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Patta C, Singchat W, Thatukan C, Jaito W, Kumnan N, Chalermwong P, Panthum T, Budi T, Wongloet W, Wattanadilokchatkun P, Thong T, Ahmad SF, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Optimizing Bangkaew dog breed identification using DNA technology. Genes Genomics 2024; 46:659-669. [PMID: 38687435 DOI: 10.1007/s13258-024-01510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/04/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND The Bangkaew dog is an indigenous dog breed in the Phitsanulok province of Thailand. This breed is recognized by the Fédération Cynologique Internationale (FCI), a global canine organization. The unique traits of the Bangkaew breed lead to purebred selection for breeding, while only their traits and pedigree from parental history are recorded. Determination of the risk of inbreeding depression and the origin of unknown DNA profiles is essential due to the challenges in predicting puppy characteristics, which are crucial for breed management and conservation. OBJECTIVE This study aimed to emphasize that current allelic frequency data for the Bangkaew dog breed must be considered for precise individual identification. METHODS Approximately 82 Bangkaew dogs from various Thai localities were studied using 15 microsatellite markers for genotypic monitoring and individual identification. Maternal genetic inheritance was assessed via mtDNA D-loop analysis. RESULTS The results revealed high genetic diversity in the Bangkaew breed, indicating low potential for inbreeding. We also found that using a 15 loci microsatellite panel was effective for the identification of Bangkaew dogs. The optimized 10 loci microsatellite genotyping panel developed in this study presents improved identification testing efficiency, promoting both time- and cost-effectiveness. CONCLUSION Analysis of microsatellite DNA markers in Bangkaew dogs using an optimized panel of 10 loci selected from 15 loci effectively facilitated individual identification. This approach not only enhances time and cost efficiency, but also provides accurate allelic frequency estimates, which are crucial for the realistic evaluation of DNA evidence.
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Affiliation(s)
- Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, 10520, Bangkok, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, 10520, Bangkok, Thailand
| | - Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, 10520, Bangkok, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, 10520, Bangkok, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, 10520, Bangkok, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, 10900, Bangkok, Thailand.
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Paulet J, Molina A, Beltzung B, Suzumura T, Yamamoto S, Sueur C. Deep learning for automatic facial detection and recognition in Japanese macaques: illuminating social networks. Primates 2024:10.1007/s10329-024-01137-5. [PMID: 38758427 DOI: 10.1007/s10329-024-01137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Individual identification plays a pivotal role in ecology and ethology, notably as a tool for complex social structures understanding. However, traditional identification methods often involve invasive physical tags and can prove both disruptive for animals and time-intensive for researchers. In recent years, the integration of deep learning in research has offered new methodological perspectives through the automatisation of complex tasks. Harnessing object detection and recognition technologies is increasingly used by researchers to achieve identification on video footage. This study represents a preliminary exploration into the development of a non-invasive tool for face detection and individual identification of Japanese macaques (Macaca fuscata) through deep learning. The ultimate goal of this research is, using identification done on the dataset, to automatically generate a social network representation of the studied population. The current main results are promising: (i) the creation of a Japanese macaques' face detector (Faster-RCNN model), reaching an accuracy of 82.2% and (ii) the creation of an individual recogniser for the Kōjima Island macaque population (YOLOv8n model), reaching an accuracy of 83%. We also created a Kōjima population social network by traditional methods, based on co-occurrences on videos. Thus, we provide a benchmark against which the automatically generated network will be assessed for reliability. These preliminary results are a testament to the potential of this approach to provide the scientific community with a tool for tracking individuals and social network studies in Japanese macaques.
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Affiliation(s)
- Julien Paulet
- Université Jean Monnet, Saint-Etienne, France
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Axel Molina
- Ecole Normale Supérieure, Université PCL, Paris, France
| | | | | | - Shinya Yamamoto
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Kyoto University Institute for Advanced Study, Kyoto, Japan
| | - Cédric Sueur
- Université de Strasbourg, IPHC UMR7178, CNRS, Strasbourg, France.
- ANTHROPO-LAB, ETHICS EA 7446, Université Catholique de Lille, Lille, France.
- Institut Universitaire de France, Paris, France.
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Liu J, Zheng Y, Zheng X, Li T, Wei R, Du W, Wang Z. Development and validation of a novel 30-plex STR assay for canine individual identification and parentage testing. Forensic Sci Int Genet 2024; 71:103056. [PMID: 38678763 DOI: 10.1016/j.fsigen.2024.103056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Domestic dogs are helpers in outdoor human work and companions for families; thus, individual canine identification and parentage testing are crucial in certain fields, including forensics and breeding programs. In this study, a six-dye fluorescent labeling multiplex amplification system containing 29 canine short tandem repeats (STRs) and the sex-determining marker DAmel was developed. The system was called the Tronfo Canine 30-plex STR Kit and was further validated according to the Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Wildlife Forensics guidelines, including tests for PCR conditions, precision, species specificity, sensitivity, stability, repeatability and reproducibility, a population study, and a study of 16 paternity test cases. The results indicated that the novel canine STR assay was accurate, specific, reproducible, stable, and robust. Complete profiles were obtained with 31.25 pg of canine DNA. Additionally, 500 unrelated canine individuals were investigated using this novel system, and the combined power of discrimination and exclusion values were 0.999999999999999999 and 0.999996451039850, respectively. These results suggest that the Tronfo Canine 30-plex STR Kit is highly polymorphic, informative, and suitable for individual canine identification and parentage testing.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yangyang Zheng
- Guangdong Homy Genetics Incorporation, Foshan 528000, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Tao Li
- Nanchang Police Dog Base of the Ministry of Public Security, Nanchang 330000, China
| | - Rongxing Wei
- Nanchang Police Dog Base of the Ministry of Public Security, Nanchang 330000, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan 528000, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Lee J, Lee J. Discovering individual fingerprints in resting-state functional connectivity using deep neural networks. Hum Brain Mapp 2024; 45:e26561. [PMID: 38096866 PMCID: PMC10789221 DOI: 10.1002/hbm.26561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024] Open
Abstract
Non-negligible idiosyncrasy due to interindividual differences is an ongoing issue in resting-state functional MRI (rfMRI) analysis. We show that a deep neural network (DNN) can be employed for individual identification by learning important features from the time-varying functional connectivity (FC) of rfMRI in the Human Connectome Project. We employed the trained DNN to identify individuals from an independent dataset acquired at our institution. The results revealed that the DNN could successfully identify 300 individuals with an error rate of 2.9% using 15 s time-window and 870 individuals with an error rate of 6.7%. A trained DNN with nonlinear hidden layers led to the proposal of the "fingerprint of FC" (fpFC) as representative edges of individual FC. The fpFCs for individuals exhibited commonly important and individual-specific edges across time-window lengths (from 5 min to 15 s). Furthermore, the utility of our model for another group of subjects was validated, supporting the feasibility of our technique in the context of transfer learning. In conclusion, our study offers an insight into the discovery of the intrinsic mode of the human brain using whole-brain resting-state FC and DNNs.
