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Soedarsono N, Hanafi MGS, Hartomo BT, Auerkari EI. ELOVL2, PRKG2, and EDARADD DNA Methylation Strongly Estimate Indonesian Adolescents. Diagnostics (Basel) 2024; 14:1767. [PMID: 39202255 PMCID: PMC11353275 DOI: 10.3390/diagnostics14161767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 09/03/2024] Open
Abstract
Recently, there has been a growing interest in using DNA methylation analysis for age estimation. Despite this growing interest, there is a scarcity of research on the potential of DNA methylation as a biomarker for age estimation in Indonesia. This study aims to investigate the applicability of ELOVL2, PRKG2, and EDARADD genes for forensic identification in the 11-20 age group among Indonesians. This research utilizes 43 archived blood samples from healthy individuals who underwent blood tests at the Gatot Soebroto Army Hospital (RSPAD) in Central Jakarta, Indonesia. The methylation-specific PCR (MSP) technique assessed the DNA methylation level. The key findings of this study include (1) a strong positive correlation between methylation levels in the ELOVL2 gene and age; (2) a strong negative correlation between methylation levels in PRKG2 and EDARADD genes with age; (3) the development of three linear regression formulas for age prediction; and (4) mean absolute error (MAE) values derived from this research, which are ±0.48 for ELOVL2 gene regression formula, ±0.58 for PRKG2 gene regression formula, and ±0.72 for EDARADD gene regression formula. In summary, this study explores the potential of DNA methylation analysis for age estimation in Indonesia, focusing on ELOVL2, PRKG2, and EDARADD genes in the 11-20 age group. The findings underscore the applicability of DNA methylation analysis in forensic identification and age estimation, paving the way for future research in this field.
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Affiliation(s)
- Nurtami Soedarsono
- Division of Forensic Odontology, Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Kota Depok, DKI, Jakarta 10430, Indonesia; (M.G.S.H.); (E.I.A.)
| | - Muhammad Garry Syahrizal Hanafi
- Division of Forensic Odontology, Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Kota Depok, DKI, Jakarta 10430, Indonesia; (M.G.S.H.); (E.I.A.)
| | - Bambang Tri Hartomo
- Department of Dental Medicine, Faculty of Medicine, Universitas Jenderal Soedirman, Purwokerto 53122, Indonesia;
| | - Elza Ibrahim Auerkari
- Division of Forensic Odontology, Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Kota Depok, DKI, Jakarta 10430, Indonesia; (M.G.S.H.); (E.I.A.)
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2
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [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: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 PMCID: PMC11050192 DOI: 10.3390/ijms25084230] [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: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
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Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
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4
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Refn MR, Andersen MM, Kampmann ML, Tfelt-Hansen J, Sørensen E, Larsen MH, Morling N, Børsting C, Pereira V. Longitudinal changes and variation in human DNA methylation analysed with the Illumina MethylationEPIC BeadChip assay and their implications on forensic age prediction. Sci Rep 2023; 13:21658. [PMID: 38066081 PMCID: PMC10709620 DOI: 10.1038/s41598-023-49064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation, a pivotal epigenetic modification, plays a crucial role in regulating gene expression and is known to undergo dynamic changes with age. The present study investigated epigenome-wide methylation profiles in 64 individuals over two time points, 15 years apart, using the Illumina EPIC850k arrays. A mixed-effects model identified 2821 age-associated differentially methylated CpG positions (aDMPs) with a median rate of change of 0.18% per year, consistent with a 10-15% change during a human lifespan. Significant variation in the baseline DNA methylation levels between individuals of similar ages as well as inconsistent direction of change with time across individuals were observed for all the aDMPs. Twenty-three of the 2821 aDMPs were previously incorporated into forensic age prediction models. These markers displayed larger changes in DNA methylation with age compared to all the aDMPs and less variation among individuals. Nevertheless, the forensic aDMPs also showed inter-individual variations in the direction of DNA methylation changes. Only cg16867657 in ELOVL2 exhibited a uniform direction of the age-related change among the investigated individuals, which supports the current knowledge that CpG sites in ELOVL2 are the best markers for age prediction.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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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: 5] [Impact Index Per Article: 5.0] [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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6
