Athina Vidaki

Athina Vidaki
Erasmus MC | Erasmus MC · Department of Genetic Identification

BSc, MSc, PhD

About

83
Publications
9,145
Reads
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831
Citations
Additional affiliations
February 2020 - present
Erasmus MC
Position
  • PostDoc Position
February 2018 - January 2020
Erasmus MC
Position
  • PostDoc Position
April 2016 - present
PostDoc Network Erasmus MC
Position
  • Chair
Education
January 2011 - January 2015
King's College London
Field of study
  • Forensic Epigenetics
September 2009 - September 2010
King's College London
Field of study
  • Forensic Science
September 2004 - July 2009

Publications

Publications (83)
Article
Full-text available
Human microbiome research is moving from characterization and association studies to translational applications in medical research, clinical diagnostics, and others. One of these applications is the prediction of human traits, where machine learning (ML) methods are often employed, but face practical challenges. Class imbalance in available microb...
Article
Full-text available
Pseudoclostridium thermosuccinogenes is a thermophilic bacterium capable of producing succinate from lignocellulosic-derived sugars and has the potential to be exploited as a platform organism. However, exploitation of P. thermosuccinogenes has been limited partly due to the genetic inaccessibility and lack of genome engineering tools. In this stud...
Article
Full-text available
Background Information on long-term alcohol consumption is relevant for medical and public health research, disease therapy, and other areas. Recently, DNA methylation-based inference of alcohol consumption from blood was reported with high accuracy, but these results were based on employing the same dataset for model training and testing, which ca...
Article
DNA methylation has become one of the most useful biomarkers for age prediction and body fluid identification in the forensic field. Therefore, several assays have been developed to detect age-associated and body fluid-specific DNA methylation changes. Among the many methods developed, SNaPshot-based assays should be particularly useful in forensic...
Article
Full-text available
Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, SNP microarrays were develop...
Article
Over the last few years, advances in massively parallel sequencing technologies (also referred to next generation sequencing) and bioinformatics analysis tools have boosted our knowledge on the human microbiome. Such insights have brought new perspectives and possibilities to apply human microbiome analysis in many areas, particularly in medicine....
Article
Full-text available
Background Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays’ probe design cannot fully consider the vast human genetic diversity, leading to genetic artifacts. Distinguishing genuine from artifactual genetic influence...
Preprint
Full-text available
Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relat...
Article
Full-text available
Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In t...
Article
Full-text available
Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blo...
Article
Full-text available
Background Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring...
Article
Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood tr...
Article
Full-text available
Forensic DNA phenotyping is gaining interest as the number of applications increases within the forensic genetics community. The possibility of providing investigative leads in addition to conventional DNA profiling for human identification provides new insights into otherwise “cold” police investigations. The ability of reporting on the bio-geogra...
Article
Full-text available
Inferring a person’s smoking habit and history from blood is relevant for complementing or replacing self-reports in epidemiological and public health research, and for forensic applications. However, a finite DNA methylation marker set and a validated statistical model based on a large dataset are not yet available. Employing 14 epigenome-wide ass...
Conference Paper
Identifying the body source of human biological traces found at crime scenes is relevant for crime reconstruction; however, the use of human cell biomarkers provides challenges. Employing the human microbiome is expected to be useful, as distinct microbial communities inhabit different body sites. Previous tissue identification attempts with microb...
Poster
Full-text available
Correct identification of human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework, providing crucial information for crime reconstruction. However, their overlap in human cell type composition provides challenges when using human cell biomarkers, while the microbiota composition of these three tissue...
Article
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and ident...
Poster
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and ident...
Article
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and ident...
Conference Paper
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and ident...
Article
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) d...
Poster
Full-text available
Traces of human epithelial materials, such as from skin, saliva and vaginal secretion, are often encountered at crime scenes, and their reliable identification is relevant for solving criminal cases. However, due to overlap in human cell composition, identifying these three tissue types via human biomarkers is challenging. By using validated 16S r...
Article
Full-text available
Monozygotic (MZ) twins are typically indistinguishable via forensic DNA profiling. Recently, we demonstrated that epigenetic differentiation of MZ twins is feasible; however, proportions of twin differentially methylated CpG sites (tDMSs) identified in reference-type blood DNA were not replicated in trace-type blood DNA. Here we investigated buccal...
Poster
Full-text available
INTRODUCTION: Traces of different human epithelial materials, such as from skin, saliva and vaginal secretion, are often encountered at crime scenes, and their reliable identification provides crucial information for crime reconstruction relevant for solving criminal cases. However, due to overlap in human cell composition between these three body...