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Affiliation(s)
- Juhyeon Lee
- Department of Brain and Cognitive EngineeringKorea UniversitySeoulRepublic of Korea
| | - Jong‐Hwan Lee
- Department of Brain and Cognitive EngineeringKorea UniversitySeoulRepublic of Korea
- Interdisciplinary Program in Precision Public HealthKorea UniversitySeoulSouth Korea
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyBostonMassachusettsUSA
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Liu Y, Fan J, Zhang M, Liu Z, Wang J, Liu J, Li Z, Yang F, Zhang G. A human identification system for hair shaft using RNA polymorphism. Forensic Sci Int Genet 2023; 67:102929. [PMID: 37611365 DOI: 10.1016/j.fsigen.2023.102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Hair is one of the common pieces of evidence at crime scenes, with abundant mitochondrial DNA but limited nuclear DNA in its shaft. It also helps to narrow the investigation scope to maternal lineage but fails to provide unique individual information. We assumed that RNA in hair shafts would be an alternative resource used to perform human identification based on the facts that (1) RNA retains the polymorphic information; (2) the multi-copy of RNA in a cell resists degradation as compared to the one-copy of nuclear DNA. In this study, we explored the potential of RNA polymorphism in hair shafts for forensic individual identification. A SNaPshot typing system was constructed using 18 SNPs located on 11 genes (ABCA13, AHNAK, EXPH5, KMT2D, KRT35, PPP1R15A, RBM33, S100A5, TBC1D4, TMC5, TRPV2). The RNA typing system was evaluated for sensitivity, species specificity, and feasibility for aged hair samples. Hair samples from a Shanxi population in China were used for the population study of the system. The detection limit of the assay was 2 ng RNA. The CDP of these 11 genes was 0.999969 in the Shanxi population. We also identified the concordance of the RNA and DNA typing results. In summary, we developed an RNA typing method to perform human identification from hair shafts, which performed as accurately as nuclear DNA typing. Our method provides a potential basis for solving the human identification problem from hair shafts, as well as other biological materials that lack nuclear DNA.
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Affiliation(s)
- Yao Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiajia Fan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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Huo DM, Mao XY, Mo WW, Zhao FM, Du M, Sun RR. 3D- 3D dentition superimposition for individual identification: A study of an Eastern Chinese population. Forensic Sci Int 2023; 350:111801. [PMID: 37536075 DOI: 10.1016/j.forsciint.2023.111801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
Recently, 3D dental intraoral scanning technology has been developed rapidly and applied widely in everyday dental practice. Since 3D dental scanning could provide valuable personal information, it enabled researchers to develop novel procedures for individual identification through 3D-3D dentition superimposition. This study aimed to test the applicability of this method in an Eastern Chinese population and propose a threshold for personal identification. For this purpose, 40 volunteers were recruited, and the initial 80 (upper and lower) 3D intraoral scans (IOS) were collected. After one year, 80 IOS of these volunteers were repeatedly collected. In addition, the other 120 IOS of 60 patients were extracted from the database. The 3D models were trimmed, aligned, and superimposed via Geomagic Control X software, and then the root mean square (RMS) value of point-to-point distance between the two models was calculated. The superimposition of two IOS belonging to the same individual was considered as a match, and superimposition of two IOS belonging to different individuals was considered as a mismatch. Totally, superimpositions of 80 matches and 3120 mismatches were obtained. Intra- and inter-observer errors were assessed through the calculation of relative technical error of measurement (rTEM). Mann-Whitney U test verified possible statistically significant differences between matches and mismatches (P < 0.05). The rTEM of intra- and inter-observer repeatability analyses was lower than 4.7 %. The range of RMS value was 0.05-0.18 mm in matches and 0.72-2.28 mm in mismatches without overlapping. The percentage of accurate identification reached 100 % in blind test through an arbitrary RMS threshold of 0.45 mm. The results indicated that individual identification through the 3D-3D dentition superimposition was effective in Eastern Chinese population. Successful identification could be achieved with high probability when the RMS value of the point-to-point distance of two dentitions is <0.45 mm.
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Affiliation(s)
- De-Min Huo
- Shanghai Key Laboratory of Forensic Medicine, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai 200063, China; Institute of Criminal Science and Technology, Jiading Branch of Shanghai Public Security Bureau, Shanghai 201822, China
| | - Xiao-Yan Mao
- Department of Orthodontics, Shanghai Jiading District Dental Research Institute, Shanghai 201800, China
| | - Wei-Wei Mo
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai 201424, China
| | - Fei-Ming Zhao
- School of Maritime Economics and Management of Dalian Maritime University, Dalian 116026, China
| | - Meng Du
- Shanghai Key Laboratory of Forensic Medicine, Key Laboratory of Forensic Science, Ministry of Justice, Shanghai 200063, China; Institute of Criminal Science and Technology, Jiading Branch of Shanghai Public Security Bureau, Shanghai 201822, China
| | - Rong-Rong Sun
- Department of Orthodontics, School & Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai 200072, China.
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Lai L, Liu L, Wang Y, Liu S, Zhang J, Zheng X. QR code technology in individual identification training provides an introduction in hands-on forensic DNA genotyping to medical students. BMC Med Educ 2023; 23:314. [PMID: 37147637 PMCID: PMC10161171 DOI: 10.1186/s12909-023-04284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Forensic biology is a subject in the field of forensic science that stresses practical teaching and training in laboratory skills. Visualization of deoxyribonucleic acid (DNA) profiles is important in individual identification and is easily performed by well-trained examiners. Therefore, developing a novel training project for obtaining individual DNA profiles can improve the quality of teaching for medical students or trainees. DNA profiles based on quick response (QR) codes can also be applied to practical teaching and operation training for individual identification. METHODS A novel training project was developed through an experimental course in forensic biology. Blood samples and buccal swabs with oral epithelial cells, as used in the forensic DNA laboratory, were obtained from medical students at Fujian Medical University. DNA was isolated, and a number of short tandem repeat (STR) loci were used as genetic markers to generate DNA profiles. The students converted DNA profiles and individual information into a QR code. The QR code could then be scanned by a mobile phone for consulting and retrieval. Gene identity cards with QR codes were produced and provided to every student. The participation rate and passing rate of students who participated in the novel training project were calculated and compared with those of students in the traditional experimental course, and a chi-square test was carried out by SPSS 23.0 software to evaluate the teaching effectiveness. p < 0.05 indicated significant differences. In addition, a survey was conducted to investigate the likelihood of using of gene identity cards with QR codes in the future. RESULTS A total of 54 of 91 medical students who studied forensic biology participated in the novel training project in 2021. Only 31 of 78 students who studied forensic biology participated in the traditional experimental course in 2020. The participation rate in the novel training project was 24% higher than that of the traditional experimental course. The participants in the novel training project showed better performance in forensic biological handling techniques. The passing rate of the students in the forensic biology course with the novel training project was approximately 17% higher than that of the students in the former course. The participation rates and passing rates of the two groups were significantly different (χ = 6.452, p = 0.008 and χ = 11.043, p = 0.001). In the novel training project, all participants made 54 gene identity cards with QR codes. Furthermore, in the DNA profiles of four African students who participated, we found two rare alleles that were not discovered in Asians. The survey showed that the use of gene identity cards with QR codes was accepted by most participants, and the likelihood of future utilization was 78%. CONCLUSION We established a novel training project to promote the learning activities of medical students in experimental forensic biology courses. The participants showed great interest in using gene identity cards with QR codes to store general individual identity information and DNA profiles. They also examined the genetic population differences between different races based on DNA profiles. Hence, the novel training project could be useful for training workshops, forensic experimental courses, and medical big data research.