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Refn MR, Kampmann ML, Morling N, Tfelt-Hansen J, Børsting C, Pereira V. Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives. Forensic Sci Res 2023; 8:85-97. [PMID: 37621446 PMCID: PMC10445583 DOI: 10.1093/fsr/owad021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/28/2023] [Indexed: 08/26/2023] Open
Abstract
Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen , Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Anić P, Golubić Talić J, Božinović K, Dediol E, Mravak-Stipetić M, Grce M, Milutin Gašperov N. Methylation of Immune Gene Promoters in Oral and Oropharyngeal Cancer. Int J Mol Sci 2023; 24:ijms24097698. [PMID: 37175405 PMCID: PMC10178514 DOI: 10.3390/ijms24097698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
The proportion of oral and oropharyngeal squamous cell carcinoma (OOSCC) that can be attributed to human papillomavirus (HPV) infection is growing nowadays. A potential factor indicating the occurrence of HPV-positive OSCC is a change in the degree of methylation of gene promoters that play a key role in the immune response. In this study, we investigated the difference in the methylation of EDARADD, GBP4, HAVCR2, HLA DPB1, IL12RB1, MARCO, and SIGLEC12 gene promoters in samples of healthy oral mucosa versus samples of oral and oropharyngeal cancer. The presence of HPV infection in samples was examined earlier. To determine the difference in methylation of those gene promotors, isolated and bisulfite-modified DNA was analysed by the methylation-specific PCR method. The investigated gene promoters were found to be more hypomethylated in the oral and oropharyngeal cancer samples in comparison to normal tissue. The proportion of unmethylated gene promoters was similar in HPV-positive and HPV-negative cancers, although the data should be confirmed on a larger set of samples. To conclude, in samples of healthy oral mucosa, the investigated gene promoters were found to be methylated in a high percentage (73.3% to 100%), while in oral and oropharyngeal cancer samples, they were methylated in a low percentage (11.1% to 37%), regardless of HPV infection.
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Affiliation(s)
- Petra Anić
- Research Department, Srebrnjak Children's Hospital, 10000 Zagreb, Croatia
| | | | - Ksenija Božinović
- Department of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Emil Dediol
- Department of Maxillofacial Surgery, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marinka Mravak-Stipetić
- Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Magdalena Grce
- Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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9
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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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Yang F, Qian J, Qu H, Ji Z, Li J, Hu W, Cheng F, Fang X, Yan J. DNA methylation-based age prediction with bloodstains using pyrosequencing and random forest regression. Electrophoresis 2023; 44:835-844. [PMID: 36739525 DOI: 10.1002/elps.202200250] [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: 10/12/2022] [Revised: 12/08/2022] [Accepted: 01/24/2023] [Indexed: 02/06/2023]
Abstract
The use of DNA methylation to predict chronological age has shown promising potential for obtaining additional information in forensic investigations. To date, several studies have reported age prediction models based on DNA methylation in body fluids with high DNA content. However, it is often difficult to apply these existing methods in practice due to the low amount of DNA present in stains of body fluids that are part of a trace material. In this study, we present a sensitive and rapid test for age prediction with bloodstains based on pyrosequencing and random forest regression. This assay requires only 0.1 ng of genomic DNA and the entire procedure can be completed within 10 h, making it practical for forensic investigations that require a short turnaround time. We examined the methylation levels of 46 CpG sites from six genes using bloodstain samples from 128 males and 113 females aged 10-79 years. A random forest regression model was then used to construct an age prediction model for males and females separately. The final age prediction models were developed with seven CpG sites (three for males and four for females) based on the performance of the random forest regression. The mean absolute deviation was less than 3 years for each model. Our results demonstrate that DNA methylation-based age prediction using pyrosequencing and random forest regression has potential applications in forensics to accurately predict the biological age of a bloodstain donor.
