative mutations identified from high-coverage sequences in the YanHuang cohort. This panel is intended to provide a new tool for forensic complex pedigree search and paternal biogeographical ancestry inference, as well as explore the general patterns of the fine-scale paternal evolutionary history of ethnolinguistically diverse Chinese populations. Results The sequencing performance of the East Asian-specific Y-chromosomal panel, including 2999-core SNP variants, was found to be robust and reliable. The YHSeqY3000 panel was designed to capture the genetic diversity of Chinese paternal lineages from 3500 years ago, identifying 408 terminal lineages in 2097 individuals across 41 genetically and geographically distinct populations. We identified a fine-scale paternal substructure that was correlating with ancient population migrations and expansions. New evidence was provided for extensive gene flow events between minority ethnic groups and Han Chinese people, based on the integrative Chinese Paternal Genomic Diversity Database. Conclusions This work successfully integrated Y-chromosome-related basic genomic science with forensic and anthropological translational applications, emphasizing the necessity of comprehensively characterizing Y-chromosome genomic diversity from genomically under-representative populations. This is particularly important in the second phase of our population-specific medical or anthropological genomic cohorts, where dense sampling strategies are employed. |
| format | Article |
| id | doaj-art-e9ce2e4ac20346019040cc7699f78d1c |
| institution | Kabale University |
| issn | 1741-7007 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj-art-e9ce2e4ac20346019040cc7699f78d1c2025-01-26T12:52:38ZengBMCBMC Biology1741-70072025-01-0123112010.1186/s12915-025-02122-0YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity databaseMengge Wang0Shuhan Duan1Qiuxia Sun2Kaijun Liu3Yan Liu4Zhiyong Wang5Xiangping Li6Lanhai Wei7Yunhui Liu8Shengjie Nie9Kun Zhou1010K_CPGDP consortium11Yongxin Ma12Huijun Yuan13Bing Liu14Lan Hu15Chao Liu16Guanglin He17Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversitySchool of International Tourism and Culture, Guizhou Normal UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversitySchool of Ethnology and Anthropology, Inner Mongolia Normal UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversitySchool of Forensic Medicine, Kunming Medical UniversityMoFang Human Genome Research InstituteInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityDepartment of Medical Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityInstitute of Forensic Science, Ministry of Public SecurityInstitute of Forensic Science, Ministry of Public SecurityAnti-Drug Technology Center of Guangdong ProvinceInstitute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan UniversityAbstract Background The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challenges posed by the lack of population-scale genomic databases, have the potential to revolutionize our approach to high-resolution, population-specific Y-chromosome panels and databases for anthropological and forensic applications. Objectives This study aimed to develop the highest-resolution Y-targeted sequencing panel, utilizing time-stamped, core phylogenetic informative mutations identified from high-coverage sequences in the YanHuang cohort. This panel is intended to provide a new tool for forensic complex pedigree search and paternal biogeographical ancestry inference, as well as explore the general patterns of the fine-scale paternal evolutionary history of ethnolinguistically diverse Chinese populations. Results The sequencing performance of the East Asian-specific Y-chromosomal panel, including 2999-core SNP variants, was found to be robust and reliable. The YHSeqY3000 panel was designed to capture the genetic diversity of Chinese paternal lineages from 3500 years ago, identifying 408 terminal lineages in 2097 individuals across 41 genetically and geographically distinct populations. We identified a fine-scale paternal substructure that was correlating with ancient population migrations and expansions. New evidence was provided for extensive gene flow events between minority ethnic groups and Han Chinese people, based on the integrative Chinese Paternal Genomic Diversity Database. Conclusions This work successfully integrated Y-chromosome-related basic genomic science with forensic and anthropological translational applications, emphasizing the necessity of comprehensively characterizing Y-chromosome genomic diversity from genomically under-representative populations. This is particularly important in the second phase of our population-specific medical or anthropological genomic cohorts, where dense sampling strategies are employed.https://doi.org/10.1186/s12915-025-02122-0YanHuang cohortGenomic diversity databaseYHSeqY3000 panelForensic genomicsHuman evolution |
| spellingShingle | Mengge Wang Shuhan Duan Qiuxia Sun Kaijun Liu Yan Liu Zhiyong Wang Xiangping Li Lanhai Wei Yunhui Liu Shengjie Nie Kun Zhou 10K_CPGDP consortium Yongxin Ma Huijun Yuan Bing Liu Lan Hu Chao Liu Guanglin He YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database BMC Biology YanHuang cohort Genomic diversity database YHSeqY3000 panel Forensic genomics Human evolution |
| title | YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database |
| title_full | YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database |
| title_fullStr | YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database |
| title_full_unstemmed | YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database |
| title_short | YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database |
| title_sort | yhseqy3000 panel captures all founding lineages in the chinese paternal genomic diversity database |
| topic | YanHuang cohort Genomic diversity database YHSeqY3000 panel Forensic genomics Human evolution |
| url | https://doi.org/10.1186/s12915-025-02122-0 |
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