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Affiliation(s)
- Li Lai
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China.
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China.
| | - Li Liu
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Yaochen Wang
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Shanlong Liu
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
- Central Laboratory of Fujian Provincial Hospital, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Jiancheng Zhang
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
| | - Xiaochun Zheng
- Provincial Clinical College of Fujian Medical University, No.134 East Road, Fujian, Fuzhou, 350001, China
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Bu WQ, Guo YX, Zhang D, Du SY, Han MQ, Wu ZX, Tang Y, Chen T, Guo YC, Meng HT. Automatic sex estimation using deep convolutional neural network based on orthopantomogram images. Forensic Sci Int 2023; 348:111704. [PMID: 37094502 DOI: 10.1016/j.forsciint.2023.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/09/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023]
Abstract
Sex estimation is very important in forensic applications as part of individual identification. Morphological sex estimation methods predominantly focus on anatomical measurements. Based on the close relationship between sex chromosome genes and facial characterization, craniofacial hard tissues morphology shows sex dimorphism. In order to establish a more labor-saving, rapid, and accurate reference for sex estimation, the study investigated a deep learning network-based artificial intelligence (AI) model using orthopantomograms (OPG) to estimate sex in northern Chinese subjects. In total, 10703 OPG images were divided into training (80%), validation (10%), and test sets (10%). At the same time, different age thresholds were selected to compare the accuracy differences between adults and minors. The accuracy of sex estimation using CNN (convolutional neural network) model was higher for adults (90.97%) compared with minors (82.64%). This work demonstrated that the proposed model trained with a large dataset could be used in automatic morphological sex-related identification with favorable performance and practical significance in forensic science for adults in northern China, while also providing a reference for minors to some extent.
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Affiliation(s)
- Wen-Qing Bu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Dong Zhang
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, People's Republic of China
| | - Shao-Yi Du
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, People's Republic of China
| | - Meng-Qi Han
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Zi-Xuan Wu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Yu Tang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Teng Chen
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an 710004, Shaanxi, People's Republic of China
| | - Yu-Cheng Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China; National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, People's Republic of China.
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an 710004, Shaanxi, People's Republic of China.
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9
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Li Y, Liu A, Fu X, Mckeown MJ, Wang ZJ, Chen X. Atlas-guided parcellation: Individualized functionally-homogenous parcellation in cerebral cortex. Comput Biol Med 2022; 150:106078. [PMID: 36155266 DOI: 10.1016/j.compbiomed.2022.106078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/03/2022] [Indexed: 11/03/2022]
Abstract
Resting-state Magnetic resonance imaging-based parcellation aims to group the voxels/vertices non-invasively based on their connectivity profiles, which has achieved great success in understanding the fundamental organizational principles of the human brain. Given the substantial inter-individual variability, the increasing number of studies focus on individual parcellation. However, current methods perform individual parcellations independently or are based on the group prior, requiring expensive computational costs, precise parcel alignment, and extra group information. In this work, an efficient and flexible parcellation framework of individual cerebral cortex was proposed based on a region growing algorithm by merging the unassigned and neighbor vertex with the highest-correlated parcel iteratively. It considered both consistency with prior atlases and individualized functional homogeneity of parcels, which can be applied to a single individual without parcel alignment and group information. The proposed framework was leveraged to 100 unrelated subjects for functional homogeneity comparison and individual identification, and 186 patients with Parkison's disease for symptom prediction. Results demonstrated our framework outperformed other methods in functional homogeneity, and the generated parcellations provided 100% individual identification accuracy. Moreover, the default mode network (DMN) exhibited higher functional homogeneity, intra-subject parcel reproducibility and fingerprinting accuracy, while the sensorimotor network did the opposite, reflecting that the DMN is the most representative, stable, and individual-identifiable network in the resting state. The correlation analysis showed that the severity of the disease symptoms was related negatively to the similarity of individual parcellation and the atlases of healthy populations. The disease severity can be correctly predicted using machine learning models based on individual topographic features such as parcel similarity and parcel size. In summary, the proposed framework not only significantly improves the functional homogeneity but also captures individualized and disease-related brain topography, serving as a potential tool to explore brain function and disease in the future.
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Affiliation(s)
- Yu Li
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China; School of Information Science and Technology, University of Science and Technology of China, Hefei, 230026, China
| | - Aiping Liu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China; School of Information Science and Technology, University of Science and Technology of China, Hefei, 230026, China.
| | - Xueyang Fu
- School of Information Science and Technology, University of Science and Technology of China, Hefei, 230026, China
| | - Martin J Mckeown
- Pacific Parkinson's Research Centre, Vancouver, British Columbia, V6E 2M6, Canada; Department of Medicine (Neurology), University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada
| | - Z Jane Wang
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Xun Chen
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China; School of Information Science and Technology, University of Science and Technology of China, Hefei, 230026, China
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10
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Hommelsen M, Viswanathan S, Daun S. Robustness of individualized inferences from longitudinal resting state EEG dynamics. Eur J Neurosci 2022; 56:3613-3644. [PMID: 35445438 DOI: 10.1111/ejn.15673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 11/27/2022]
Abstract
Tracking how individual human brains change over extended timescales is crucial to clinical scenarios ranging from stroke recovery to healthy aging. The use of resting state (RS) activity for tracking is a promising possibility. However, it is unresolved how a person's RS activity over time can be decoded to distinguish neurophysiological changes from confounding cognitive variability. Here, we develop a method to screen RS activity changes for these confounding effects by formulating it as a problem of change classification. We demonstrate a novel solution to change classification by linking individual-specific change to inter-individual differences. Individual RS-EEG was acquired over five consecutive days including task states devised to simulate the effects of inter-day cognitive variation. As inter-individual differences are shaped by neurophysiological differences, the inter-individual differences in RS activity on one day were analyzed (using machine learning) to identify distinctive configurations in each individual's RS activity. Using this configuration as a decision-rule, an individual could be re-identified from 2-second samples of the instantaneous oscillatory power spectrum acquired on a different day both from RS and confounded-RS with a limited loss in accuracy. Importantly, the low loss in accuracy in cross-day vs same-day classification was achieved with classifiers that combined information from multiple frequency bands at channels across the scalp (with a concentration at characteristic fronto-central and occipital zones). Taken together, these findings support the technical feasibility of screening RS activity for confounding effects and the suitability of longitudinal RS for robust individualized inferences about neurophysiological change in health and disease.
