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Zeng K, Du J, Chen YZ, Wang DY, Sun ML, Li YZ, Wang DY, Liu SH, Zhu XM, Lv P, Du Z, Liu K, Yao J. Metabolomics efficiently discriminates monozygotic twins in peripheral blood. Int J Legal Med 2024:10.1007/s00414-024-03269-1. [PMID: 38858273 DOI: 10.1007/s00414-024-03269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Monozygotic (MZ) twins cannot be distinguished using conventional forensic STR typing because they present identical STR genotypings. However, MZ twins do not always live in the same environment and often have different dietary and other lifestyle habits. Metabolic profiles are deyermined by individual characteristics and are also influenced by the environment in which they live. Therefore, they are potential markers capable of identifying MZ twins. Moreover, the production of proteins varies from organism to organism and is influenced by both the physiological state of the body and the external environment. Hence, we used metabolomics and proteomics to identify metabolites and proteins in peripheral blood to discriminate MZ twins. We identified 1749 known metabolites and 622 proteins in proteomic analysis. The metabolic profiles of four pairs of MZ twins revealed minor differences in intra-MZ twins and major differences in inter-MZ twins. Each pair of MZ twins exhibited distinct characteristics, and four metabolites-methyl picolinate, acesulfame, paraxanthine, and phenylbenzimidazole sulfonic acid-were observed in all four MZ twin pairs. These four differential exogenous metabolites conincidently show that the different external environments and life styles can be well distinguished by metabolites, considering that twins do not all have the same eating habits and living environments. Moreover, MZ twins showed different protein profiles in serum but not in whole blood. Thus, our results indicate that differential metabolites provide potential biomarkers for the personal identification of MZ twins in forensic medicine.
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Affiliation(s)
- Kuo Zeng
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Jiang Du
- Department of Pathology, School of Basic Medicine, China Medical University, Shenyang, P.R. China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dan-Yang Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China
| | - Kun Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, P.R. China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, P.R. China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, P.R. China.
- China Medical University Center of Forensic Investigation, Shenyang, P.R. China.
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Procopio N, Bonicelli A. From flesh to bones: Multi-omics approaches in forensic science. Proteomics 2024; 24:e2200335. [PMID: 38683823 DOI: 10.1002/pmic.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.
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Affiliation(s)
- Noemi Procopio
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Experimental Taphonomy, School of Law and Policing, University of Central Lancashire, Preston, UK
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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4
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Filoglu G, Sımsek SZ, Ersoy G, Can K, Bulbul O. Epigenetic-based age prediction in blood samples: Model development. J Forensic Sci 2024; 69:869-879. [PMID: 38308398 DOI: 10.1111/1556-4029.15478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Aging is a complex process influenced by genetic, epigenetic, and environmental factors that lead to tissue deterioration and frailty. Epigenetic mechanisms, such as DNA methylation, play a significant role in gene expression regulation and aging. This study presents a new age estimation model developed for the Turkish population using blood samples. Eight CpG sites in loci TOM1L1, ELOVL2, ASPA, FHL2, C1orf132, CCDC102B, cg07082267, and RASSF5 were selected based on their correlation with age. Methylation patterns of these sites were analyzed in blood samples from 100 volunteers, grouped into age categories (20-35, 36-55, and ≥56). Sensitivity analysis indicated a reliable performance with DNA inputs ≥1 ng. Statistical modeling, utilizing Multiple Linear Regression, underscores the reliability of the primary 6-CpG model, excluding cg07082267 and TOM1L1. This model demonstrates strong correlations with chronological age (r = 0.941) and explains 88% of the age variance with low error rates (MAE = 4.07, RMSE = 5.73 years). Validation procedures, including a training-test split and fivefold cross-validation, consistently confirm the model's accuracy and consistency. The study indicates minimal variation in error scores across age cohorts and no significant gender differences. The developed model showed strong predictive accuracy, with the ability to estimate age within certain prediction intervals. This study contributes to the age prediction by using DNA methylation patterns, which can have disparate applications, including forensic and clinical assessments.
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Affiliation(s)
- Gonul Filoglu
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Sumeyye Zulal Sımsek
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gokhan Ersoy
- Department of Forensic Medicine, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Kadriye Can
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ozlem Bulbul
- Department of Science, Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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5
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Marcante B, Delicati A, Onofri M, Tozzo P, Caenazzo L. Estimation of Human Chronological Age from Buccal Swab Samples through a DNA Methylation Analysis Approach of a Five-Locus Multiple Regression Model. Int J Mol Sci 2024; 25:935. [PMID: 38256009 PMCID: PMC10815300 DOI: 10.3390/ijms25020935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Recent advancements in forensic genetics have facilitated the extraction of additional characteristics from unidentified samples. This study delves into the predictive potential of a five-gene (ELOVL2, FHL2, KLF14, C1orf132, and TRIM59) methylation rate analysis for human age estimation using buccal swabs collected from 60 Italian volunteers. The methylation levels of specific CpG sites in the five genes were analyzed through bisulfite conversion, single-base extension, and capillary electrophoresis. A multivariate linear regression model was crafted on the training set, then the test set was employed to validate the predictive model. The multivariate predictive model revealed a mean absolute deviation of 3.49 years in the test set of our sample. While limitations include a modest sample size, the study provides valuable insights into the potential of buccal swab-based age prediction, aiding in criminal investigations where accurate age determination is crucial. Our results also highlight that it is necessary to investigate the effectiveness of predictive models specific to biological tissues and individual populations, since models already proven effective for other populations or different tissues did not show the same effectiveness in our study.
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Affiliation(s)
- Beatrice Marcante
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Arianna Delicati
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Martina Onofri
- Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy;
| | - Pamela Tozzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
| | - Luciana Caenazzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (B.M.); (A.D.); (P.T.)
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Popovic N, Ždralević M, Vujosevic S, Radunović M, Adžić Zečević A, Rovčanin Dragović I, Vukčević B, Popovic T, Radulović L, Vuković T, Eraković J, Lazović R, Radunović M. Retinal microvascular complexity as a putative biomarker of biological age: a pilot study. Biogerontology 2023; 24:971-985. [PMID: 37572202 DOI: 10.1007/s10522-023-10057-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
Physiological changes associated with aging increase the risk for the development of age-related diseases. This increase is non-specific to the type of age-related disease, although each disease develops through a unique pathophysiologic mechanism. People who age at a faster rate develop age-related diseases earlier in their life. They have an older "biological age" compared to their "chronological age". Early detection of individuals with accelerated aging would allow timely intervention to postpone the onset of age-related diseases. This would increase their life expectancy and their length of good quality life. The goal of this study was to investigate whether retinal microvascular complexity could be used as a biomarker of biological age. Retinal images of 68 participants ages ranging from 19 to 82 years were collected in an observational cross-sectional study. Twenty of the old participants had age-related diseases such as hypertension, type 2 diabetes, and/or Alzheimer's dementia. The rest of the participants were healthy. Retinal images were captured by a hand-held, non-mydriatic fundus camera and quantification of the microvascular complexity was performed by using Sholl's, box-counting fractal, and lacunarity analysis. In the healthy subjects, increasing chronological age was associated with lower retinal microvascular complexity measured by Sholl's analysis. Decreased box-counting fractal dimension was present in old patients, and this decrease was 2.1 times faster in participants who had age-related diseases (p = 0.047). Retinal microvascular complexity could be a promising new biomarker of biological age. The data from this study is the first of this kind collected in Montenegro. It is freely available for use.
