Decoding Clues Beyond DNA: Forensic Epigenomics in Crime Investigations
Introduction
Developments in forensic genetics involve new ways to determine identity beyond traditional methods which look solely at sequences of nucleotides. Now forensic epigenomics examines the additional dimension of the molecular modifications that determine whether a gene is active. Among these modifications the methylation of DNA stands out as a means of identifying specific biological tissue, inferring age, and determining certain lifestyle attributes of a suspect or victim [1].
Extracting the biological context of a DNA profile evidencing a forensic case is a paradigm shift in the interpretation of biological evidence in a criminal investigation and has been discussed in Forensic Science International: Genetics [1]. This shift is possible because of the substantial information that a forensic investigator can derive from methylation-based forensic science.
What is Epigenomics?
Epigenomics is the study of heritable changes in genome function that do not involve changes to the DNA sequence, but are handed down to daughter cells [2].
The best known of these is DNA methylation, which involves a methyl group being slapped onto cytosine bases at CpG sites, silencing some genes and activating others.
Unlike static DNA sequences, methylation patterns are dynamic, they shift with cell type, age, health and environmental exposure [3]. This diversity makes them highly valuable in forensic applications, providing information that cannot be obtained using the routine DNA profiling.
Advances in Forensic Epigenomics
i) Identification of Tissue and Body Fluids
Methylation is how the instruction manual encoded in our genes remains locked inside each cell. It’s as if a flashing ‘Do not enter’ appears over the DNA for any kind of tissue; such methylation marks are present on, say, all body fluid like blood but also semen or saliva or vaginal fluid and skin with its own molecular identity (or epigenetic).
Those panels of markers have fixed tissue-specific CpG sites that allow forensic scientists to establish the biological source of minute samples found at a crime scene, where serological tests commonly do not work [2],[4].
For instance, Naue et al. Mujibe et al(2017) has shown the potential of methylation patterns in differentiating semen from vaginal speak and can be useful sexual assault evidence [4].
ii) Forensic Age Estimation
Forensic age prediction can even tap into intracellular age markers epigenetic “methylation clocks” that tick with time itself, shifting so precisely they can place a person’s age within about three years, as clearly as rings inside a tree trunk. Since there’s no skeletal or morphological evidence to work with no bones, no trace of form genes like ELOVL2 and FHL2 take the spotlight [5],[6].
iii) Lifestyle Inference:
DNA methylation changes will play the leading role in estimating chronological age (Terram et al., 2016), a remarkably handy tool like watching the years unfold in fine lines and silver strands.
Leading research shows that shifts in DNA methylation mirror our daily habits and the world we move through like the trace of smoke that lingers after a single cigarette. Researchers have discovered that smoking leaves a hypomethylation mark on the AHRR and F2RL3 genes, a pattern easy to spot, like faint fingerprints on glass. Alcohol consumption alters the methylation of PER2 and SLC7A111, shifting how these genes behave like a subtle change in tone when a drop of wine hits a clear solution [1].
Differentiating Identical Twins
Identical twins, by nature, have the same DNA sequence, thus traditional genetic profiling cannot be used to distinguish them.
However, epigenomic experiments reveal minute changes in methylation that are dependent on the environment and the age of the individuals, which provides a novel manner for distinguishing identical twins in forensic situations [1],[3].
Applications in Forensics
Body Fluid Source Attribution: Enables DNA material to be attributed to blood, saliva, or seminal fluid so evidence can be interpreted more reliably [2],[4].
Age and Lifestyle Profiling: Can generate a rough age of a person and some clues about the lifestyle as well, which will be extremely useful to match suspects [5],[6].
Events Reconstruction: Aids in determining the time obtained from a biological deposit that has been taken recently or even prior to commission of crime [3].
Cold Case Review: The methylation marks are more rare than RNA or proteins but they also occur in old and degraded samples, so they're great if you have an old cold case [1],[6].
Challenges and Limitations:
The science of epigenomics in forensic is very promising but it still deals with some issues:
Environmental Influences: The stability of methylation may depend on environmental factors such as temperature, humidity and storage [1].
Standardization: Worldwide consensus on marker panels, analytical thresholds for forensic threshold is not yet available [3].
Interpretation of Data: Methylation is naturally variable between individuals, and as such it can be extremely challenging distinguishing environmental from natural biological variation [3].