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Affiliation(s)
- Fenglong Yang
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Jialin Qian
- Beijing Center for Physical and Chemical Analysis, Beijing, P. R. China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, P. R. China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Shanxi, P. R. China
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11
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Manco L, Dias HC. DNA methylation analysis of ELOVL2 gene using droplet digital PCR for age estimation purposes. Forensic Sci Int 2022; 333:111206. [DOI: 10.1016/j.forsciint.2022.111206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 11/16/2022]
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12
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Correia Dias H, Manco L, Corte Real F, Cunha E. A Blood-Bone-Tooth Model for Age Prediction in Forensic Contexts. BIOLOGY 2021; 10:biology10121312. [PMID: 34943227 PMCID: PMC8698317 DOI: 10.3390/biology10121312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary DNA methylation age estimation is one of the hottest topics in forensic field nowadays. Age estimation can be improved under a multidisciplinary approach, the role of a forensic anthropologist and forensic epigeneticist being crucial in the establishment of new basis for age estimation. The development of epigenetic models for bones and tooth samples is crucial in this way. Moreover, developing models for age estimation using several samples can be a useful tool in forensics. In this study, we built two multi-tissue models for age estimation, combining blood, bones and tooth samples and using two different methodologies. Through the Sanger sequencing methodology, we built a model with seven age-correlated markers and a mean absolute deviation between predicted and chronological ages of 6.06 years. Using the SNaPshot assay, a model with three markers has been developed revealing a mean absolute deviation between predicted and chronological ages of 6.49 years. Our results showed the usefulness of DNA methylation age estimation in forensic contexts and brought new insights into the development of multi-tissue models applied to blood, bones and teeth. In the future, we expected that these procedures can be applied to the Medico-Legal facilities to use DNA methylation in routine practice for age estimation. Abstract The development of age prediction models (APMs) focusing on DNA methylation (DNAm) levels has revolutionized the forensic age estimation field. Meanwhile, the predictive ability of multi-tissue models with similar high accuracy needs to be explored. This study aimed to build multi-tissue APMs combining blood, bones and tooth samples, herein named blood–bone–tooth-APM (BBT-APM), using two different methodologies. A total of 185 and 168 bisulfite-converted DNA samples previously addressed by Sanger sequencing and SNaPshot methodologies, respectively, were considered for this study. The relationship between DNAm and age was assessed using simple and multiple linear regression models. Through the Sanger sequencing methodology, we built a BBT-APM with seven CpGs in genes ELOVL2, EDARADD, PDE4C, FHL2 and C1orf132, allowing us to obtain a Mean Absolute Deviation (MAD) between chronological and predicted ages of 6.06 years, explaining 87.8% of the variation in age. Using the SNaPshot assay, we developed a BBT-APM with three CpGs at ELOVL2, KLF14 and C1orf132 genes with a MAD of 6.49 years, explaining 84.7% of the variation in age. Our results showed the usefulness of DNAm age in forensic contexts and brought new insights into the development of multi-tissue APMs applied to blood, bone and teeth.
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Affiliation(s)
- Helena Correia Dias
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- National Institute of Legal Medicine and Forensic Sciences, 3000-548 Coimbra, Portugal;
- Correspondence: ; Tel.: +351-239240700; Fax: +351-239855211
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
| | - Francisco Corte Real
- National Institute of Legal Medicine and Forensic Sciences, 3000-548 Coimbra, Portugal;
- Faculty of Medicine, University of Coimbra, 3000-370 Coimbra, Portugal
| | - Eugénia Cunha
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- National Institute of Legal Medicine and Forensic Sciences, 3000-548 Coimbra, Portugal;
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13
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Habibe JJ, Clemente-Olivo MP, de Vries CJ. How (Epi)Genetic Regulation of the LIM-Domain Protein FHL2 Impacts Multifactorial Disease. Cells 2021; 10:2611. [PMID: 34685595 PMCID: PMC8534169 DOI: 10.3390/cells10102611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
Susceptibility to complex pathological conditions such as obesity, type 2 diabetes and cardiovascular disease is highly variable among individuals and arises from specific changes in gene expression in combination with external factors. The regulation of gene expression is determined by genetic variation (SNPs) and epigenetic marks that are influenced by environmental factors. Aging is a major risk factor for many multifactorial diseases and is increasingly associated with changes in DNA methylation, leading to differences in gene expression. Four and a half LIM domains 2 (FHL2) is a key regulator of intracellular signal transduction pathways and the FHL2 gene is consistently found as one of the top hyper-methylated genes upon aging. Remarkably, FHL2 expression increases with methylation. This was demonstrated in relevant metabolic tissues: white adipose tissue, pancreatic β-cells, and skeletal muscle. In this review, we provide an overview of the current knowledge on regulation of FHL2 by genetic variation and epigenetic DNA modification, and the potential consequences for age-related complex multifactorial diseases.