Article
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laborato...
Presentation
The ability to estimate the age of the donor from recovered biological material at a crime scene can be valuable in forensic investigations by providing additional intelligence information to narrow down suspect pools. Age-associated DNA methylation patterns can be used for this purpose, to build accurate prediction tools in various forensically re...
Article
Full-text available
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...
Presentation
Estimating an individual’s biological age can be of great use in studying ageing or predicting disease susceptibility; however, estimating one’s chronological age would also be of a significant value in criminal investigations. In cases where there are no suspects or eye-witnesses available to provide investigative leads, predicting a crime scene s...
Poster
Full-text available
Introduction Standard DNA profiling is typically non-informative for differentiating between monozygotic (MZ) twins. Whole genome sequencing was recently proposed as a solution; however, both the rarity of such autosomal SNPs and required ultra-high coverage resulting in immense costs, make this approach impractical. Epigenetic variation was identi...
Presentation
During this seminar, an introduction to the potential, challenges and future of forensic DNA methylation profiling was delivered.
Article
Monozygotic (MZ) twins share the same STR profile, demonstrating a practical problem in forensic casework. DNA methylation has provided a suitable resource for MZ twin differentiation; however, studies addressing the forensic feasibility are lacking. Here, we investigated epigenetic MZ twin differentiation from blood under the forensic scenario com...
Conference Paper
Standard DNA profiling is typically non-informative for differentiating between monozygotic (MZ) twins in paternity or criminal forensic casework, since MZ twins originate from the same zygote. Whole genome sequencing for detecting ‘random’ autosomal SNPs was recently proposed as a solution; however, both the rarity of such SNPs (only 5 were detect...
Presentation
During this seminar, an introduction to the potential, challenges and future of forensic DNA methylation profiling was presented including current applications of 1) the identification of forensically relevant tissues and body fluids, 2) the estimation of an unknown individual’s chronological age, and 3) the discrimination between identical twins.
Conference Paper
Standard DNA profiling is typically non-informative for differentiating between monozygotic (MZ) twins. Whole genome sequencing was recently proposed as a solution; however, both the rarity of such autosomal SNPs and required ultra-high coverage resulting in immense costs, make this approach impractical. Epigenetic variation was identified as suita...
Presentation
Full-text available
As part of the Beyond DNA profiling workship, this presentation will provide an introduction to tissue-specific DNA methylation and its potentail in forensic applications. During the presentation, strategies for marker discovery, targeted methylation assays and technical challenges will be discussed driven by my pyrosequencing experience.
Conference Paper
Monozygotic (MZ) twins share the same STR profile, demonstrating a practical problem in forensic casework. Here, we investigated epigenetic MZ twin differentiation from blood and saliva under the forensic scenario comprising the i) discovery of candidate twin-differentially methylated sites (tDMSs) in reference-type DNA via genome-wide analysis, ii...
Poster
Full-text available
Monozygotic (MZ) twins share the same STR profile, demonstrating a practical problem in forensic casework. DNA methylation has provided a suitable resource for MZ twin differentiation; however, studies addressing the forensic feasibility are lacking. Here, we investigated epigenetic MZ twin differentiation from blood under the forensic scenario com...
Presentation
The presentation was in Greek. Τίτλος: ’Η μεθυλίωση του DNA - Ξεπερνώντας τους περιορισμούς της συμβατικής ανάλυσης’ Ημερίδα: ’Η διεπιστημονική προσέγγιση στην εξιχνίαση μιας υπόθεσης’ Οργανωτές: Ομάδα ReAcTiON, Αριστοτέλειο Πανεπιστήμιο Θεσσαλονίκης
Article
DNA methylation patterns have the ability to reveal the activities of genes within a certain tissue at a particular time point. Tissue-specific DNA methylation patterns have been previously investigated for their applicability in the identification of forensically relevant body fluids, however there is still a lack in robust markers. While followin...
Poster
Full-text available
Introduction: Monozygotic (MZ) twins share ‘identical’ genomic sequences, except for very rare somatic mutations. Therefore, conventional forensic DNA profiling is non-informative when trying to differentiate these individuals in a forensic investigation, as MZ twins result in the same DNA profiles. Epigenetics has the potential to serve a solution...
Conference Paper
Full-text available
The ability to estimate the age of the donor from recovered biological material at a crime scene can be valuable in forensic investigations. Here, the aim was to use age-specific DNA methylation patterns to predict age from blood. Based on previous findings, 45 CpG sites were investigated using publicly available data obtained from 953 blood sample...
Presentation
Guest lecture as part of the MSc course ’Forensic Medicine and Criminology – Newly introduced scientific tools for criminal case investigations’ at the School of Medicine.
Article
Full-text available
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person’s lifetime including epigenetic patterns. The aim of this study was to use age-spe...
Conference Paper
The ability to estimate the age of the donor from recovered biological material at a crime scene can be valuable in forensic investigations. Here, the aim was to use age-specific DNA methylation patterns to predict age from blood. Based on previous findings, 45 CpG sites were investigated using publicly available data obtained from 953 blood sample...
Article
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination o...
Article