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Affiliation(s)
- Natasa Popovic
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro.
| | - Maša Ždralević
- Institute for Advanced Studies, University of Montenegro, Podgorica, Montenegro
| | - Stela Vujosevic
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Eye Clinic, IRCCS MultiMedica, Milan, Italy
| | | | - Antoaneta Adžić Zečević
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
- Clinical Center of Montenegro, Podgorica, Montenegro
| | | | | | - Tomo Popovic
- Faculty for Information Systems and Technologies, University of Donja Gorica, Podgorica, Montenegro
| | - Ljiljana Radulović
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
- Clinical Center of Montenegro, Podgorica, Montenegro
| | | | | | - Ranko Lazović
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
- Clinical Center of Montenegro, Podgorica, Montenegro
| | - Miodrag Radunović
- Faculty of Medicine, University of Montenegro, Podgorica, Montenegro
- Clinical Center of Montenegro, Podgorica, Montenegro
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Guo Y, Zhang X, Zhang H, Liu Y, Shi J, Meng H, Chen X, Lan Q, Zhu B. Application of microfluidic technologies in forensic analysis. Electrophoresis 2023; 44:1725-1743. [PMID: 37857551 DOI: 10.1002/elps.202200268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 10/21/2023]
Abstract
The application of microfluidic technology in forensic medicine has steadily expanded over the last two decades due to the favorable features of low cost, rapidity, high throughput, user-friendliness, contamination-free, and minimum sample and reagent consumption. In this context, bibliometric methods were adopted to visualize the literature information contained in the Science Citation Index Expanded from 1989 to 2022, focusing on the co-occurrence analysis of forensic and microfluidic topics. A deep interpretation of the literature was conducted based on co-occurrence results, in which microfluidic technologies and their applications in forensic medicine, particularly forensic genetics, were elaborated. The purpose of this review is to provide an impartial evaluation of the utilization of microfluidic technology in forensic medicine. Additionally, the challenges and future trends of implementing microfluidic technology in forensic genetics are also addressed.
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Affiliation(s)
- Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, P. R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yaoshun Liu
- Ankang Hospital of Traditional Chinese Medicine, Ankang, Shaanxi, P. R. China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xin Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Zhong Y, Zeng K, Adnan A, Li YZ, Hou XK, Pan Y, Li A, Zhu XM, Lv P, Du Z, Yang Y, Yao J. Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing. Int J Legal Med 2023; 137:1337-1345. [PMID: 37270462 DOI: 10.1007/s00414-023-03033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
Differentiating between monozygotic (MZ) twins remains difficult because they have the same genetic makeup. Applying the traditional STR genotyping approach cannot differentiate one from the other. Heteroplasmy refers to the presence of two or more different mtDNA copies within a single cell and this phenomenon is common in humans. The levels of heteroplasmy cannot change dramatically during transmission in the female germ line but increase or decrease during germ-line transmission and in somatic tissues during life. As massively parallel sequencing (MPS) technology has advanced, it has shown the extraordinary quantity of mtDNA heteroplasmy in humans. In this study, a probe hybridization technique was used to obtain mtDNA and then MPS was performed with an average sequencing depth of above 4000. The results showed us that all ten pairs of MZ twins were clearly differentiated with the minor heteroplasmy threshold at 1.0%, 0.5%, and 0.1%, respectively. Finally, we used a probe that targeted mtDNA to boost sequencing depth without interfering with nuclear DNA and this technique can be used in forensic genetics to differentiate the MZ twins.
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Affiliation(s)
- Yang Zhong
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ang Li
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China
- China Medical University Center of Forensic Investigation, Chengdu, China
| | - Ying Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No.77, Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-evidence Sciences, Shenyang, Liaoning Province, China.
- China Medical University Center of Forensic Investigation, Chengdu, China.
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10
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Konrad H, Lawniczek J, Bajramjan C, Weber L, Bajanowski T, Poetsch M. Knife wound or nosebleed-where does the blood at the crime scene come from? Int J Legal Med 2023:10.1007/s00414-023-03012-2. [PMID: 37148347 PMCID: PMC10247842 DOI: 10.1007/s00414-023-03012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/14/2023] [Indexed: 05/08/2023]
Abstract
Secretion analysis is a useful tool in forensic genetics, since it establishes the (cellular) origin of the DNA prior in addition to the identification of the DNA donor. This information can be crucial for the construction of the crime sequence or verification of statements of people involved in the crime. For some secretions, rapid/pretests already exist (blood, semen, urine, and saliva) or can be determined via published methylation analyses or expression analyses (blood, saliva vaginal secretions, menstrual blood, and semen). To discriminate nasal secretion/blood from other secretions (like oral mucosa/saliva, blood, vaginal secretion, menstrual blood, and seminal fluid), assays based on specific methylation patterns at several CpGs were set up in this study. Out of an initial 54 different CpG markers tested, two markers showed a specific methylation value for nasal samples: N21 and N27 with a methylation mean value of 64.4% ± 17.6% and 33.2% ± 8.7%, respectively. Although identification or discrimination was not possible for all nasal samples (due to partial overlap in methylation values to other secretions), 63% and 26% of the nasal samples could be unambiguously identified and distinguished from the other secretions using the CpG marker N21 and N27, respectively. In combination with a blood pretest/rapid test, a third marker (N10) was able to detect nasal cells in 53% of samples. Moreover, the employment of this pretest increases the proportion of identifiable or discriminable nasal secretion samples using marker N27 to 68%. In summary, our CpG assays proved to be promising tools in forensic analysis for the detection of nasal cells in samples from a crime scene.
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Affiliation(s)
- Helen Konrad
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Janina Lawniczek
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Christine Bajramjan
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Lisa Weber
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Thomas Bajanowski
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany.
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11
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Vidaki A, Planterose Jiménez B, Poggiali B, Kalamara V, van der Gaag KJ, Maas SCE, Ghanbari M, Sijen T, Kayser M. Targeted DNA methylation analysis and prediction of smoking habits in blood based on massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102878. [PMID: 37116245 DOI: 10.1016/j.fsigen.2023.102878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Tobacco smoking is a frequent habit sustained by > 1.3 billion people in 2020 and the leading preventable factor for health risk and premature mortality worldwide. In the forensic context, predicting smoking habits from biological samples may allow broadening DNA phenotyping. In this study, we aimed to implement previously published smoking habit classification models based on blood DNA methylation at 13 CpGs. First, we developed a matching lab tool based on bisulfite conversion and multiplex PCR followed by amplification-free library preparation and targeted paired-end massively parallel sequencing (MPS). Analysis of six technical duplicates revealed high reproducibility of methylation measurements (Pearson correlation of 0.983). Artificially methylated standards uncovered marker-specific amplification bias, which we corrected via bi-exponential models. We then applied our MPS tool to 232 blood samples from Europeans of a wide age range, of which 90 were current, 71 former and 71 never smokers. On average, we obtained 189,000 reads/sample and 15,000 reads/CpG, without marker drop-out. Methylation distributions per smoking category roughly corresponded to previous microarray analysis, showcasing large inter-individual variation but with technology-driven bias. Methylation at 11 out of 13 smoking-CpGs correlated with daily cigarettes in current smokers, while solely one was weakly correlated with time since cessation in former smokers. Interestingly, eight smoking-CpGs correlated with age, and one displayed weak but significant sex-associated methylation differences. Using bias-uncorrected MPS data, smoking habits were relatively accurately predicted using both two- (current/non-current) and three- (never/former/current) category model, but bias correction resulted in worse prediction performance for both models. Finally, to account for technology-driven variation, we built new, joint models with inter-technology corrections, which resulted in improved prediction results for both models, with or without PCR bias correction (e.g. MPS cross-validation F1-score > 0.8; 2-categories). Overall, our novel assay takes us one step closer towards the forensic application of viable smoking habit prediction from blood traces. However, future research is needed towards forensically validating the assay, especially in terms of sensitivity. We also need to further shed light on the employed biomarkers, particularly on the mechanistics, tissue specificity and putative confounders of smoking epigenetic signatures.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Brando Poggiali
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vivian Kalamara
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Silvana C E Maas
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, The Hague, the Netherlands; Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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12
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Watanabe K, Yamagishi T, Toyomane K, Akutsu T. Validation of a novel fluorescent probe-based real-time PCR assay to detect saliva-specific unmethylated CpG sites for saliva identification. Leg Med (Tokyo) 2023; 63:102260. [PMID: 37094513 DOI: 10.1016/j.legalmed.2023.102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
The identification of saliva from forensic samples is often important to establish what happened at a crime scene, especially in sexual assault cases. Recently, CpG sites that are specifically methylated or unmethylated in saliva have been reported as markers for saliva identification. In this study, we designed a fluorescent probe-based real-time polymerase chain reaction (PCR) assay for analyzing the methylation status of two neighboring CpG sites, which we previously found were saliva-specifically unmethylated. Specificity analysis using various types of body fluid/tissue samples demonstrated a probe detecting the unmethylation of the two CpG sites reacted only to saliva DNA, indicating this probe as an all-or-nothing marker for the presence of saliva DNA. Sensitivity analysis demonstrated that the detection limit was 0.5 ng saliva DNA as input for bisulfite conversion, while we confirmed a negative effect of larger amounts of non-saliva DNA on sensitivity in the analysis of saliva-vaginal DNA mixtures. We finally validated the applicability of this test to swabs from licked skin and bottles after drinking as mock forensic samples in comparison with other saliva-specific markers. We confirmed the potential usefulness of this test for skin samples, from which a saliva-specific mRNA was not detected reliably, while the ingredients in several beverages might affect methylation analysis. Given the simplicity of real-time PCR as well as the high specificity and sensitivity of the test, we believe the developed method is suitable for routine forensic analysis and can play an important role in saliva identification.