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Affiliation(s)
- Jayron J. Habibe
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
- Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Maria P. Clemente-Olivo
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
| | - Carlie J. de Vries
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
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14
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Simpson DJ, Chandra T. Epigenetic age prediction. Aging Cell 2021; 20:e13452. [PMID: 34415665 PMCID: PMC8441394 DOI: 10.1111/acel.13452] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.
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Affiliation(s)
- Daniel J. Simpson
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Tamir Chandra
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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15
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Weisz NA, Roberts KA, Hardy WR. Reliability of phenotype estimation and extended classification of ancestry using decedent samples. Int J Legal Med 2021; 135:2221-2233. [PMID: 34436656 DOI: 10.1007/s00414-021-02631-x] [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: 12/16/2020] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Abstract
The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent's biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.
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Affiliation(s)
- Naomi A Weisz
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA
| | - Katherine A Roberts
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA. .,California Forensic Science Institute, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA.
| | - W Reef Hardy
- Human Genomics Unit, Los Angeles County Department of Medical Examiner-Coroner, 1104 N Mission Road, Los Angeles, CA, 90033, USA
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16
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Di Lena P, Sala C, Nardini C. Estimage: a webserver hub for the computation of methylation age. Nucleic Acids Res 2021; 49:W199-W206. [PMID: 34038548 PMCID: PMC8262735 DOI: 10.1093/nar/gkab426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022] Open
Abstract
Methylage is an epigenetic marker of biological age that exploits the correlation between the methylation state of specific CG dinucleotides (CpGs) and chronological age (in years), gestational age (in weeks), cellular age (in cell cycles or as telomere length, in kilobases). Using DNA methylation data, methylage is measurable via the so called epigenetic clocks. Importantly, alterations of the correlation between methylage and age (age acceleration or deceleration) have been stably associated with pathological states and occur long before clinical signs of diseases become overt, making epigenetic clocks a potentially disruptive tool in preventive, diagnostic and also in forensic applications. Nevertheless, methylage dependency from CpGs selection, mathematical modelling, tissue specificity and age range, still makes the potential of this biomarker limited. In order to enhance model comparisons, interchange, availability, robustness and standardization, we organized a selected set of clocks within a hub webservice, EstimAge (Estimate of methylation Age, http://estimage.iac.rm.cnr.it), which intuitively and informatively enables quick identification, computation and comparison of available clocks, with the support of standard statistics.
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Affiliation(s)
- Pietro Di Lena
- Department of Computer Science and Engineering - DISI, University of Bologna, Bologna 40100, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna 40100, Italy
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17
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DNA methylation of decedent blood samples to estimate the chronological age of human remains. Int J Legal Med 2021; 135:2163-2173. [PMID: 34245337 DOI: 10.1007/s00414-021-02650-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/24/2021] [Indexed: 01/21/2023]
Abstract
Chronological age estimation may offer valuable investigative leads in human identification cases. Bisulfite pyrosequencing analysis of single CpG sites on five genes (KLF14, ELOVL2, C1orf132, TRIM59, and FHL2) was performed on 264 postmortem blood samples from individuals aged 3 months to 93 years. The goals were to develop age prediction models based on the correlation between the methylation profile and chronological age and to assess the accuracy of the prediction. Linear regression between methylation levels and age at each CpG site revealed that the five markers show a statistically significant correlation with age. The methylation data from a training set of 160 postmortem blood samples were used to develop an age prediction model with a correlation coefficient of 0.65, explaining 73.1% of age variation, with a mean absolute deviation from the chronological age of 7.60 years. The accuracy of the model was evaluated with a test set of 72 samples producing a mean absolute deviation of 7.42 years. The training and test sets were also categorized by specific age groups to assess accuracy and deviation from chronological age. The data for both sets revealed a lower prediction potential as an individual increases in age, particularly for the age categories above 50 years.
