A Genome-Wide Scan of DNA Methylation Markers for Distinguishing Monozygotic Twins

Abstract

Identification of individuals within pairs of monozygotic (MZ) twins remains unresolved using common forensic DNA typing technology. For some criminal cases involving MZ twins as suspects, the twins had to be released due to inability to identify which of the pair was the perpetrator. In this study, we performed a genome-wide scan on whole blood-derived DNA from four pairs of healthy phenotypically concordant MZ twins using the methylated DNA immunoprecipitation sequencing technology to identify candidate DNA methylation markers with capacity to distinguish MZ twins within a pair. We identified 38 differential methylation regions showing within-pair methylation differences in all four MZ pairs. These are all located in CpG islands, 17 of which are promoter-associated, 17 are intergenic islands, and four are intragenic islands. Genes associated with these markers are related with cell proliferation, differentiation, and growth and development, including zinc finger proteins, PRRX2, RBBP9, or are involved in G-protein signaling, such as the regulator of G-protein signaling 16. Further validation studies on additional MZ twins are now required to evaluate the broader utility of these 38 markers for forensic use.

Epigenetic discrimination of identical twins from blood under the forensic scenario

“…We investigated whether tDMSs appear more often in specific chromosomal regions according to CpG content, and observed that 27% of tDMSs are annotated to fall in CGIs, 25% in CGI shores, 6% in CGI shelves and 42% are non-CGI probes [ Figure S3D]. At this cutoff, it seems that CGI probes are highly represented, which has been previously supported by similar studies [25,28]. 20…”

“…Although the extent of these differences, and to what degree they are shared by different MZ twin pairs, is yet not understood, the potential of using DNA methylation to distinguish between MZ twins for forensic purposes has already been recognized [23][24][25][26][27][28], albeit via limited studies. In an initial study, Li et al tested blood DNA samples of 22 adult MZ twin pairs by using the Illumina Infinium Human Methylation 27K BeadChip array that allows for the co-analysis of 27,578 CpG sites, which revealed significant DNA methylation differences (377 CpG sites, methylation difference >0.17) [23].…”

“…Applying the criterion of how frequent the observed methylation differences were amongst MZ twin pairs, authors sub-selected a total of 92 CpGs, that were differentially methylated in all 22 pairs [24]. Furthermore, in another candidate-finding approach, Du et al [25] analysed four MZ twin pairs with methylated DNA immunoprecipitation (MeDIP) and identified a set of 38 differential methylation regions demonstrating pair-specific methylation differences, all of which are located within CpG islands (<500bp long, >55% GC content, [29]). The majority of these markers are associated with cell differentiation, proliferation and development, but future validation is necessary to reveal whether they can be used for MZ twin differentiation in routine forensic practice.…”

From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence

“…Genetically identical MZ twins are sometimes discordant for certain phenotypes [ 61 ], indicating epigenetic involvement [ 6 ], and several studies have demonstrated that there is considerable epigenetic variation within MZ twin pairs. Although some studies have explored the value of epigenetic profiling in forensically discriminating MZ twins [ 62 , 63 ], it is not yet fully established whether the observed twin-to-twin differences are twin pair-specific, or might be universal and applicable across twin pairs, as would be preferred. Recently, a first attempt was made to demonstrate the feasibility of differentiating between MZ twins using forensic epigenetics [ 15 ].…”

Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting

“…Observed epigenetic drifts within MZ twin pairs can be seen not only at specific genomic loci [ 15 , 16 ], but also at a global level [ 12 ], which has unraveled epigenetics’ role in development, ageing, and disease [ 17 , 18 , 19 , 20 , 21 , 22 ]. The potential of DNA methylation profiling for the discrimination between MZ twins in the forensic setting has already been proposed [ 23 , 24 , 25 , 26 , 27 , 28 ]; however, these previous studies mainly included reference-type DNA such as whole blood or buccal swabs. Investigations were not extended to trace-type DNA such as from blood or saliva stains, while combining both parts is needed in the forensic setting.…”