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Affiliation(s)
- Ken Watanabe
- National Research Institute of Police Science, Chiba 277-0882, Japan.
| | | | - Kochi Toyomane
- National Research Institute of Police Science, Chiba 277-0882, Japan
| | - Tomoko Akutsu
- National Research Institute of Police Science, Chiba 277-0882, Japan
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13
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Forensic Age Estimation through a DNA Methylation-Based Age Prediction Model in the Italian Population: A Pilot Study. Int J Mol Sci 2023; 24:ijms24065381. [PMID: 36982454 PMCID: PMC10049185 DOI: 10.3390/ijms24065381] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
DNA methylation is one of the epigenetic marks which has been studied intensively in recent years for age predicting purposes in the forensic area. In order to integrate age prediction into routine forensic workflow, the purpose of this study was to standardize and optimize a DNA methylation-based protocol tailored to the Italian context. A previously published protocol and age-predictive method was implemented for the analysis of 84 blood samples originating from Central Italy. The study here presented is based on the Single Base Extension method, considering five genes: ELOVL2, FHL2, KLF14, C1orf132, now identified as MIR29B2C, and TRIM59. The precise and specific steps consist of DNA extraction and quantification, bisulfite conversion, amplification of converted DNA, first purification, single base extension, second purification, capillary electrophoresis, and analysis of the results to train and test the tool. The prediction error obtained, expressed as mean absolute deviation, showed a value of 3.12 years in the training set and 3.01 years in the test set. Given that population-based differences in DNA methylation patterns have been previously reported in the literature, it would be useful to further improve the study implementing additional samples representative of the entire Italian population.
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14
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Foley MM, Oldoni F. A global snapshot of current opinions of next-generation sequencing technologies usage in forensics. Forensic Sci Int Genet 2023; 63:102819. [PMID: 36509023 DOI: 10.1016/j.fsigen.2022.102819] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
The future of forensic DNA testing is being shaped by the research and usage of next-generation systems, which have increased the multiplexing capabilities of the field and the type and amount of genetic data that can be utilized for investigations. The NGS adoption for casework has been slow, albeit the plethora of data that has been published. This study evaluated the current opinions on sequencing in forensics. A 20-question online-survey focusing on NGS knowledge, training, and usage was distributed to 6001 forensic DNA researchers and practitioners worldwide. A total of 367 responses were obtained from all continents (North/South America (69.8%), Europe (21.2%), Asia (5.5%), Oceania (2.5%), and Africa (1%)). The respondents consisted of 50% practitioners, 31% researchers, and 19% both. Of these, 38% already own a next-gen sequencing instrument, and 13% are planning to purchase one. Overall, there exists an extensive knowledge on next-gen sequencing within the forensic community, including among laboratories that have not yet implemented this high-throughput technology in their workflows. Current usage focuses primarily on SNP analysis for investigative leads and mitochondrial DNA analysis while future applications included both STR and SNP testing applied to general casework. The major overall concerns respondents have for implementing a sequencing instrument include limited funding, staffing, lack of time, and the cost-effectiveness of providing this service. Specific technical concerns that the respondents had are the lack of training, statistical applications, bioinformatics support, and of rigorous guidelines and recommendations. Most of the respondents do believe there will be a technology shift from using CE only to the use of NGS on casework in 5-10 years. In addition, around 66% of respondents believe that it is moderately to very likely that the court will accept sequencing analysis. Sixteen percent fell in the middle, and the remaining 15% believe it is more unlikely, with 3% of respondents believing it is very unlikely. In conclusion, this work outlines current analytical challenges experienced by the global forensic DNA community and addresses different strategies for the implementation of next-gen sequencing technologies in casework.
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Affiliation(s)
- Megan M Foley
- The George Washington University, Department of Forensic Sciences, 2100 Foxhall Rd, Washington, DC 20007, United States
| | - Fabio Oldoni
- Arcadia University, Department of Chemistry & Physics, 450 S Easton Rd, Glenside, PA 19038, United States.
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15
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Akash MSH, Rasheed S, Rehman K, Ibrahim M, Imran M, Assiri MA. Biochemical Activation and Regulatory Functions of Trans-Regulatory KLF14 and Its Association with Genetic Polymorphisms. Metabolites 2023; 13:metabo13020199. [PMID: 36837818 PMCID: PMC9962810 DOI: 10.3390/metabo13020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Krüpple-Like family of transcription factor-14 (KLF14) is a master trans-regulatory gene that has multiple biological regulatory functions and is involved in many pathological mechanisms. It controls the expressions of several other genes which are involved in multiple regulatory functions. KLF14 plays a significant role in lipid metabolism, glucose regulation and insulin sensitivity. Cell apoptosis, proliferation, and differentiation are regulated by the KLF14 gene, and up-regulation of KLF14 prevents cancer progression. KLF14 has been used as an epigenetic biomarker for the estimation of chronological age due to the presence of different age-related CpG sites on genes that become methylated with age. Different genome-wide association studies have identified several KLF14 variants in adipose tissues. These single nucleotide polymorphisms in KLF14 have been associated with dyslipidemia, insulin resistance, and glucose intolerance. Moreover, the prevalence of genetic polymorphism is different in different populations due to ethnic differences and epigenetic modifications. In addition, environmental and physiological factors such as diet, age, gender, and obesity are also responsible for genetic mutations in KLF14.
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Affiliation(s)
- Muhammad Sajid Hamid Akash
- Department of Pharmaceutical Chemistry, Government College University, Faisalabad 38000, Pakistan
- Correspondence: (M.S.H.A.); (K.R.)
| | - Sumbal Rasheed
- Department of Pharmaceutical Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, The Women University, Multan 60000, Pakistan
- Correspondence: (M.S.H.A.); (K.R.)
| | - Muhammad Ibrahim
- Department of Applied Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Imran
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62413, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 62413, Saudi Arabia
| | - Mohammed A. Assiri
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 62413, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 62413, Saudi Arabia
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16
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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17
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Ambroa-Conde A, Girón-Santamaría L, Mosquera-Miguel A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, de la Puente M, Ruiz-Ramírez J, Lareu M, Freire-Aradas A. Epigenetic age estimation in saliva and in buccal cells. Forensic Sci Int Genet 2022; 61:102770. [DOI: 10.1016/j.fsigen.2022.102770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/04/2022]
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18
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Ogata A, Kondo M, Yoshikawa M, Okano M, Tsutsumi T, Aboshi H. Dental age estimation based on DNA methylation using real-time methylation-specific PCR. Forensic Sci Int 2022; 340:111445. [DOI: 10.1016/j.forsciint.2022.111445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/17/2022] [Accepted: 08/28/2022] [Indexed: 11/28/2022]
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19
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Ye Z, Jiang L, Zhao M, Liu J, Dai H, Hou Y, Wang Z. Epigenome-wide screening of CpG markers to develop a multiplex methylation SNaPshot assay for age prediction. Leg Med (Tokyo) 2022; 59:102115. [PMID: 35810521 DOI: 10.1016/j.legalmed.2022.102115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/05/2022] [Accepted: 07/02/2022] [Indexed: 11/30/2022]
Abstract
Age prediction can provide important information about the contributors of biological evidence left at crime scenes. DNA methylation has been regarded as the most promising age-predictive biomarker. Measuring themethylation level at the genome-wide scaleis an important step to screen specific markers for forensic age prediction. In present study, we screened out five age-related CpG sites from the public EPIC BeadChip data and evaluated them in a training set (115 blood) by multiplex methylation SNaPshot assay. Through full subset regression, the five markers were narrowed down to three, namely cg10501210 (C1orf132), cg16867657 (ELOVL2), and cg13108341 (DNAH9), of which the last one was a newly discovered age-related CpG site. An age prediction model was built based on these three markers, explaining 86.8% of the variation of age with a mean absolute deviation (MAD) of 4.038 years. Then, the multiplex methylation SNaPshot assay was adjusted according to the age prediction model. Considering that bloodstains are one of the most common biological samples in practical cases, three validation sets composed of 30 blood, 30 fresh bloodstains and 30 aged bloodstains were used for evaluation of the age prediction model. The MAD of each set was estimated as 4.734, 4.490, and 5.431 years, respectively, suggesting that our age prediction model was applicable for age prediction for blood and bloodstains in Chinese Han population of 11-71 age. In general, this study describes a workflow of screening CpG markers from public chip data and presents a 3-CpG markers model for forensic age prediction.