The presence of specific body fluids at crime scenes could be linked with particular types of crime, therefore attributing a DNA profile to a specific tissue could increase the evidential significance of a match with a suspect. Current methodologies like tissue-specific mRNA profiling are useful but drawbacks include low tissue specificity and appl...
Presentation
Delivering the award-winning presentation at the ISFG Congress 2015.
Presentation
Here, we present the results of the first part of the EDNAP Meth-Age exercise.
Conference Paper
Full-text available
Attending this presentation will give attendees the opportunity to learn about the potential of applying epigenetic markers in forensic age prediction. This presentation will impact the forensic science community by proposing a quantitative next generation sequencing (NGS) approach in estimating chronological age and demonstrating its accuracy, re...
Conference Paper
Estimating an individual's biological age can be of great use in studying ageing or predicting disease susceptibility; however, estimating someone's chronological age would also be of a significant value in criminal investigations. In cases where there are no suspects or no eye-witnesses available to provide investigative leads, predicting a bloods...
Chapter
Epigenetics can offer a forensic investigator intelligence to help identify a perpetrator when a DNA profile is available, but this does not match with any database held by law enforcement. Using a hypothetical crime, we illustrate its future potential. The methodologies of linking a biological stain to the cellular source of the DNA profile are di...
Thesis
Full-text available
Body fluids such as blood are amongst the most important biological evidence recovered from crime scenes. Identification of the donor can be achieved through STR profiling; however, extracting additional information regarding the tissue type or the donor’s physical appearance such as age could prove very useful in police investigations. Firstly, th...
Presentation
During this presentation, both mRNA- and DNA methylation-approaches for identifying forensically relevant tissues and body fluids were discussed. The first application to a forensic case was also demonstrated.
Presentation
Delivering the award-winning presentation at the ISFG Congress 2015.
Presentation
Here, we propose to conduct a collaborative EDNAP exercise to test a novel DNA methylation-based NGS method for forensic age prediction.
Conference Paper
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging is complex and associated with various molecular modifications in cells that accumulate over a person’s lifetime. The aim of this study was to use age-specific DNA methylation patterns to pre...
Conference Paper
Full-text available
Determining the cellular origin of body fluid stains is very important in police investigations as it could provide crucial information concerning the sequence of events that has taken place at a crime scene. Particularly in sexual assault cases differentiating between peripheral and menstrual blood is often necessary; however, this is not possible...
Article
The European DNA Profiling Group (EDNAP) organized a fourth and fifth collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling. The task was to identify dried menstrual blood and vaginal secretion stains using specific RNA biomarkers, and additionally test 3 housekeeping genes for their suitability as reference...
Conference Paper
DNA profiling is the most powerful tool for identifying individuals; however, there are also heritable changes caused by mechanisms other than differences in the DNA sequence, such as DNA methylation. The aim of this study was to determine body fluid- and age-specific alterations in DNA methylation patterns. Determining the tissue source or the age...
Conference Paper
Introduction: Estimating the biological age of an individual could be very beneficial in forensic investigations. Ageing is biologically complex and leads to a series of biochemical changes in cells and tissues. A simple and accurate molecular estimation would be advantageous; however this remains a challenge. Although various genetic methods based...
Poster
Full-text available
Estimating the age of the donor from a bloodstain would be very beneficial in police investigations as it could reduce the number of suspects. A decline of gene regulation occurs over time; DNA methylation patterns have been proven to modify with age and have shown to be associated with age-related diseases. Hannum et al. (2013) identified 71 age-a...
Poster
Full-text available
Body fluid analysis does not only aid potential identification of the donor, but also can help reconstruct the sequence of events. Determining whether the biological material originates from semen may be very informative in sexual assault cases. Current confirmatory testing, such as microscopic identification of sperm heads or mRNA profiling, is of...
Conference Paper
Full-text available
Background: Body fluid analysis does not only aid in identifying its potential donor, but also reconstructing the sequence of events taken place at a crime scene. Determining whether the biological material originates from semen can be extremely informative in sexual assault or rape cases. Despite its usefulness, current presumptive or confirmatory...
Presentation
This presentation includes a PhD update on our results regarding this topic.
Article
A third collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling was organized by the European DNA Profiling Group (EDNAP). Twenty saliva and semen stains, four dilution series (10-0.01μl saliva, 5-0.01μl semen) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 20...
Conference Paper
Analysis of body fluid stains found at a crime scene does not only aid in identifying its potential donor, but also in reconstructing the sequence of events that took place. Despite their usefulness, current enzymatic and immunologic presumptive tests are applicable only to a subset of body fluids and might suffer limitations such as low specificit...
Article
Inhibitor of DNA binding 2 (Id2), a helix-loop-helix protein of the inhibitor of differentiation (ID) family, is involved in hematopoiesis, mainly through interaction with the E-family of transcription factors. Recent studies have shown that Id2 is overexpressed in some types of B-cell lymphoma, including classical Hodgkin lymphoma. The authors of...