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18
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Nutzung von Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung zur postmortalen Lebensaltersschätzung. Rechtsmedizin (Berl) 2021. [DOI: 10.1007/s00194-021-00489-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
ZusammenfassungMit der Identifikation und Beschreibung „molekularer Uhren“ (posttranslationale Proteinmodifikationen, DNA-Methylierung) eröffnen sich neue Möglichkeiten zur Entwicklung von Verfahren zur postmortalen Lebensaltersschätzung. Bislang werden diese Ansätze aber nur unabhängig voneinander eingesetzt. Ihre Verknüpfung verspricht eine bessere Erfassung hochkomplexer Alterungsprozesse und damit die Möglichkeit zur Entwicklung optimierter Verfahren zur Altersschätzung für verschiedenste Szenarien der forensischen Praxis.In Vorbereitung umfangreicher Untersuchungen zur Überprüfung dieser Hypothese wurden verschiedene molekulare Uhren (Akkumulation von D‑Asparaginsäure, Akkumulation von Pentosidin und DNA-Methylierungsmarker [RPA2, ZYG11A, F5, HOXC4, NKIRAS2, TRIM59, ELOVL2, DDO, KLF14 und PDE4C]) in 4 fäulnisresistenten Geweben (Knochen, Sehne, Bandscheibe, Epiglottis) von 15 Individuen untersucht.In allen untersuchten Geweben fand sich eine starke Korrelation beider Proteinmarker sowie jeweils mehrerer DNA-Methylierungsmarker mit dem Lebensalter. Dabei zeigten die untersuchten Parameter gewebsspezifische Veränderungen mit dem Alter.Die Ergebnisse der Pilotstudie belegen das Potenzial der Verknüpfung molekularer Verfahren für die postmortale Altersschätzung. Weitere Untersuchungen werden zeigen, wie genau postmortale Altersschätzungen sein können, wenn Altersinformationen aus posttranslationalen Proteinmodifikationen und DNA-Methylierung aus verschiedenen Geweben in multivariaten Modellen verknüpft werden.
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19
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Identifying Methylation Patterns in Dental Pulp Aging: Application to Age-at-Death Estimation in Forensic Anthropology. Int J Mol Sci 2021; 22:ijms22073717. [PMID: 33918302 PMCID: PMC8038189 DOI: 10.3390/ijms22073717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Age-at-death estimation constitutes one of the key parameters for identification of human remains in forensic investigations. However, for applications in forensic anthropology, many current methods are not sufficiently accurate for adult individuals, leading to chronological age estimates erring by ±10 years. Based on recent trends in aging studies, DNA methylation has great potential as a solution to this problem. However, there are only a few studies that have been published utilizing DNA methylation to determine age from human remains. The aim of the present study was to expand the range of this work by analyzing DNA methylation in dental pulp from adult individuals. Healthy erupted third molars were extracted from individuals aged 22–70. DNA from pulp was isolated and bisulfite converted. Pyrosequencing was the chosen technique to assess DNA methylation. As noted in previous studies, we found that ELOVL2 and FHL2 CpGs played a role in age estimation. In addition, three new markers were evaluated—NPTX2, KLF14, and SCGN. A set of CpGs from these five loci was used in four different multivariate regression models, providing a Mean Absolute Error (MAE) between predicted and chronological age of 1.5–2.13 years. The findings from this research can improve age estimation, increasing the accuracy of identification in forensic anthropology.