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Affiliation(s)
- Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hao Dai
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China.
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20
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DNA Methylation Biomarkers-Based Human Age Prediction Using Machine Learning. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:8393498. [PMID: 35111213 PMCID: PMC8803417 DOI: 10.1155/2022/8393498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/20/2021] [Accepted: 12/22/2021] [Indexed: 12/28/2022]
Abstract
Purpose. Age can be an important clue in uncovering the identity of persons that left biological evidence at crime scenes. With the availability of DNA methylation data, several age prediction models are developed by using statistical and machine learning methods. From epigenetic studies, it has been demonstrated that there is a close association between aging and DNA methylation. Most of the existing studies focused on healthy samples, whereas diseases may have a significant impact on human age. Therefore, in this article, an age prediction model is proposed using DNA methylation biomarkers for healthy and diseased samples. Methods. The dataset contains 454 healthy samples and 400 diseased samples from publicly available sources with age (1–89 years old). Six CpG sites are identified from this data having a high correlation with age using Pearson’s correlation coefficient. In this work, the age prediction model is developed using four different machine learning techniques, namely, Multiple Linear Regression, Support Vector Regression, Gradient Boosting Regression, and Random Forest Regression. Separate models are designed for healthy and diseased data. The data are split randomly into 80 : 20 ratios for training and testing, respectively. Results. Among all the techniques, the model designed using Random Forest Regression shows the best performance, and Gradient Boosting Regression is the second best model. In the case of healthy samples, the model achieved a MAD of 2.51 years for training data and 4.85 for testing data. Also, for diseased samples, a MAD of 3.83 years is obtained for training and 9.53 years for testing. Conclusion. These results showed that the proposed model can predict age for healthy and diseased samples.
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21
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Fan H, Xie Q, Zhang Z, Wang J, Chen X, Qiu P. Chronological Age Prediction: Developmental Evaluation of DNA Methylation-Based Machine Learning Models. Front Bioeng Biotechnol 2022; 9:819991. [PMID: 35141217 PMCID: PMC8819006 DOI: 10.3389/fbioe.2021.819991] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetic clock, a highly accurate age estimator based on DNA methylation (DNAm) level, is the basis for predicting mortality/morbidity and elucidating the molecular mechanism of aging, which is of great significance in forensics, justice, and social life. Herein, we integrated machine learning (ML) algorithms to construct blood epigenetic clock in Southern Han Chinese (CHS) for chronological age prediction. The correlation coefficient (r) meta-analyses of 7,084 individuals were firstly implemented to select five genes (ELOVL2, C1orf132, TRIM59, FHL2, and KLF14) from a candidate set of nine age-associated DNAm biomarkers. The DNAm-based profiles of the CHS cohort (240 blood samples differing in age from 1 to 81 years) were generated by the bisulfite targeted amplicon pyrosequencing (BTA-pseq) from 34 cytosine-phosphate-guanine sites (CpGs) of five selected genes, revealing that the methylation levels at different CpGs exhibit population specificity. Furthermore, we established and evaluated four chronological age prediction models using distinct ML algorithms: stepwise regression (SR), support vector regression (SVR-eps and SVR-nu), and random forest regression (RFR). The median absolute deviation (MAD) values increased with chronological age, especially in the 61–81 age category. No apparent gender effect was found in different ML models of the CHS cohort (all p > 0.05). The MAD values were 2.97, 2.22, 2.19, and 1.29 years for SR, SVR-eps, SVR-nu, and RFR in the CHS cohort, respectively. Eventually, compared to the MAD range of the meta cohort (2.53–5.07 years), a promising RFR model (ntree = 500 and mtry = 8) was optimized with an MAD of 1.15 years in the 1–60 age categories of the CHS cohort, which could be regarded as a robust epigenetic clock in blood for age-related issues.
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Affiliation(s)
- Haoliang Fan
- *Correspondence: Haoliang Fan, ; Xuncai Chen, ; Pingming Qiu,
| | | | | | | | - Xuncai Chen
- *Correspondence: Haoliang Fan, ; Xuncai Chen, ; Pingming Qiu,
| | - Pingming Qiu
- *Correspondence: Haoliang Fan, ; Xuncai Chen, ; Pingming Qiu,
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22
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Tyazhelova TV, Kuznetsova IL, Andreeva TV, Kunizheva SS, Rogaev EI. Application of Massive Parallel Sequencing Technology in Forensics: Comparative Analysis of Sequencing Platforms. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Wienroth M, Granja R, Lipphardt V, Nsiah Amoako E, McCartney C. Ethics as Lived Practice. Anticipatory Capacity and Ethical Decision-Making in Forensic Genetics. Genes (Basel) 2021; 12:1868. [PMID: 34946816 PMCID: PMC8701090 DOI: 10.3390/genes12121868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023] Open
Abstract
Greater scrutiny and demands for innovation and increased productivity place pressures on scientists. Forensic genetics is advancing at a rapid pace but can only do so responsibly, usefully, and acceptably within ethical and legal boundaries. We argue that such boundaries require that forensic scientists embrace 'ethics as lived practice'. As a starting point, we critically discuss 'thin' ethics in forensic genetics, which lead to a myopic focus on procedures, and to seeing 'privacy' as the sole ethical concern and technology as a mere tool. To overcome 'thin' ethics in forensic genetics, we instead propose understanding ethics as an intrinsic part of the lived practice of a scientist. Therefore, we explore, within the context of three case studies of emerging forensic genetics technologies, ethical aspects of decision-making in forensic genetics research and in technology use. We discuss the creation, curation, and use of databases, and the need to engage with societal and policing contexts of forensic practice. We argue that open communication is a vital ethical aspect. Adoption of 'ethics as lived practice' supports the development of anticipatory capacity-empowering scientists to understand, and act within ethical and legal boundaries, incorporating the operational and societal impacts of their daily decisions, and making visible ethical decision making in scientific practice.
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Affiliation(s)
- Matthias Wienroth
- Centre for Crime and Policing, Department of Social Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Rafaela Granja
- Communication and Society Research Centre, University of Minho, 4710-057 Braga, Portugal
| | - Veronika Lipphardt
- University College Freiburg, Albert-Ludwigs-Universität, 79098 Freiburg, Germany
| | - Emmanuel Nsiah Amoako
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
| | - Carole McCartney
- Science & Justice Research Interest Group, Law School, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
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Olivares-Castro G, Cáceres-Jensen L, Guerrero-Bosagna C, Villagra C. Insect Epigenetic Mechanisms Facing Anthropogenic-Derived Contamination, an Overview. INSECTS 2021; 12:780. [PMID: 34564220 PMCID: PMC8468710 DOI: 10.3390/insects12090780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022]
Abstract
Currently, the human species has been recognized as the primary species responsible for Earth's biodiversity decline. Contamination by different chemical compounds, such as pesticides, is among the main causes of population decreases and species extinction. Insects are key for ecosystem maintenance; unfortunately, their populations are being drastically affected by human-derived disturbances. Pesticides, applied in agricultural and urban environments, are capable of polluting soil and water sources, reaching non-target organisms (native and introduced). Pesticides alter insect's development, physiology, and inheritance. Recently, a link between pesticide effects on insects and their epigenetic molecular mechanisms (EMMs) has been demonstrated. EMMs are capable of regulating gene expression without modifying genetic sequences, resulting in the expression of different stress responses as well as compensatory mechanisms. In this work, we review the main anthropogenic contaminants capable of affecting insect biology and of triggering EMMs. EMMs are involved in the development of several diseases in native insects affected by pesticides (e.g., anomalous teratogenic reactions). Additionally, EMMs also may allow for the survival of some species (mainly pests) under contamination-derived habitats; this may lead to biodiversity decline and further biotic homogenization. We illustrate these patterns by reviewing the effect of neonicotinoid insecticides, insect EMMs, and their ecological consequences.