Ethical considerations: The notion of predicting health/lifestyle traits may give rise to privacy matters and would therefore require robust ethical guidelines and consent procedures [1].
Future Directions
One day forensic epigenomics will be able to combine with portable AI, bioinformatics, and sequencing technologies. Mobile devices such as Oxford Nanopore’s MinION will be capable of identifying and performing methylation sequencing in-silico, thus accelerating investigations [1],[6].
Machine learning models are also being developed which can accommodate challenging methylation data and improve tissue or age prediction accuracy. The International Society for Forensic Genetics (ISFG) is pushing the envelope toward norm-setting international collaboration methylation marker panel(s) that are reproducible and acceptable by court [6].
Forensic DNA Profiling vs Epigenomic Analysis - A Comparison
| Aspect | Conventional DNA Profiling | Forensic Epigenomics |
|---|---|---|
| Target | Sequence variation (STRs) | Epigenetic alteration (DNA methylation) |
| Aim | Identify individuals | Determine tissue type, age, lifestyle, and biological context |
| Information Yield | Identity of person | Source and biological background |
| Methods | PCR, STR typing, capillary electrophoresis | Bisulfite conversion, qPCR, Next-Generation Sequencing (NGS) |
| Applications | Suspect identification and relationship testing | Identification of body fluids, estimation of age, lifestyle inference |
| Advantages | High accuracy for identity confirmation | Adds depth — reveals biological and environmental details |
| Limitations | Provides no biological context | Influenced by environment and requires standardization |
| Result | Links an individual to the crime scene | Adds variation and context to DNA evidence |
Conclusion
Forensic epigenomics is a paradigm shift that moves the focus from who brought their DNA to the investigation scene to what, when and how.
By studying patterns of DNA methylation, forensics experts would know what kind of tissue it was from, have a rough idea of the donor’s age and lifestyle and could even distinguish between identical twins coming from one biological source.
In the end, due to technological advancement and standardization being advanced, forensic epigenomics will develop into an indispensable forensic tool in current society, which can provide the substance of case but also the depth，the accuracy and context to this science that are used for solving crimes [1],[6].
References
- Vidaki, A., & Kayser, M. (2018). Recent progress, methods and perspectives in forensic epigenetics. Forensic Science International: Genetics, 37, 180–195. https://pubmed.ncbi.nlm.nih.gov/30176440/
- Naue, J. et al. (2017). Proof of concept study of age-dependent DNA methylation in various tissues. Forensic Science International: Genetics, 31, 19–28. https://pubmed.ncbi.nlm.nih.gov/30031222/
- Maulani, C. (2020). Age estimation using DNA methylation technique in forensics: A systematic review. Egyptian Journal of Forensic Sciences. https://ejfs.springeropen.com/articles/10.1186/s41935-020-00214-2
- Onofri, M. et al. (2023). Forensic age estimation through a DNA methylation-based age prediction model in the Italian population. International Journal of Molecular Sciences, 24(6), 5381. https://www.mdpi.com/1422-0067/24/6/5381
- Hasnain, S. E. et al. (2019). Forensic Epigenetic Analysis: The Path Ahead. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639569/
- Lee, H. Y. et al. (2016). Forensic DNA methylation profiling from evidence material. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032003/
- Kim, B. M. et al. (2024). DNA methylation-based organ tissue identification: Marker discovery. Forensic Science International: Genetics. https://www.sciencedirect.com/science/article/abs/pii/S1872497324000462
- Ambroa-Conde, A. et al. (2024). Inference of tobacco & alcohol consumption via DNA methylation. Forensic Science International: Genetics. https://www.sciencedirect.com/science/article/pii/S1872497324000164
- Gerra, M. C. et al. (2024). Epigenetic analyses in forensic medicine: future and perspectives. International Journal of Legal Medicine. https://link.springer.com/article/10.1007/s00414-024-03165-8
- Castagnola, M. J. et al. (2024). Uncovering forensic evidence: A path to age estimation using DNA methylation. International Journal of Molecular Sciences, 25(9), 4917. https://www.mdpi.com/1422-0067/25/9/4917
- Gomaa, R. et al. (2021). Application of DNA methylation-based markers in forensic tissue identification. Egyptian Journal of Forensic Sciences. https://ejfs.springeropen.com/articles/10.1186/s41935-021-00226-6