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20
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Woźniak A, Heidegger A, Piniewska-Róg D, Pośpiech E, Xavier C, Pisarek A, Kartasińska E, Boroń M, Freire-Aradas A, Wojtas M, de la Puente M, Niederstätter H, Płoski R, Spólnicka M, Kayser M, Phillips C, Parson W, Branicki W. Development of the VISAGE enhanced tool and statistical models for epigenetic age estimation in blood, buccal cells and bones. Aging (Albany NY) 2021; 13:6459-6484. [PMID: 33707346 PMCID: PMC7993733 DOI: 10.18632/aging.202783] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/16/2021] [Indexed: 01/07/2023]
Abstract
DNA methylation is known as a biomarker for age with applications in forensics. Here we describe the VISAGE (VISible Attributes through GEnomics) Consortium's enhanced tool for epigenetic age estimation in somatic tissues. The tool is based on eight DNA methylation markers (44 CpGs), bisulfite multiplex PCR followed by sequencing on the MiSeq FGx platform, and three statistical prediction models for blood, buccal cells and bones. The model for blood is based on six CpGs from ELOVL2, MIR29B2CHG, KLF14, FHL2, TRIM59 and PDE4C, and predicts age with a mean absolute error (MAE) of 3.2 years, while the model for buccal cells includes five CpGs from PDE4C, MIR29B2CHG, ELOVL2, KLF14 and EDARADD and predicts age with MAE of 3.7 years, and the model for bones has six CpGs from ELOVL2, KLF14, PDE4C and ASPA and predicts age with MAE of 3.4 years. The VISAGE enhanced tool for age estimation in somatic tissues enables reliable collection of DNA methylation data from small amounts of DNA using a sensitive multiplex MPS assay that provides accurate estimation of age in blood, buccal swabs, and bones using the statistical model tailored to each tissue.
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Affiliation(s)
- Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Wojtas
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Maria de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Rafał Płoski
- Department Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wojciech Branicki
- Central Forensic Laboratory of the Police, Warsaw, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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21
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Soedarsono N, Hanafi MS, Auerkari E. Biological age estimation using DNA methylation analysis: A systematic review. SCIENTIFIC DENTAL JOURNAL 2021. [DOI: 10.4103/sdj.sdj_27_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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22
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Correia Dias H, Corte-Real F, Cunha E, Manco L. DNA methylation age estimation from human bone and teeth. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1805011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Helena Correia Dias
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - Francisco Corte-Real
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Eugénia Cunha
- Centre for Functional Ecology (CEF), Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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23
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Koop BE, Mayer F, Gündüz T, Blum J, Becker J, Schaffrath J, Wagner W, Han Y, Boehme P, Ritz-Timme S. Postmortem age estimation via DNA methylation analysis in buccal swabs from corpses in different stages of decomposition-a "proof of principle" study. Int J Legal Med 2020; 135:167-173. [PMID: 32632799 PMCID: PMC7782454 DOI: 10.1007/s00414-020-02360-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
Age estimation based on the analysis of DNA methylation patterns has become a focus of forensic research within the past few years. However, there is little data available regarding postmortem DNA methylation analysis yet, and literature mainly encompasses analysis of blood from corpses without any signs of decomposition. It is not entirely clear yet which other types of specimen are suitable for postmortem epigenetic age estimation, and if advanced decomposition may affect methylation patterns of CpG sites. In living persons, buccal swabs are an easily accessible source of DNA for epigenetic age estimation. In this work, the applicability of this approach (buccal swabs as source of DNA) under different postmortem conditions was tested. Methylation levels of PDE4C were investigated in buccal swab samples collected from 73 corpses (0–90 years old; mean: 51.2) in different stages of decomposition. Moreover, buccal swab samples from 142 living individuals (0–89 years old; mean 41.2) were analysed. As expected, methylation levels exhibited a high correlation with age in living individuals (training set: r2 = 0.87, validation set: r2 = 0.85). This was also the case in postmortem samples (r2 = 0.90), independent of the state of decomposition. Only in advanced putrified cases with extremely low DNA amounts, epigenetic age estimation was not possible. In conclusion, buccal swabs are a suitable and easy to collect source for DNA methylation analysis as long as sufficient amounts of DNA are present.
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Affiliation(s)
- Barbara Elisabeth Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - Felix Mayer
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Tanju Gündüz
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Jacqueline Blum
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Judith Schaffrath
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Petra Boehme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Stefanie Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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