Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures
DNA mixtures containing semen and vaginal fluid are common biological samples in forensic analysis. However, the analysis of semen–vaginal fluid mixtures remains challenging. In this study, to solve these problems, it is proposed to combine semen-specific CpG sites and closely related microhaplotype...
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The Royal Society
2025-01-01
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| Series: | Royal Society Open Science |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsos.241565 |
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| author | Dan Wen Hao Xing Xuan Tang Yue Wang Bowei Jiang Jienan Li Ying Liu Lagabaiyila Zha |
| author_facet | Dan Wen Hao Xing Xuan Tang Yue Wang Bowei Jiang Jienan Li Ying Liu Lagabaiyila Zha |
| author_sort | Dan Wen |
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| description | DNA mixtures containing semen and vaginal fluid are common biological samples in forensic analysis. However, the analysis of semen–vaginal fluid mixtures remains challenging. In this study, to solve these problems, it is proposed to combine semen-specific CpG sites and closely related microhaplotype sites to form a new composite genetic marker (semen-specific methylation-microhaplotype). Six methylation-microhaplotype loci were selected. To further improve discrimination power, five methylation-SNP loci were also included. The methylation levels and genotypes of these selected loci were obtained using massively parallel sequencing technology. Except for loci MMH04ZHA019 and MMH17ZHA059, the remaining nine loci were successfully sequenced. For the successfully sequenced loci, they performed well in identifying individuals and body fluids. An allele categorization model was developed using K-nearest neighbour algorithm, which was then used to predict allele types in semen–vaginal fluid mixtures. These loci were able to confirm the presence of semen and link semen to a true donor in semen–vaginal fluid mixtures with mixing ratios of 10:1, 9:1, 5:1, 4:1, 1:1, 1:3, 1:4, 1:8 and 1:9 (semen:vaginal fluid). This preliminary study suggests that this new composite genetic marker has great potential as a supplementary tool to commonly used genetic markers (STR, etc.) for analysing semen–vaginal fluid mixtures. |
| format | Article |
| id | doaj-art-f72d5b44898544518f68e41d5ca7472b |
| institution | Kabale University |
| issn | 2054-5703 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | The Royal Society |
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| series | Royal Society Open Science |
| spelling | doaj-art-f72d5b44898544518f68e41d5ca7472b2025-01-15T00:06:00ZengThe Royal SocietyRoyal Society Open Science2054-57032025-01-0112110.1098/rsos.241565Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixturesDan Wen0Hao Xing1Xuan Tang2Yue Wang3Bowei Jiang4Jienan Li5Ying Liu6Lagabaiyila Zha7Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaDepartment of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaDepartment of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaDepartment of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaThe First Research Institute of the Ministry of Public Security of P.R.C, No.1. Shouti South Road, Haidian District, Beijing 100044, People’s Republic of ChinaDepartment of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaDepartment of Oral Implantology, Xiangya Hospital of Stomatology, Central South University, No72. Xiangya Road, Changsha, Hunan 410028, People’s Republic of ChinaDepartment of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People’s Republic of ChinaDNA mixtures containing semen and vaginal fluid are common biological samples in forensic analysis. However, the analysis of semen–vaginal fluid mixtures remains challenging. In this study, to solve these problems, it is proposed to combine semen-specific CpG sites and closely related microhaplotype sites to form a new composite genetic marker (semen-specific methylation-microhaplotype). Six methylation-microhaplotype loci were selected. To further improve discrimination power, five methylation-SNP loci were also included. The methylation levels and genotypes of these selected loci were obtained using massively parallel sequencing technology. Except for loci MMH04ZHA019 and MMH17ZHA059, the remaining nine loci were successfully sequenced. For the successfully sequenced loci, they performed well in identifying individuals and body fluids. An allele categorization model was developed using K-nearest neighbour algorithm, which was then used to predict allele types in semen–vaginal fluid mixtures. These loci were able to confirm the presence of semen and link semen to a true donor in semen–vaginal fluid mixtures with mixing ratios of 10:1, 9:1, 5:1, 4:1, 1:1, 1:3, 1:4, 1:8 and 1:9 (semen:vaginal fluid). This preliminary study suggests that this new composite genetic marker has great potential as a supplementary tool to commonly used genetic markers (STR, etc.) for analysing semen–vaginal fluid mixtures.https://royalsocietypublishing.org/doi/10.1098/rsos.241565forensic geneticsDNA methylationmicrohaplotypesemen–vaginal fluid mixturesK-nearest neighbour algorithmmassively parallel sequencing |
| spellingShingle | Dan Wen Hao Xing Xuan Tang Yue Wang Bowei Jiang Jienan Li Ying Liu Lagabaiyila Zha Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures Royal Society Open Science forensic genetics DNA methylation microhaplotype semen–vaginal fluid mixtures K-nearest neighbour algorithm massively parallel sequencing |
| title | Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures |
| title_full | Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures |
| title_fullStr | Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures |
| title_full_unstemmed | Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures |
| title_short | Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen–vaginal fluid mixtures |
| title_sort | application of a new composite genetic marker semen specific methylation microhaplotype in the analysis of semen vaginal fluid mixtures |
| topic | forensic genetics DNA methylation microhaplotype semen–vaginal fluid mixtures K-nearest neighbour algorithm massively parallel sequencing |
| url | https://royalsocietypublishing.org/doi/10.1098/rsos.241565 |
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