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Affiliation(s)
- Maximilian Hommelsen
- Cognitive Neuroscience, Institute of Neuroscience and Medicine (INM-3), Jülich, Germany
| | | | - Silvia Daun
- Cognitive Neuroscience, Institute of Neuroscience and Medicine (INM-3), Jülich, Germany.,Institute of Zoology, University of Cologne, Cologne, Germany
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11
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Tie J, Uchigasaki S, Isobe E, Iwakami E, Okuda T. Detection of deletion/insertion polymorphism profiles from single human hair shafts. Mol Biol Rep 2021; 49:1017-1025. [PMID: 34739693 DOI: 10.1007/s11033-021-06921-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Hair is a frequently encountered biological evidence in personal identification. The amount of nuclear DNA that can be extracted from a single strand of rootless hair is most limited, making the detection of short tandem repeat (STR) polymorphisms difficult. To overcome these limitations, deletion/insertion polymorphisms (DIP) as a new type of genetic marker have shown their benefits in detecting low-copy-number DNA. The Investigator DIPplex kit contains 30 biallelic autosomal DIP and amelogenin. The analysis of DIPs combines the advantages of both STR and single nucleotide polymorphism analyses. Thus, this study aimed to detect the DIP distribution of individual hair shafts from individuals. METHODS AND RESULTS DNA was extracted from the shaft of fresh, aged, and shed hair. After DNA was evaluated, the DIP profiles were detected by capillary electrophoresis. The results indicated that the amount of DNA extracted from hair roots was much higher than that from the hair shafts in the same individual for all samples. The degradation index values of DNA from the aged hair shafts were highest. It is classified to be "mildly degraded." Compared with their hair roots, the full DIP profiles were detected for fresh hair, 70% for aged hair, and 92% for shed hair. Contrarily, except for fresh hair shafts, only three STR loci of the aged and shed strands of hair could be genotyped using AmpFlSTR MiniFiler PCR Amplification Kit. CONCLUSIONS These results indicate that the detection of DIP profile is an effective tool for personal identification from hair shafts, including aged hair.
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Affiliation(s)
- Jian Tie
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan.
| | - Seisaku Uchigasaki
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Eiji Isobe
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Etsuko Iwakami
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
| | - Takahisa Okuda
- Division of Legal Medicine, Department of Social Medicine, Nihon University School of Medicine, Tokyo, 1738610, Japan
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12
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Zhao GB, Ma GJ, Zhang C, Kang KL, Li SJ, Wang L. BGISEQ-500RS sequencing of a 448-plex SNP panel for forensic individual identification and kinship analysis. Forensic Sci Int Genet 2021; 55:102580. [PMID: 34454122 DOI: 10.1016/j.fsigen.2021.102580] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/13/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023]
Abstract
Next generation sequencing (NGS)-based single nucleotide polymorphism (SNP) genotyping is widely used in the field of forensics. SNP genotyping data from several NGS platforms have been published, but forensic application trials of DNA nanoball sequencing platforms have been very limited. In this work, we developed a 448-plex SNP panel on the BGISEQ-500RS platform. The sequencing metrics of a total of 261 samples that were sequenced with this panel are reported in detail. The average sequencing depth was 8373 × and the average heterozygosity of the 448-plex assay was 0.85. Sensitivity analysis showed that 325 SNPs were successfully genotyped with as little as 50 pg of genomic DNA, with the mean quality score of the sequencing data above Q30. Forensic parameters were calculated based on the data of 142 unrelated Chinese Han individuals and the combined matching probability was as low as 5.21 × 10-101. Kinship analyses based on experiments and computer simulations showed that the 448-panel was as effective as the ForenSeq™ DNA Signature Prep Kit for second-degree kinship identification, and when the two panels were merged, the related pairs were almost completely distinguished from unrelated pairs. The 448-plex SNP panel on the BGISEQ-500RS platform provides a powerful tool for forensic individual identification and kinship analysis.
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Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Guan-Ju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Shu-Jin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
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Scarpulla E, Boattini A, Cozzo M, Giangregorio P, Ciucci P, Mucci N, Randi E, Davoli F. First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach. BMC Genomics 2021; 22:623. [PMID: 34407764 PMCID: PMC8371798 DOI: 10.1186/s12864-021-07915-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. RESULTS We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. CONCLUSIONS The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.
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Affiliation(s)
- Erminia Scarpulla
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Mario Cozzo
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Patrizia Giangregorio
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnology "Charles Darwin" (BBCD), Sapienza University of Rome, Rome, Italy
| | - Nadia Mucci
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Faculty of Engineering and Science, Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | - Francesca Davoli
- Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca' Fornacetta, 9 - 40064 Ozzano dell'Emilia, Bologna, Italy.
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De R, Kumar V, Ankit K, Khan KA, Kumar H, Kumar N, Habib B, Goyal SP. Cross-amplification of ungulate microsatellite markers in the endemic Indian antelope or blackbuck (Antilope cervicapra) for population monitoring and conservation genetics studies in south Asia. Mol Biol Rep 2021; 48:5151-60. [PMID: 34213708 DOI: 10.1007/s11033-021-06514-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023]
Abstract
The Indian antelope or blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent, inhabiting scrublands and dry grasslands. Most of the blackbuck populations are small, isolated, and threatened by habitat fragmentation and degradation. Management of such disjunct populations requires genetic characterization, which is critical for assessing hazards of stochastic events and inbreeding. Addressing the scarcity of such information on the blackbuck, we describe a novel panel of microsatellite markers that could be used to monitor blackbuck demography and population genetic parameters using non-invasive faecal sampling. We screened microsatellites (n = 40) that had been reported to amplify in bovid and cervid species using faecal samples of the blackbuck collected from Kaimoor Wildlife Sanctuary, Uttar Pradesh, India and its vicinities. We selected 12 markers for amplification using faecal DNA extracts (n = 140) in three multiplex reactions. We observed a mean amplification success rate of 72.4% across loci (92.1-25.7%) with high allele diversity (mean number of alleles/locus = 8.67 ± 1.03). Mean genotyping error rates across the markers were low to moderate (allelic drop-out rate = 0.09; false allele rate = 0.11). The proportions of first- and second-order relatives in the study population were 0.69% and 6.21%, respectively. Based on amplification success, genotyping error rates and the probability of identity (PID), we suggest (i) a panel of five microsatellite markers (cumulative PID = 1.24 × 10-5) for individual identification and population monitoring and (ii) seven additional markers for conservation genetics studies. This study provides essential tools capable of augmenting blackbuck conservation strategies at the landscape level, integral to protecting the scrubland-grassland ecosystem.