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Affiliation(s)
- Gabriela Olivares-Castro
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| | - Lizethly Cáceres-Jensen
- Laboratorio de Físicoquímica Analítica, Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Santiago 7760197, Chile;
| | - Carlos Guerrero-Bosagna
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden;
- Environmental Toxicology Program, Department of Integrative Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Cristian Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
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Li Z, Li J, Li Y, Liu N, Liu F, Ren J, Yun K, Yan J, Zhang G. Development of a multiplex methylation-sensitive restriction enzyme-based SNP typing system for deconvolution of semen-containing mixtures. Int J Legal Med 2021; 135:1281-1294. [PMID: 33813614 DOI: 10.1007/s00414-021-02552-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/24/2021] [Indexed: 11/30/2022]
Abstract
The identification of mixed stains has always been a difficult problem in personal identification in the forensic field. In recent years, tissue-specific methylation sites have proven to be very stable biomarkers for distinguishing tissue origin. However, it is still challenging to perform tissue source identification and individual identification simultaneously. In this study, we developed a method that uses tissue-specific methylation markers combined with single-nucleotide polymorphism (SNP) markers to detect semen from mixed biofluids and to identify individuals simultaneously. Semen-specific CpG markers were chosen from the literature and further validated utilizing methylation-sensitive restriction endonuclease (MSRE) combined with PCR technology. The neighboring SNP markers were searched in the flanking sequence of the target CpG within 400 bp, and SNP typing was then carried out through a single-base extension reaction followed by capillary electrophoresis. Eventually, a method of MSRE combined with SNaPshot that could detect 12 compound CpG-SNP markers was developed. Using this system, 10 ng of total DNA and DNA mixture with semen content up to 25% could be typed successfully. Moreover, the cumulative discrimination power of the system in the northern Chinese Han population is 0.9998. This study provides a valuable strategy for forensic practice to perform tissue origin and individual identification from mixed stains simultaneously.
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Affiliation(s)
- Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Yidan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Na Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
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de Assis Pinheiro J, Freitas FV, Borçoi AR, Mendes SO, Conti CL, Arpini JK, Dos Santos Vieira T, de Souza RA, Dos Santos DP, Barbosa WM, Archanjo AB, de Oliveira MM, Dos Santos JG, Sorroche BP, Casali-da-Rocha JC, Trivilin LO, Borloti EB, Louro ID, Arantes LMRB, Alvares-da-Silva AM. Alcohol consumption, depression, overweight and cortisol levels as determining factors for NR3C1 gene methylation. Sci Rep 2021; 11:6768. [PMID: 33762648 PMCID: PMC7990967 DOI: 10.1038/s41598-021-86189-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
The NR3C1 glucocorticoid receptor (GR) gene is a component of the stress response system, which can be regulated by epigenetic mechanisms. NR3C1 methylation has been associated with trauma and mental issues, including depression, post-traumatic stress, anxiety, and personality disorders. Previous studies have reported that stressful events are involved in NR3C1 gene methylation, suggesting that its regulation under environmental effects is complex. The present study aimed to analyze associations involving stressors such as socioeconomic status, health conditions, and lifestyle in relation to NR3C1 methylation in adults. This study included 386 individual users of the Brazilian Public Unified Health System (SUS), and evaluated socioeconomic and health conditions, body mass index, cortisol levels, and lifestyle. Data were correlated with NR3C1 methylation, determined using DNA pyrosequencing. The results showed that alcohol consumption, overweight, and high cortisol levels were related to NR3C1 demethylation, while depression was related to its methylation. Habits, lifestyle, and health status may influence NR3C1 gene regulation via methylation, revealing the complexity of environmental impacts on NR3C1 methylation.
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Affiliation(s)
- Júlia de Assis Pinheiro
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | - Flávia Vitorino Freitas
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil.,Department of Pharmacy and Nutrition, Universidade Federal do Espirito Santo, Alegre, ES, Brazil
| | - Aline Ribeiro Borçoi
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | - Suzanny Oliveira Mendes
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | - Catarine Lima Conti
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | - Juliana Krüger Arpini
- Graduate Program in Forest Sciences, Universidade Federal do Espirito Santo, Alegre, ES, Brazil
| | - Tamires Dos Santos Vieira
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | | | | | - Wagner Miranda Barbosa
- Department of Pharmacy and Nutrition, Universidade Federal do Espirito Santo, Alegre, ES, Brazil
| | - Anderson Barros Archanjo
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | - Mayara Mota de Oliveira
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | | | - Bruna Pereira Sorroche
- Molecular Oncology Research Center, Hospital do Câncer de Barretos, Barretos, SP, Brazil
| | | | | | - Elizeu Batista Borloti
- Department of Social and Developmental Psychology, Universidade Federal do Espírito Santo, Vitoria, ES, Brazil
| | - Iuri Drumond Louro
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil
| | | | - Adriana Madeira Alvares-da-Silva
- Biotechnology/Renorbio Graduate Program, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil. .,Department of Morphology, Health Science Center, Universidade Federal do Espirito Santo, Vitoria, ES, Brazil. .,Departamento de Biologia, Universidade Federal do Espirito Santo, Alto Universitário Sem Número, Alegre, ES, 29500000, Brazil.
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Application of fragment analysis based on methylation status mobility difference to identify vaginal secretions. Sci Justice 2021; 61:384-390. [PMID: 34172127 DOI: 10.1016/j.scijus.2021.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/16/2021] [Accepted: 03/13/2021] [Indexed: 11/21/2022]
Abstract
Identifying vaginal secretions attaching or adhering to a suspect's belongings would be beneficial for reconstructing the events that have taken place during a sexual assault. The present study describes a novel approach to identify vaginal secretions by fragment analysis using capillary electrophoresis, based on the mobility differences of PCR amplicons from bisulfite-treated DNA depending on methylation status. We targeted three genome regions including each of three vaginal secretion-specific methylated CpG sites reported previously: cg25416153, cg09765089, and cg14991487. In all three genome regions, the amplicon peaks for methylated genomic DNA (gDNA) sequences were only detected in vaginal samples, whereas samples of other body fluids (blood, saliva, semen, and deposit on skin surface) only showed amplicon peaks for unmethylated gDNA sequences. In vaginal secretions, the methylation ratio of each of the three targeted regions between samples was variable, while the ratios at the three regions in each sample were similar. Furthermore, commercial vaginal epithelial cells were completely methylated at the three regions. Therefore, vaginal secretion-specific methylation may derive from vaginal epithelial cells present in the sample. In forensic cases with a limited amount of DNA, the reproducibility of a detected peak using the present method is not high due to degradation of DNA by bisulfite treatment and subsequent stochastic PCR bias. However, it was possible to detect peaks from methylated DNA sequences by performing PCR and capillary electrophoresis in triplicate after bisulfite treatment, even when bisulfite treatment was performed using 0.5 ng of gDNA from vaginal secretions. In addition, the level of methylation at each targeted region was found to be stable in vaginal secretions stored for 1 year at room temperature. Therefore, we conclude that detection of the visual peak from vaginal secretion-specific methylated DNA sequence is useful to prove the presence of vaginal secretions. This approach has the potential to analyze multiple marker regions simultaneously, and may provide a new multiplex assay to identify various body fluids.
