Epigenetic-based chronological age-prediction: a new objective tool for forensic case work
A team of researchers led by Pernette Verschure and Ate Kloosterman of the Swammerdam Institute for Life Sciences at the UvA have developed an age prediction tool for forensic application based on DNA methylation. Their findings were recently published in three successive articles in Forensic Science International: Genetics.
The code for life is written in DNA. But it’s not only the code itself that determines genome functioning. Chemical modifications can be made to the DNA that determine the composition of our epigenome. The addition of a methyl group to the DNA includes such an epigenetic modification. Our epigenome plays a crucial role in establishing and maintaining cell identity of the cells in our body by coordinating the level and timing of its thousands of genes. The study of such epigenetic regulatory functions is called epigenetics.
Age prediction through epigenetic changes in cells
The epigenetic composition of the genome changes when we age. This is reflected by alterations in the DNA methylation pattern. Based on this principle, an assay was developed to predict the chronological age of individuals measuring epigenetic DNA methylation changes in white blood cells.
Epigenetic age determination is an essential addition to already existing tools in forensic genetics. The epigenetic assay is expected to become a useful objective tool for forensic case work. For instance to narrow down a pool of suspects, to help identify unknown persons, or to determine illegal movement of individuals below adult age across borders.
Three consecutive papers on the epigenetic assay
In three separate papers, Pernette Verschure of the Swammerdam Institute of Life Sciences and Ate Kloosterman of the Institute for Biodiversity and Ecosystem Dynamics published the development, the limits and applicability of the epigenetic assay. These papers are:
- Epigenetic age prediction with a variance up to 5 years
The authors describe the development of the epigenetic age-prediction assay that is based on measuring DNA methylation levels in blood samples of individuals within a broad age-range (18-69 years). 15 DNA methylation sites of different genomic loci were identified as informative epigenetic age-prediction markers. Of interest, the genomic regions of the age-prediction markers are involved in multiple biological pathways such as developmental biology, metabolism, homeostasis, metabolism, immune system, transcription, repair, replication, cell cycle and cellular response.
- Epigenetic profiling at the limits
The research team investigated how biological fluctuations in epigenetic DNA methylation levels influence epigenetic age-prediction outcomes. This concept is especially important in samples with low DNA level, which is rather the norm then the exception in forensic cases. The researchers used computer simulation to illustrate biological variability in DNA methylation. The simulation typically represents drawing samples with small numbers of cells from a large population of cells. They compared a basic model with a more flexible model, providing 0%, 50% or 100% methylation of DNA at one site. The simulation data clearly pointed out that stochastic effects should be taken into account when analyzing minimal sample sizes for epigenetic chronological age determination.
- Age prediction across different tissues
The applicability of the blood-based epigenetic age-dependent loci was tested in other forensic relevant cell types, i.e. brain, bone, muscle, buccal swaps. The data are very promising since seven of the loci did show age-dependency in all tested tissues. Nevertheless, a different reference set for each tissue is needed to adapt for epigenetic tissue-specific changes upon ageing. Especially the analysis of bone tissue for age determination of an unidentified skeleton or bone fragment is of large forensic interest. The data of this study implicate that epigenetic age determination from skeletal remains is within reach.
The research depended largely on funding from the Dutch Ministry of Justice and Security (NCTV). Additional funding was provided by the Amsterdam University (UvA) and the Wissenschaftliche Gesellschaft Freiburg.
- Naue J, Hoefsloot HCJ, Mook ORF, Rijlaarsdam-Hoekstra L, van der Zwalm MCH, Henneman P, Kloosterman AD, Verschure PJ. Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression. Forensic Sci Int Genet. 2017 Nov;31:19-28. doi: 10.1016/j.fsigen.2017.07.01
- Naue J, Hoefsloot HCJ, Kloosterman AD, Verschure PJ. Forensic DNA methylation profiling from minimal traces: How low can we go? Forensic Sci Int Genet. 2018 Mar;33:17-23. doi: 10.1016/j.fsigen.2017.11.004
- Naue J, Sänger T, Hoefsloot HCJ, Lutz-Bonengel S, Kloosterman AD, Verschure PJ. Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing. Forensic Sci Int Genet. 2018 Jul 7;36:152-159. doi: 10.1016/j.fsigen.2018.07.007
More information on the research group of Pernette Verschure can be found at the website of UvA-Swammerdam Institute for Life Sciences.