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15
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Tian L, Ye M, Chen C, Cao X, Shen T. Consistency of functional connectivity across different movies. Neuroimage 2021; 233:117926. [PMID: 33675997 DOI: 10.1016/j.neuroimage.2021.117926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/24/2021] [Accepted: 02/28/2021] [Indexed: 10/22/2022] Open
Abstract
Movie fMRI has emerged as a powerful tool for investigating human brain function, and functional connectivity (FC) plays a predominant role in fMRI-based studies. Accordingly, movie-watching FC may have great potential for future studies on human brain function. Before wide application of movie-watching FC, however, it is essential to evaluate how much it is influenced by differences in movies. The main aim of this study was to investigate the consistency of movie-watching FC across different movies. For this purpose, we performed three sets of analyses on the four movie fMRI runs (with different movie stimuli) included in the HCP dataset. The first set was performed to evaluate the agreement of movie-watching FC in exact values using intra-class correlation (ICC), and the ICC of movie-watching FC across different movies (0.37 on average) was found to be comparable to that of resting-state FC across repeated scans. The second set was performed to evaluate the agreement of movie-watching FC in connectivity patterns, and the results indicate that individuals could be identified with relatively high accuracies (94%-99%) across different movies based on their FC matrices. The final set was performed to test the generalizability of predictive models based on movie-watching FC, as this generalizability is highly dependent on the consistency of the FC. The results indicate that predictive models trained based on FC extracted from one movie fMRI run can make good predictions on FC extracted from runs with different movie stimuli. Taken together, our findings indicate that movie-watching FC is highly consistent across different movies, and conclusions drawn based on movie-watching FC are generalizable.
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Affiliation(s)
- Lixia Tian
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044, China.
| | - Mengting Ye
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044, China; Beijing Key Laboratory of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
| | - Chen Chen
- Beijing Key Laboratory of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
| | - Xuyu Cao
- Beijing Key Laboratory of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
| | - Tianhui Shen
- Beijing Key Laboratory of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China
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Mou QN, Ji LL, Liu Y, Zhou PR, Han MQ, Zhao JM, Cui WT, Chen T, Du SY, Hou YX, Guo YC. Three-dimensional superimposition of digital models for individual identification. Forensic Sci Int 2020; 318:110597. [PMID: 33279768 DOI: 10.1016/j.forsciint.2020.110597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/02/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022]
Abstract
Dentition is an individualizing structure in humans that may be potentially utilized in individual identification. However, research on the use of three-dimensional (3D) digital models for personal identification is rare. This study aimed to develop a method for individual identification based on a 3D image registration algorithm and assess its feasibility in practice. Twenty-eight college students were recruited; for each subject, a dental cast and an intraoral scan were taken at different time points, and digital models were acquired. The digital models of the dental casts and intraoral scans were assumed as antemortem and postmortem dentition, respectively. Additional 72 dental casts were extracted from a hospital database as a suspect pool together with 28 antemortem models. The dentition images of all of the models were extracted. Correntropy was introduced into the traditional iterative closest point algorithm to compare each postmortem 3D dentition with 3D dentitions in the suspect pool. Point-to-point root mean square (RMS) distances were calculated, and then 28 matches and 2772 mismatches were obtained. Statistical analysis was performed using the Mann-Whitney U test, which showed significant differences in RMS between matches (0.18±0.03mm) and mismatches (1.04±0.67mm) (P<0.05). All of the RMS values of the matched models were below 0.27mm. The percentage of accurate identification reached 100% in the present study. These results indicate that this method for individual identification based on 3D superimposition of digital models is effective in personal identification.
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Affiliation(s)
- Qing-Nan Mou
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China
| | - Ling-Ling Ji
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China
| | - Yan Liu
- Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 28 Xianning West Road, Xi'an, 710049, Shaanxi, PR China
| | - Pei-Rong Zhou
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China
| | - Meng-Qi Han
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China
| | - Jia-Min Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China
| | - Wen-Ting Cui
- Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 28 Xianning West Road, Xi'an, 710049, Shaanxi, PR China
| | - Teng Chen
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, 76 West Yanta Road, Xi'an, 710004, Shaanxi, PR China
| | - Shao-Yi Du
- Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 28 Xianning West Road, Xi'an, 710049, Shaanxi, PR China
| | - Yu-Xia Hou
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China.
| | - Yu-Cheng Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Department of Orthodontics, Stomatological Hospital of Xi'an Jiaotong University, 98 XiWu Road, Xi'an, 710004, Shaanxi, PR China; Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 28 Xianning West Road, Xi'an, 710049, Shaanxi, PR China.
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Hull JM, Sage GK, Sonsthagen SA, Gravley MC, Martinico BL, Booms TL, Swem T, Talbot SL. Isolation and characterization of microsatellite loci in merlins (Falco columbarius) and cross-species amplification in gyrfalcons (F. rusticolus) and peregrine falcons (F. peregrinus). Mol Biol Rep 2020; 47:8377-83. [PMID: 33099758 DOI: 10.1007/s11033-020-05842-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Merlins, Falco columbarius, breed throughout temperate and high latitude habitats in Asia, Europe, and North America. Like peregrine falcons, F. peregrinus, merlins underwent population declines during the mid-to-late twentieth century, due to organochlorine-based contamination, and have subsequently recovered, at least in North American populations. To better understand levels of genetic diversity and population structuring in contemporary populations and to assess the impact of the twentieth century decline, we used genomic data archived in public databases and constructed genomic libraries to isolate and characterize a suite of 17 microsatellite markers for use in merlins. We also conducted cross-amplification experiments to determine the markers' utility in peregrine falcons and gyrfalcons, F. rusticolus. These markers provide a valuable addition to marker suites that can be used to determine individual identity and conduct genetic analyses on merlins and congeners.
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18
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Ottewell K, Thavornkanlapachai R, McArthur S, Spencer PBS, Tedeschi J, Durrant B, Knuckey C, Armstrong K, Byrne M. Development and optimisation of molecular assays for microsatellite genotyping and molecular sexing of non-invasive samples of the ghost bat, Macroderma gigas. Mol Biol Rep 2020; 47:5635-5641. [PMID: 32577991 DOI: 10.1007/s11033-020-05544-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/23/2020] [Indexed: 01/04/2023]
Abstract
The ghost bat (Macroderma gigas) is endemic to Australia but is under threat, with scarce information available on the genetic health of remaining populations. Here, we develop molecular assays for microsatellite genotyping and molecular sexing of non-invasive samples as a genetic monitoring tool to identify individuals, measure genetic diversity and investigate spatial and temporal patterns of habitat use by ghost bats. We identified novel microsatellites through high-throughput sequencing on the Illumina MiSeq platform. Of 48 loci tested, six markers were added to five previously developed microsatellite loci. We developed three Y-linked (DDX3Y, Zfy and SRY) and one X-linked markers (Zfx) to enable molecular identification of sex. To assess performance, all 11 microsatellite and four sex-linked markers were amplified in three multiplex reactions in 160 M. gigas faecal samples from the Pilbara region, Western Australia. The combined markers offered a high level of individual discrimination (PIDsibs = 0.00002) and we detected 19 bats in total (11 males, 4 females and 4 sex undetermined). The number of alleles per locus ranged from 5 to 14 and the average observed and expected heterozygosity across loci were Ho = 0.735 (0.58-0.91) and uHe = 0.785 (0.59-0.89) respectively. Our molecular assays allowed identification of individuals from faecal samples at multiple time points and spatial locations and enabled us to elucidate patterns of habitat usage at the study site. This study highlights the value of our molecular assays as a potential capture-mark-recapture technique for population monitoring for this species.