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Romanos P, Borjac J. Epigenetic Discrimination of Lebanese Monozygotic Twins as a Promising Forensic Approach. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Turrina S, Bortoletto E, Giannini G, De Leo D. Monozygotic twins: Identical or distinguishable for science and law? MEDICINE, SCIENCE, AND THE LAW 2021; 61:62-66. [PMID: 33591870 DOI: 10.1177/0025802420922335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Monozygotic twins, also known as monovular twins, share an identical genetic heritage because they are two individuals who derive from the same zygote. For this reason, they have been considered indistinguishable. They represent a limit for the application of markers and analytical methods that are routinely used in forensic science because analyses of DNA fragments (short tandem repeats analysed by capillary electrophoresis) are unable to distinguish monozygotic twins. The recent introduction of ultra-deep next generation sequencing in forensic genetics, also known as massively parallel sequencing, has made it possible to identify a number of genetic variations through genome sequencing (such as copy number variations, single nucleotide polymorphisms and DNA methylation) that make it possible to distinguish monozygotic twins. Here, we present a case of ascertaining biological paternity, in which the alleged father had a monozygotic twin brother. This case led to the examination of international law in similar cases in which the only available biological evidence derives from classical forensic genetic analysis, performed with short tandem repeat (autosomal and/or gonosomal) capillary electrophoresis and the probative value, if recognised, of the next generation sequencing technology in the courtroom.
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Affiliation(s)
- Stefania Turrina
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Elena Bortoletto
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Giacomo Giannini
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
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31
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Kondo M, Aboshi H, Yoshikawa M, Ogata A, Murayama R, Takei M, Aizawa S. A newly developed age estimation method based on CpG methylation of teeth-derived DNA using real-time methylation-specific PCR. J Oral Sci 2020; 63:54-58. [PMID: 33281149 DOI: 10.2334/josnusd.20-0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Age estimation of unidentified bodies is important in forensic medicine and crime scenes. There is accumulating evidence that DNA methylation in the human genome isolated from body fluids changes with age. Most of the data have been obtained by pyrosequencing. In the forensic field, a simple, quick, and economical method is required to evaluate the age of various types of samples. In this study, an age estimation method based on methylation levels of DNA extracted from teeth using real-time methylation-specific PCR (MSP) was developed. The CpG island in the upstream region of ELOVL2, which is known as a validated biomarker in blood samples, was selected as a target site. The CpG methylation levels highly correlated with age (r = 0.843, n = 29). Age-related increase in DNA methylation levels was not affected by sex differences. In addition, the simple regression model based on methylation status of the CpG island exhibited moderate accuracy with a mean absolute deviation between chronological age and predicted age of 8.94 years. The results imply that real-time MSP can be a new tool to perform age prediction of unidentified bodies in forensic scenes.
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Affiliation(s)
- Masahiro Kondo
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Hirofumi Aboshi
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Masaaki Yoshikawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine
| | - Ayano Ogata
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Ryosuke Murayama
- Department of Legal Medicine, Nihon University School of Dentistry
| | - Masami Takei
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine
| | - Shin Aizawa
- Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine
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Alghanim H, Balamurugan K, McCord B. Development of DNA methylation markers for sperm, saliva and blood identification using pyrosequencing and qPCR/HRM. Anal Biochem 2020; 611:113933. [PMID: 32891597 DOI: 10.1016/j.ab.2020.113933] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
Discrimination of body fluids can provide important information in the investigation of crime scenes. The goal of this project was to identify new sets of tissue specific differentially methylated regions (tDMRs) and develop assays that can be utilized for forensic discrimination of body fluids, in particular sperm, saliva and blood. In this study, a sample set containing semen with sperm, semen without sperm, buccal swabs, saliva (oral fluids), venous blood, menstrual blood, vaginal secretions, and sweat/skin samples were used to develop four assays. Two methods for the analysis of DNA methylation biomarkers were developed in this paper: pyrosequencing and quantitative PCR/high resolution melt (HRM) analysis. Using an epigenome wide association study, two markers, NMUR2 and UBE2U, were found to be specific for sperm, based on the fact that mean DNA methylation levels for semen (containing sperm cells) were significantly lower than mean DNA methylation levels of other body fluids. In addition, one marker (SA-6) was hypermethylated in saliva when compared to other body fluids. The assays developed for NMUR2, UBE2U and SA-6 markers can be applied in forensic tissue identification using both pyrosequencing and HRM analysis. Additionally, a set of CpG sites in the AHRR locus were hypomethylated in blood when compared to other tissues using pyrosequencing. However, this locus was not amenable to HRM analysis. Overall, this work demonstrates the discovery and application of tDMRs for forensic applications.
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Affiliation(s)
- Hussain Alghanim
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA; General Department of Forensic Science and Criminology, Dubai Police, Dubai, United Arab Emirates
| | - Kuppareddi Balamurugan
- School of Criminal Justice, Forensic Science and Security, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA.
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Maulani C, Auerkari EI. Age estimation using DNA methylation technique in forensics: a systematic review. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00214-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AbstractBackgroundIn addition to the DNA sequence, epigenetic markers have become substantial forensic tools during the last decade. Estimating the age of an individual from human biological remains may provide information for a forensic investigation. Age estimation in molecular strategies can be obtained by telomere length, mRNa mutation, or by sjTRECs but the accuracy is not sufficient in forensic practice because of high margin error.Main bodyOne solution to this problem is to use DNA methylation methods. DNA methylation markers for tissue identification at age-associated CpG sites have been suggested as the most informative biomarkers for estimating the age of an unknown donor. This review aims to give an overview of DNA methylation profiling for estimating the age in cases of forensic relevance and the important aspects in determining the mean absolute deviation (MAD) or mean absolute error (MAE) of the estimated age. Online database searching was performed through PubMed, Scopus, and Google Scholar with keywords selected for forensic age estimation. Thirty-two studies were included in the review, with variable DNA samples but blood commonly as a source. Pyrosequencing and EpiTYPER were methods mostly used in DNA analysis. The MAD in the estimates from DNA methylation was about 3 to 5 years, which was better than other methods such as those based on telomere length or signal-joint T-cell receptor excision circles. The ELOVL2 gene was a commonly used DNA methylation marker in age estimation.ConclusionDNA methylation is a favorable candidate for estimating the age at the time of death in forensic profiling, with an uncertainty mean absolute deviation of about 3 to 5 years in the predicted age. The sample type, platform techniques used, and methods to construct age predictive models were important in determining the accuracy in mean absolute deviation or mean absolute error. The DNA methylation outcome suggests good potential to support conventional STR profiling in forensic cases.
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Kong FC, Ma CL, Zhong MK. Epigenetic Effects Mediated by Antiepileptic Drugs and their Potential Application. Curr Neuropharmacol 2020; 18:153-166. [PMID: 31660836 PMCID: PMC7324883 DOI: 10.2174/1570159x17666191010094849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/01/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
An epigenetic effect mainly refers to a heritable modulation in gene expression in the short term but does not involve alterations in the DNA itself. Epigenetic molecular mechanisms include DNA methylation, histone modification, and untranslated RNA regulation. Antiepileptic drugs have drawn attention to biological and translational medicine because their impact on epigenetic mechanisms will lead to the identification of novel biomarkers and possible therapeutic strategies for the prevention and treatment of various diseases ranging from neuropsychological disorders to cancers and other chronic conditions. However, these transcriptional and posttranscriptional alterations can also result in adverse reactions and toxicity in vitro and in vivo. Hence, in this review, we focus on recent findings showing epigenetic processes mediated by antiepileptic drugs to elucidate their application in medical experiments and shed light on epigenetic research for medicinal purposes.
