Improved age determination of blood and teeth samples using a selected set of DNA methylation markers

Abstract

Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0-91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R 2 of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19-70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R 2 of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals

Crime investigation through DNA methylation analysis: methods and applications in forensics

“…DNA methylation particularly cytosine methylation at the CpG sites, the major epigenetic and chemical change in the DNA which without altering the DNA sequence leads to phenotypic variation among the various tissues, monozygotic twins or among humans has provided a new vista to distinguish cell types or tissues (Brunner et al, 2009;Lokk et al, 2014), monozygotic twins (Fraga et al, 2005;Heyn et al, 2013;Kaminsky et al, 2009), age of humans (Bekaert et al, 2015;Horvath, 2013;Yi et al, 2015), human races (Adkins et al, 2011;Heyn et al, 2013) or even can be used to predict certain criminal behaviours (Day & Sweatt, 2010;Szyf, 2011;Szyf, 2013).…”

“…The current approach of age determination which is based on an assessment of bone and teeth structure and composition is practically vague, rather methylation marks on the DNA obtained from these hard tissues can be used to accurately predict the chronological age of individuals (Bekaert et al, 2015;Giuliani et al, 2015). DNA methylation has an inheritable effect with age acceleration and is close to zero at the embryonic stage of an individual (Guo et al, 2014;Horvath, 2013).…”

“…Further researches in concert have developed the epigenetic markers (cg06304190, cg06979108, and cg12837463) for age prediction using semen samples . In an another research work, some of the CpG DNA methylation loci (ASPA, PDE4C, ELOVL2, FHL2, CCDC102B, C1orf132, chr16:85395429 and EDARADD) have been used to predict accurately the age of deceased or live individuals using their blood samples (Bekaert et al, 2015;Freire-Aradas et al, 2016). Beside accurate age prediction, DNA methylation can also help to measure the rate of aging (Horvath, 2013).…”

“…5mC profiling with the advent of NGS platform, Illumina (Masser et al, 2015) has provided a boost to the BS-seq method as well as led to the creation of many methylation databases (Grunau et al, 2001;Hackenberg et al, 2011). The detection of DNA methylation patterns is an advancing area of research in forensic science, which promises to distinguish various cell/tissue types or monozygotic twins (Levesque et al, 2014;Li et al, 2013), accurately estimate human age (Bekaert et al, 2015;Horvath, 2013), identify human bio-geographic/ethnicity type (Heyn et al, 2013;Xia et al, 1846) and can be applied to predict human behaviour as a new part of investigative forensic (Kockler et al, 2006;Kovatsi et al, 2011).…”

The Future of Forensic Biology

“…DNA methylation particularly 5mC (5-methylcytosine) methylation at the CpG sites, the major epigenetic and chemical change in the DNA [41] which without altering the DNA sequence leads to phenotypic variation among the various tissues, monozygotic twins or among humans has provided a new vista to distinguish cell types or tissues [42,43], monozygotic twins [44][45][46], age of humans [47][48][49], human bio-geographic types [44,50] or even can be used to predict certain criminal behaviors [51][52][53]. This 15-dalton mark of methylation in the bases of DNA sequence can help to solve an array of critical cases in forensic biology which when stands gloomy with current polymorphic STR technology.…”