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Affiliation(s)
- Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA, 6151, Australia.
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA, 6151, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA, 6151, Australia
| | - Peter B S Spencer
- Environmental and Conservation Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Jamie Tedeschi
- Environmental and Conservation Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Brad Durrant
- Biologic Environmental Survey, 24 Wickham Street, East Perth, WA, 6004, Australia
| | - Chris Knuckey
- Biologic Environmental Survey, 24 Wickham Street, East Perth, WA, 6004, Australia
| | - Kyle Armstrong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington, WA, 6151, Australia
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19
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Abstract
Background Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human, dog, cat, cattle, etc. Maintaining these systems simultaneously can be costly. These mammals share many high similar regions along their genomes. With the availability of the massive amount of the whole genomics data of these species, it is possible to develop a unified STR profiling system. In this study, our objective is to propose and develop a unified set of STR loci that could be simultaneously applied to multiple species. Result To find a unified STR set, we collected the whole genome sequence data of the concerned species and mapped them to the human genome reference. Then we extracted the STR loci across the species. From these loci, we proposed an algorithm which selected a subset of loci by incorporating the optimized combined power of discrimination. Our results show that the unified set of loci have high combined power of discrimination, >1−10−9, for both individual species and the mixed population, as well as the random-match probability, <10−7 for all the involved species, indicating that the identified set of STR loci could be applied to multiple species. Conclusions We identified a set of STR loci which shared by multiple species. It implies that a unified STR profiling system is possible for these species under the forensic scenes. The system can be applied to the individual identification or paternal test of each of the ten common species which are Sus scrofa (pig), Bos taurus (cattle), Capra hircus (goat), Equus caballus (horse), Canis lupus familiaris (dog), Felis catus (cat), Ovis aries (sheep), Oryctolagus cuniculus (rabbit), and Bos grunniens (yak), and Homo sapiens (human). Our loci selection algorithm employed a greedy approach. The algorithm can generate the loci under different forensic parameters and for a specific combination of species.
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Affiliation(s)
- Yilin Liu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Jiao Xu
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Miaoxia Chen
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China.
| | - Shuaicheng Li
- City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China.
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20
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Sun L, Liu Q, Li S, Ma G, Wang Z, Ma C, Cong B, Fu L. A new strategy to confirm the identity of tumour tissues using single-nucleotide polymorphisms and next-generation sequencing. Int J Legal Med 2019; 134:399-409. [PMID: 31811377 DOI: 10.1007/s00414-019-02216-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/15/2019] [Indexed: 11/25/2022]
Abstract
With growing cancer morbidity, forensics cases in which archived tumour tissues can be used as biological samples are increasing, and an effective method to identify the body source of tumour tissues is needed. Single nucleotide polymorphisms (SNPs) may be a promising biomarker to identify the source of tumour tissues because of their low mutation rate and small amplicon size. Next-generation sequencing techniques offers the ability to detect hundreds of SNPs in a single run. The Precision ID Identity Panel (Thermo Fisher Scientific, Waltham, MA, USA) detects 90 autosomal SNPs for individual identification and 34 lineage-informative SNPs on Y chromosome using the Ion PGM system (Thermo Fisher Scientific). In this study, we evaluated performance of the panel for individual identification of tumour tissues. One hundred and fifty pairs of tumour tissues and corresponding normal tissues were analysed. Loss of heterozygosity was detected only in tumour tissues. The identity-by-state (IBS) scoring system was adopted to identify the body source of tumour tissues. The IBS score, as well as the number of loci with 2 alleles (A2), 1 allele (A1) and 0 alleles (A0) shared, were analysed within each tumour-normal pair, unrelated individual pairs, parent-offspring pairs and full-sibling pairs. According to the probability distribution, threshold of A2 in the range of 69 to 89 could achieve accuracy > 99% in identifying the source of tumour tissues. Thus, we developed a new strategy (process and criteria) to identify the source of tumour tissues that could be used in practice.
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Affiliation(s)
- Lijuan Sun
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Qi Liu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Zhandong Wang
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, Xuzhou Cancer Hospital, Xuzhou, China
| | - Chunling Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China.
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China.
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21
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Modi S, Habib B, Ghaskadbi P, Nigam P, Mondol S. Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog ( Cuon alpinus). PeerJ 2019; 7:e7453. [PMID: 31534835 PMCID: PMC6727832 DOI: 10.7717/peerj.7453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 07/10/2019] [Indexed: 11/20/2022] Open
Abstract
Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.
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Affiliation(s)
- Shrushti Modi
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Bilal Habib
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Pallavi Ghaskadbi
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
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22
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Yang J, Lin D, Deng C, Li Z, Pu Y, Yu Y, Li K, Li D, Chen P, Chen F. The advances in DNA mixture interpretation. Forensic Sci Int 2019; 301:101-106. [PMID: 31153987 DOI: 10.1016/j.forsciint.2019.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
In forensic genetics, the analysis of DNA in biological samples is a valuable tool for personal identification. There is an increasing demand in analyzing of the mixed DNA which may provide insightful investigative instructions. With the continuous effort for the improvement of individual identification, complicated mixed stains represent a growing fraction of the samples processed by forensic laboratories. Recent technological advances have enabled quantitative analysis of DNA mixture and emerging sequencing approaches to decipher the complicated DNA mixture. Here, we describe the use of different genetic markers, typing approaches and analytical methods in mixture analysis, and how useful information can be obtained from complicated DNA mixture.
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Affiliation(s)
- Jiawen Yang
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Donghai Lin
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Chuwei Deng
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Zheng Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Yan Pu
- School of Medicine, Southeast University, Nanjing, Jiangsu 210009, PR China
| | - Yanfang Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Kai Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Ding Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China.
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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23
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Chen P, Luo L, Gao H, Wu J, Wang Y, He G, Han Y. Forensic performance of 30 InDels included in the Investigator DIPplex system in Miao population and comprehensive genetic relationship in China. Int J Legal Med 2019; 133:1389-1392. [PMID: 30989323 DOI: 10.1007/s00414-019-02057-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
Abstract
Binary markers of insertion and deletion (InDel) play an important role in forensic personal identification, parentage testing, and individual ancestry inference. We first genotyped 30 InDels included in the Investigator DIPplex in 403 unrelated healthy Zunyi Miao people and analyzed the genetic polymorphisms, as well as explored the genetic relationship between Miao and 32 Chinese reference populations. No departures from the HWE were observed. The combined power of discrimination and the combined probability of exclusion were 0.99999999998 and 0.9884, respectively. Forensic parameters demonstrated that 30 markers are polymorphic and informative in the Zunyi Miao population and can be used as a tool for forensic personal identification and parentage testing. Allele frequency divergence analysis found that 12 out of 30 displaying high allele frequency difference between Turkic-speaking populations and other Chinese populations can be used as candidates of ancestry informative markers for ancestry inference of sub-population in East Asia. Population genetic parameters in the comprehensive population comparison among 33 Chinese populations indicated that our studied Hmong-Mien-speaking Miao has a close genetic relationship with geographically adjacent Enshi Tujia and genetically differentiate from Turkic-speaking populations.