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Affiliation(s)
- Fan-Cheng Kong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Chun-Lai Ma
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming-Kang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
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Kader F, Ghai M, Zhou M. Ethnicity, age and disease-associated variation in body fluid-specific CpG sites in a diverse South African cohort. Forensic Sci Int 2020; 314:110372. [PMID: 32623090 DOI: 10.1016/j.forsciint.2020.110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/11/2022]
Abstract
Tissue-specific differential DNA methylation has been an attractive target for the development of markers for discrimination of body fluids found at crime scenes. Though mostly stable, DNA methylation patterns have been shown to vary between different ethnic groups, in different age groups as well as between healthy and diseased individuals. To the best of our knowledge, none of the markers for body fluid identification have been applied to different ethnic groups to ascertain if variability exists. In the present study, saliva and blood were collected to determine the effects of ethnicity (Blacks, Whites, Coloureds and Indians), age (20-30 years, 40-50years and above 60 years) and diabetes on methylation profiles of potential saliva- and blood-specific DMSs. Both DMSs were previously shown to exhibit hypermethylation in their target body fluids at single CpG sites, however in the present study, additional CpG sites flanking the reported sites were also screened. Bisulfite sequencing revealed that Coloureds showed highest methylation levels for both body fluids, and blacks displayed significant differences between other ethnic groups in the blood-specific CpG sites. A decline in methylation for both potential DMRs was observed with increasing age. Heavily methylated CpG sites in different ethnic groups and previously reported DMSs displayed hypomethylation with increasing age and disease status. Diabetic status did not show any significant difference in methylation when compared to healthy counterparts. Thus, the use of methylation markers for forensics needs thorough investigation of influence of external factors and ideally, several CpG sites should be co-analysed instead of a single DMS.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Marvellous Zhou
- South African Sugarcane Research Institute, Mount Edgecombe, Durban, South Africa; University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa.
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McCord B, Gauthier Q, Alghanim H, Antunes J, Fernandez Tejero N, Duncan G, Balamurugan K. Applications of epigenetic methylation in body fluid identification, age determination and phenotyping. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Yuan L, Chen X, Liu Z, Liu Q, Song A, Bao G, Wei G, Zhang S, Lu J, Wu Y. Identification of the perpetrator among identical twins using next-generation sequencing technology: A case report. Forensic Sci Int Genet 2019; 44:102167. [PMID: 31605960 DOI: 10.1016/j.fsigen.2019.102167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/12/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Monozygotic (MZ) twins, considered genetically identical, cannot be distinguished using regular short tandem repeats (STR) typing, thus presenting a challenge for forensic geneticists. In paternity testing, single nucleotide polymorphisms (SNPs) in nuclear DNA can help distinguish MZ twins. However, the unique features of the mitochondrial genome, such as high copy number, small genome size, and high substitution rate, make it a promising source for applications in forensic science. METHODS Whole-genome sequencing (WGS) was performed on blood samples, and bioinformatic analysis was used to distinguish between MZ twins. Amplification refractory mutation system polymerase chain reaction (ARMS-PCR) was used to confirm the WGS results. This methodology was further applied to forensic samples from criminal cases. Amplicon sequencing was also performed to further exclude the innocent twin. RESULTS The monozygosity of the twins was confirmed using STR typing. Only one potential somatic mutation, m.6903 T > C (2.6%), in the mitochondrial genome of one of the twins was verified when the sequence depth was set to 2000-fold, while no other distinguishing locus in the nuclear genome was identified. By dividing the number of C-reads by total reads, WGS data confirmed the amount of the minor component C to be 2.6%, which was further confirmed by ARMS-PCR. In addition, the heterogeneous locus was used to identify samples obtained from four criminal cases for forensic testing. Two heterogeneous loci in the sperm DNA of the other twin were identified by amplicon sequencing, and the amount of minor component T in m.6935C > T and m.6938C > T was estimated to be 17.91% and 18.79%, respectively. CONCLUSION The biological samples taken from the MZ twins were distinguished using a combination of WGS, allele-specific PCR, and deep-amplicon sequencing. Compared with nuclear DNA, mitochondrial DNA exhibited a higher potential for distinguishing between the MZ twins. The distinguishing feature of the mitochondrial DNA was the heterogeneous SNPs that occurred in only one twin. One SNP was further verified in the samples from the criminal cases and helped identify the perpetrator in case 1 and case 2. Furthermore, two heterogeneous SNPs found by amplicon sequencing helped to exclude the innocent twin in all four cases. Our findings demonstrated that a combination of deep sequencing and molecular analysis can be an effective way to distinguish between identical twins and can be used to analyze samples from criminal cases.
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Affiliation(s)
- Lijuan Yuan
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China; Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Xihui Chen
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Ziyu Liu
- Department of Microbiology, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Qingbo Liu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - An Song
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Guoqiang Bao
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Gang Wei
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China
| | - Sijia Zhang
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China
| | - Jianguo Lu
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an, Shaanxi 710038, PR China.
| | - Yuanming Wu
- Department of Biochemistry and Molecular Biology, Center for DNA Typing, Air Force Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, PR China.
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Alsaleh H, Haddrill PR. Identifying blood-specific age-related DNA methylation markers on the Illumina MethylationEPIC® BeadChip. Forensic Sci Int 2019; 303:109944. [PMID: 31546163 DOI: 10.1016/j.forsciint.2019.109944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/14/2019] [Accepted: 09/01/2019] [Indexed: 01/02/2023]
Abstract
The past decade has seen rapid development in DNA methylation (DNAm) microarrays, including the Illumina HumanMethylation27 and HumanMethylation450 (450K) chips, which have played an essential role in identifying and evaluating age-related (AR) DNAm markers in different tissues. Recently, a new array, the Illumina MethylationEPIC (EPIC) was introduced, with nearly double the number of probes as the 450K (∼850,000 probes). In this study, we test these newly added probes for age association using a large cohort of 754 DNAm profiles from blood samples assayed on the EPIC BeadChip, for individuals aged 0-88 years old. 52 AR CpG sites (Spearman's abs(rho) >0.6 and P-value <10-83) were identified, 21 of which were novel sites and mapped to 18 genes, nine of which (LHFPL4, SLC12A8, EGFEM1P, GPR158, TAL1, KIAA1755, LOC730668, DUSP16, and FAM65C) have never previously been reported to be associated with age. The data were subsequently split into a 527-sample training set and a 227-sample testing set to build and validate two age prediction models using elastic net regression and multivariate regression. Elastic net regression selected 425 CpG markers with a mean absolute deviation (MAD) of 2.6 years based on the testing set. To build a multivariate linear regression model, AR CpG sites with R2 > 0.5 at FDR < 0.05 were input into stepwise regression to select the best subset for age prediction. The resulting six CpG markers were linearly modelled with age and explained 81% of age-correlated variation in DNAm levels. Age estimation accuracy using bootstrap analysis was 4.5 years, with 95% confidence intervals of 4.56 to 4.57 years based on the testing set. These results suggest that EPIC BeadChip probes for age estimation fall within the range of probes found on the previous Illumina HumanMethylation platforms in terms of their age-prediction ability.
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Affiliation(s)
- Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK; General Department for Forensic Evidence, State of Kuwait Ministry of Interior, Kuwait.
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, Scotland, UK
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Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
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40
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Abstract
Identifying and validating molecular targets of interventions that extend the human health span and lifespan has been difficult, as most clinical biomarkers are not sufficiently representative of the fundamental mechanisms of ageing to serve as their indicators. In a recent breakthrough, biomarkers of ageing based on DNA methylation data have enabled accurate age estimates for any tissue across the entire life course. These 'epigenetic clocks' link developmental and maintenance processes to biological ageing, giving rise to a unified theory of life course. Epigenetic biomarkers may help to address long-standing questions in many fields, including the central question: why do we age?
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41
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Xin Y, Dong K, Cao F, Tian Y, Sun J, Peng M, Liu W, Shi P. Studies of hTERT DNA methylation assays on the human age prediction. Int J Legal Med 2019; 133:1333-1339. [PMID: 31165262 DOI: 10.1007/s00414-019-02076-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/17/2019] [Indexed: 11/25/2022]
Abstract
As an important aspect of epigenetics, DNA methylation has been proven to be suitable for forensic DNA analysis. By detecting changes in DNA methylation, it is desirable to construct a model of age patterns associated with it to infer the age of the individual. The hTERT gene methylation is closely related to tumors, but there are few reports on the relationship between hTERT gene promoter methylation and age. In this study, we utilized the methylation-specific polymerase chain reaction and real-time PCR (relative quantification and absolute quantification) approach to explore the connection between hTERT DNA methylation and age prediction. We fit three models for age prediction based on methylation assay for 90 blood samples from donors aged 1-79 years old. Among them, the model of absolute quantification of real-time enabled the age prediction with R2 = 0.9634. We verified the linear regression model with a validation set of 30 blood samples where prediction average error was 4.29 years. Generally, this reliable method improves the DNA methylation analysis of forensic samples.