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Affiliation(s)
- Pengyu Chen
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Zunyi, 563099, Guizhou, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, 563099, Guizhou, China
| | - Li Luo
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Zunyi, 563099, Guizhou, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, 563099, Guizhou, China
| | - Hongyan Gao
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Zunyi, 563099, Guizhou, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, 563099, Guizhou, China
| | - Jian Wu
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Zunyi, 563099, Guizhou, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, 563099, Guizhou, China
| | - Yudan Wang
- Center of Forensic Expertise, Affiliated hospital of Zunyi Medical University, Zunyi, 563099, Guizhou, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, 563099, Guizhou, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yanyan Han
- School of Public Health, Zunyi Medical University, Zunyi, 563099, Guizhou, China.
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24
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Hwa HL, Wu MY, Lin CP, Hsieh WH, Yin HI, Lee TT, Lee JCI. A single nucleotide polymorphism panel for individual identification and ancestry assignment in Caucasians and four East and Southeast Asian populations using a machine learning classifier. Forensic Sci Med Pathol 2019; 15:67-74. [PMID: 30649693 DOI: 10.1007/s12024-018-0071-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 11/26/2022]
Abstract
Single nucleotide polymorphism (SNP) profiling is an effective means of individual identification and ancestry inferences in forensic genetics. This study established a SNP panel for the simultaneous individual identification and ancestry assignment of Caucasian and four East and Southeast Asian populations. We analyzed 220 SNPs (125 autosomal, 17 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs) of the DNA samples from 563 unrelated individuals of five populations (89 Caucasian, 234 Taiwanese Han, 90 Filipino, 79 Indonesian and 71 Vietnamese) and 18 degraded DNA samples. Informativeness for assignment (In) was used to select ancestry informative SNPs (AISNPs). A machine learning classifier, support vector machine (SVM), was used for ancestry assignment. Of the 220 SNPs, 62 were individual identification SNPs (IISNPs) (51 autosomal and 11 X-chromosomal SNPs) and 191 were AISNPs (100 autosomal, 13 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs). The 51 autosomal IISNPs offered cumulative random match probabilities (cRMPs) ranging from 1.56 × 10-21 to 3.16 × 10-22 among these five populations. Using AISNPs with the SVM, the overall accuracy rate of ancestry inference achieved in the testing dataset between Caucasian, Taiwanese Han, and Filipino populations was 88.9%, whereas it was 70.0% between Caucasians and each of the four East and Southeast Asian populations. For the 18 degraded DNA samples with incomplete profiling, the accuracy rate of ancestry assignment was 94.4%. We have developed a 220-SNP panel for simultaneous individual identification and ethnic origin differentiation between Caucasian and the four East and Southeast Asian populations. This SNP panel may assist with DNA analysis of forensic casework.
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Affiliation(s)
- Hsiao-Lin Hwa
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Ming-Yih Wu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Wei Hsin Hsieh
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - James Chun-I Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan.
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25
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Philippe C, Isabelle HC, Philippe F, Russell S, Nadia B, Alain F, Dominique GH, Saudamini D, Anaïs A, Lou A, Antoine B. The brain of René Descartes (1650): A neuro-anatomical analysis. J Neurol Sci 2017; 378:12-8. [PMID: 28566145 DOI: 10.1016/j.jns.2017.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 11/22/2022]
Abstract
The skull of René Descartes is held in the National Museum of Natural History since the 19th c. Up to date, only anthropological examinations were carried out, focusing on the cranial capacity and phrenological interpretation of the skull morphology. Using CT-scan based 3D technology, a reconstruction of the endocast was performed, allowing for its first complete description and inter-disciplinary analysis: assessment of metrical and non-metrical features, retrospective diagnosis of anatomical anomalies, and confrontation with neuro-psychological abilities of this well-identified individual.
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26
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Zhang L, Ding M, Pang H, Xing J, Xuan J, Wang C, Lin Z, Han S, Liang K, Li C, Yao J, Wang B. Mitochondrial DNA typing of laser-captured single sperm cells to differentiate individuals in a mixed semen stain. Electrophoresis 2016; 37:2273-7. [PMID: 27225075 DOI: 10.1002/elps.201600009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 03/17/2016] [Accepted: 05/18/2016] [Indexed: 11/11/2022]
Abstract
The identification of individuals in a mixture of two semen samples usually involves an analysis of autosomal and Y chromosomal short tandem repeats (STR) which can exclude unrelated individuals but cannot achieve the purpose of individual identification. In sperm cells, there are multiple copies of mitochondrial DNAs (mtDNA) which exhibit genetic polymorphisms in different matrilineal-related individuals. Single-cell capture technology can be applied to obtain some single sperm cells in a mixed semen sample, then polymerase chain reaction can be employed to amplify the mtDNA hypervariable region I (HVR I) from each cell. By pooling the cells with the same HVR I sequence, we can obtain the sufficient nuclear DNA for STR typing.
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Affiliation(s)
- Lu Zhang
- China Medical University School of Forensic Medicine, Shenyang, P. R. China.,Department of Forensic Medicine, National Police University of China, Shenyang, P. R. China
| | - Mei Ding
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | - Hao Pang
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | - Jiaxin Xing
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | - Jinfeng Xuan
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | | | - Ziqing Lin
- Department of Forensic Medicine, National Police University of China, Shenyang, P. R. China
| | - Song Han
- Shenyang Medical College, Shenyang, P. R. China
| | - Kewei Liang
- Department of Forensic Medicine, National Police University of China, Shenyang, P. R. China
| | - Chunmei Li
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | - Jun Yao
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
| | - Baojie Wang
- China Medical University School of Forensic Medicine, Shenyang, P. R. China
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27
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Wang Q, Fu L, Zhang X, Dai X, Bai M, Fu G, Cong B, Li S. Expansion of a SNaPshot assay to a 55-SNP multiplex: Assay enhancements, validation, and power in forensic science. Electrophoresis 2016; 37:1310-7. [PMID: 26864788 DOI: 10.1002/elps.201500353] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/04/2015] [Accepted: 01/30/2016] [Indexed: 11/08/2022]
Abstract
A previously developed multiplex assay with 44 individual identification SNPs was expanded to a 55plex assay. Fifty-four highly informative SNPs and an amelogenin sex marker were amplified in one PCR reaction and then detected with two SNaPshot reactions using CE. PCR primers for four loci, 28 single-base extension primers, and the reaction conditions were altered to improve the robustness of the method. A detailed approach for allele calling was developed to guide analysis of the electropherogram. One hundred and eighty unrelated individuals and 100 father-child-mother trios of the Han population in Hebei, China were analyzed. No mutation was found in the SNP loci. The combined mean match probability and cumulative probability of exclusion were 1.327 × 10(-22) and 0.999932, respectively. Analysis of the 54 SNPs and 26 STRs (included in the AmpFLSTR Identifiler and Investigator HDplex kits) showed no significant linkage disequilibriums. Our research shows that the expanded SNP multiplex assay is an easily performed and valuable method to supplement STR analysis.
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Affiliation(s)
- Qian Wang
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Lihong Fu
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Xiaojing Zhang
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Xinyu Dai
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Mei Bai
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Guangping Fu
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
| | - Shujin Li
- Hebei Key Laboratory of Forensic Medicine, Department of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei, P. R. China
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28
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Zubakov D, Kokmeijer I, Ralf A, Rajagopalan N, Calandro L, Wootton S, Langit R, Chang C, Lagace R, Kayser M. Towards simultaneous individual and tissue identification: A proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM. Forensic Sci Int Genet 2015; 17:122-128. [PMID: 25966466 DOI: 10.1016/j.fsigen.2015.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 04/03/2015] [Indexed: 11/26/2022]
Abstract
DNA-based individual identification and RNA-based tissue identification represent two commonly-used tools in forensic investigation, aiming to identify crime scene sample donors and helping to provide links between DNA-identified sample donors and criminal acts. Currently however, both analyses are typically performed separately. In this proof-of-principle study, we developed an approach for the simultaneous analysis of forensic STRs, amelogenin, and forensic mRNAs based on parallel targeted DNA/RNA sequencing using the Ion Torrent Personal Genome Machine(®) (PGM™) System coupled with the AmpliSeq™ targeted amplification. We demonstrated that 9 autosomal STRs commonly used for individual identification (CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX, and vWA), the AMELX/AMELY system widely applied for sex identification, and 12 mRNA markers previously established for forensic tissue identification (ALAS2 and SPTB for peripheral blood, MMP10 and MMP11 for menstrual blood, HTN3 and STATH for saliva, PRM1 and TGM4 for semen, CYP2B7P1 and MUC4 for vaginal secretion, CCL27 and LCE1C for skin) together with two candidate reference mRNA markers (HPRT1 and SDHA) can all be successfully combined. Unambiguous mRNA-based tissue identification was achieved in all samples from all forensically relevant tissues tested, and STR sequencing analysis of the tissue sample donors was 100% concordant with conventional STR profiling using a commercial kit. Successful STR analysis was obtained from 1ng of genomic DNA and mRNA analysis from 10ng total RNA; however, sensitivity limits were not investigated in this proof-of-principle study and are expected to be much lower. Since dried materials with noticeable RNA degradation and small DNA/RNA amplicons with high-coverage sequencing were used, the achieved correct individual and tissue identification demonstrates the suitability of this approach for analyzing degraded materials in future forensic applications. Overall, our study demonstrates the feasibility of simultaneously obtaining multilocus STR, amelogenin, and multilocus mRNA information for combined individual and tissue identification from a small sample of degraded biological material. Moreover, our study marks the first step towards combining many DNA/RNA markers for various forensic purposes to increase the effectiveness of molecular forensic analysis and to allow more forensically relevant information to be obtained from limited forensic material.
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Affiliation(s)
- D Zubakov
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - I Kokmeijer
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - A Ralf
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - N Rajagopalan
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - L Calandro
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - S Wootton
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - R Langit
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - C Chang
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - R Lagace
- Thermo Fisher Scientific/Life Technologies, South San Francisco, CA, USA
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Rogalla U, Woźniak M, Swobodziński J, Derenko M, Malyarchuk BA, Dambueva I, Koziński M, Kubica J, Grzybowski T. A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate. Forensic Sci Int Genet 2014; 15:49-55. [PMID: 25487077 DOI: 10.1016/j.fsigen.2014.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 12/09/2022]
Abstract
As microsatellites located on Y chromosome mutate with different rates, they may be exploited in evolutionary studies, genealogical testing of a variety of populations and even, as proven recently, aid individual identification. Currently available commercial Y-STR kits encompass mostly low to moderately mutating loci, making them a perfect choice for the first two applications. Some attempts have been made so far to utilize Y-STRs to provide a discriminatory tool for forensic purposes. Although all 13 rapidly mutating Y-STRs were already multiplexed, no single assay based on single-copy markers allowing at least a portion of close male relatives to be differentiated from one another is available. To fill in the blanks, we constructed and validated an assay comprised of single-copy Y-STR markers only with a mutation rate ranging from 8×10(-3) to 1×10(-2). Performance of the resulting combination of nine RM Y-STRs and four moderately mutating ones was tested on 361 father-son pairs and 1326 males from 9 populations revealing an overall mutation rate of 1.607×10(-1) for the assay as a whole. Application of the proposed 13 Y-STR set to differentiation of haplotypes present among homogenous population of Buryats resulted in a threefold increase of discrimination as compared with 10 Y-STRs from the PowerPlex(®) Y.
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Affiliation(s)
- Urszula Rogalla
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Marcin Woźniak
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Jacek Swobodziński
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia.
| | - Boris A Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia.
| | - Irina Dambueva
- Institute of General and Experimental Biology, Institute of Mongolian, Buddhist and Tibetan Studies Russian Academy of Sciences, Ulan-Ude, Russia.
| | - Marek Koziński
- Department of Cardiology and Internal Disease, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Jacek Kubica
- Department of Cardiology and Internal Disease, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Tomasz Grzybowski
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
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Abstract
The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.
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Affiliation(s)
- Xiao-Hong Liu
- Kunming Institute of Zoology, Kunming, Yunnan, China
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31
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Sugiyama S, Chong YH, Shito M, Kasuga M, Kawakami T, Udagawa C, Aoki H, Bonkobara M, Tsuchida S, Sakamoto A, Okuda H, Nagai A, Omi T. Analysis of mitochondrial DNA HVR1 haplotype of pure-bred domestic dogs in Japan. Leg Med (Tokyo) 2013; 15:303-9. [PMID: 24120304 DOI: 10.1016/j.legalmed.2013.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/20/2022]
Abstract
To develop DNA markers for forensic analysis, we examined the hypervariable region 1 (HVR1) sequences of 447 pure-bred domestic dogs (Canis lupus familiaris) that had been bred and raised in Japan. HVR1 is a 660-bp stretch of mitochondrial (mt) DNA. Among the 447 HVR1 sequences examined, we identified 58 haplotypes from 47 single nucleotide polymorphisms (SNPs) and two insertion-deletion (InDel) polymorphisms. The haplotype diversity inferred from inter-breed analysis (N=154, 88 breeds) was 0.929±0.011. Intra-breed analysis showed that the haplotype diversity of Golden Retrievers (N=53), Labrador Retrievers (N=67), Miniature Dachshunds (N=61), Toy Poodles (N=62), and Welsh Corgis (N=50) was 0.624±0.052, 0.722±0.029, 0.922±0.010, 0.877±0.020, and 0.443±0.084, respectively. The results of this genotype analysis were used to construct a dataset consisting of dog mtDNA HVR1 sequences for use in forensic applications in Japan.
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