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Affiliation(s)
- Ye Xin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Kaikai Dong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Fangqi Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai, 200083, China
| | - Yuxiang Tian
- Department of Clinical Laboratory, Shanghai Xuhui District Dahua Hospital, Shanghai, 200237, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China
| | - Min Peng
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai, 200083, China.
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, The Chinese Academy of Sciences, Xiguan Avenue 59, Xining, 11 Qinghai Province, 810001, China.
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42
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Dyke SOM, Saulnier KM, Dupras C, Webster AP, Maschke K, Rothstein M, Siebert R, Walter J, Beck S, Pastinen T, Joly Y. Points-to-consider on the return of results in epigenetic research. Genome Med 2019; 11:31. [PMID: 31122281 PMCID: PMC6533659 DOI: 10.1186/s13073-019-0646-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies, will be of growing importance. Members of the International Human Epigenome Consortium (IHEC) Bioethics Workgroup considered the potential ethical, legal, and social issues (ELSI) involved in returning epigenetic research results and incidental findings in order to produce a set of 'Points-to-consider' (P-t-C) for the epigenetics research community. These P-t-C draw on existing guidance on the return of genetic research results, while also integrating the IHEC Bioethics Workgroup's ELSI research on and discussion of the issues associated with epigenetic data as well as the experience of a return of results pilot study by the Personal Genome Project UK (PGP-UK). Major challenges include how to determine the clinical validity and actionability of epigenetic results, and considerations related to environmental exposures and epigenetic marks, including circumstances warranting the sharing of results with family members and third parties. Interdisciplinary collaboration and good public communication regarding epigenetic risk will be important to advance the return of results framework for epigenetic science.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 2B4, Canada.
| | - Katie M Saulnier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Dupras
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | | | - Mark Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University Medical Center, 89091, Ulm, Germany
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, H3A 0G1, Canada
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Yann Joly
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
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43
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Stewart V, Deacon P, Zahra N, Uchimoto ML, Farrugia KJ. The effect of mark enhancement techniques on the presumptive and confirmatory tests for blood. Sci Justice 2018; 58:386-396. [DOI: 10.1016/j.scijus.2018.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/16/2018] [Accepted: 06/24/2018] [Indexed: 01/25/2023]
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44
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Recent progress, methods and perspectives in forensic epigenetics. Forensic Sci Int Genet 2018; 37:180-195. [PMID: 30176440 DOI: 10.1016/j.fsigen.2018.08.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 01/19/2023]
Abstract
Forensic epigenetics, i.e., investigating epigenetics variation to resolve forensically relevant questions unanswerable with standard forensic DNA profiling has been gaining substantial ground over the last few years. Differential DNA methylation among tissues and individuals has been proposed as useful resource for three forensic applications i) determining the tissue type of a human biological trace, ii) estimating the age of an unknown trace donor, and iii) differentiating between monozygotic twins. Thus far, forensic epigenetic investigations have used a wide range of methods for CpG marker discovery, prediction modelling and targeted DNA methylation analysis, all coming with advantages and disadvantages when it comes to forensic trace analysis. In this review, we summarize the most recent literature on these three main topics of current forensic epigenetic investigations and discuss limitations and practical considerations in experimental design and data interpretation, such as technical and biological biases. Moreover, we provide future perspectives with regard to new research questions, new epigenetic markers and recent technological advances that - as we envision - will move the field towards forensic epigenomics in the near future.
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45
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Naue J, Sänger T, Hoefsloot HCJ, Lutz-Bonengel S, Kloosterman AD, Verschure PJ. Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing. Forensic Sci Int Genet 2018; 36:152-159. [PMID: 30031222 DOI: 10.1016/j.fsigen.2018.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022]
Abstract
The use of DNA methylation (DNAm) for chronological age determination has been widely investigated within the last few years for its application within the field of forensic genetics. The majority of forensic studies are based on blood, saliva, and buccal cell samples, respectively. Although these types of samples represent an extensive amount of traces found at a crime scene or are readily available from individuals, samples from other tissues can be relevant for forensic investigations. Age determination could be important for cases involving unidentifiable bodies and based on remaining soft tissue e.g. brain and muscle, or completely depend on hard tissue such as bone. However, due to the cell type specificity of DNAm, it is not evident whether cell type specific age-dependent CpG positions are also applicable for age determination in other cell types. Within this pilot study, we investigated whether 13 previously selected age-dependent loci based on whole blood analysis including amongst others ELOVL2, TRIM59, F5, and KLF14 also have predictive value in other forensically relevant tissues. Samples of brain, bone, muscle, buccal swabs, and whole blood of 29 deceased individuals (age range 0-87 years) were analyzed for these 13 age-dependent markers using massive parallel sequencing. Seven of these loci did show age-dependency in all five tissues. The change of DNAm during lifetime was different in the set of tissues analyzed, and sometimes other CpG sites within the loci showed a higher age-dependency. This pilot study shows the potential of existing blood DNAm markers for age-determination to analyze other tissues than blood. We identified seven known blood-based DNAm markers for use in muscle, brain, bone, buccal swabs, and blood. Nevertheless, a different reference set for each tissue is needed to adapt for tissue-specific changes of the DNAm over time.
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Affiliation(s)
- Jana Naue
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands; Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Timo Sänger
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Huub C J Hoefsloot
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ate D Kloosterman
- Netherlands Forensic Institute, Biological Traces, Laan van Ypenburg 6, 2497GB Den Haag, The Netherlands; University of Amsterdam, Institute for Biodiversity and Dynamics, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Pernette J Verschure
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands.
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46
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Mahna D, Puri S, Sharma S. DNA methylation signatures: Biomarkers of drug and alcohol abuse. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:19-28. [DOI: 10.1016/j.mrrev.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023]
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47
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Richards R, Patel J, Stevenson K, Harbison S. Evaluation of massively parallel sequencing for forensic DNA methylation profiling. Electrophoresis 2018; 39:2798-2805. [DOI: 10.1002/elps.201800086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/06/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Rebecca Richards
- Forensic Science Programme, School of Chemical Sciences; University of Auckland; Auckland New Zealand
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - Jayshree Patel
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - Kate Stevenson
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
| | - SallyAnn Harbison
- Institute of Environmental Science & Research Ltd. (ESR); Auckland New Zealand
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48
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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49
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Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
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50
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Stafford-Allen B, Dawnay N, Hanson EK, Ball G, Gupta A, Blackman S, French DJ, Duxbury N, Ballantyne J, Wells S. Development of HyBeacon ® probes for specific mRNA detection using body fluids as a model system. Mol Cell Probes 2017; 38:51-59. [PMID: 29175285 DOI: 10.1016/j.mcp.2017.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022]
Abstract
HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods. The work presented here details the development of a single-step one-tube RT-PCR assay to detect the presence of body fluids of forensic interest (saliva, blood, seminal fluid, vaginal fluid and menstrual blood) using HyBeacon® probes and melt curve analysis. Each assay shows a high degree of specificity to the target body fluid mRNA suggesting there is no requirement to remove genomic DNA prior to analysis. Of the five assays developed, four were able to detect between 10 and 100 copies of target cDNA, the fifth 1000 copies of target. The results presented here demonstrate that such an approach can be optimised for non-expert users and further areas of work are discussed.
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Affiliation(s)
- Beccy Stafford-Allen
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK.
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Erin K Hanson
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA
| | - Glyn Ball
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Ambika Gupta
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Stephen Blackman
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - David J French
- Product Development Group, LGC Ltd, Queens Road, Teddington, TW11 0LY, UK
| | - Nicola Duxbury
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Jack Ballantyne
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA; Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL, 32816-2366, USA
| | - Simon Wells
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
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