Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis. (January 2022)

• Record Type: Journal Article
• Authors: Heidegger, A.; Pisarek, A.; de la Puente, M.; Niederstätter, H.; Pośpiech, E.; Woźniak, A.; Schury, N.; Unterländer, M.; Sidstedt, M.; Junker, K.; Ventayol Garcia, M.; Laurent, FX; Ulus, A.; Vannier, J.; Bastisch, I.; Hedman, J.; Sijen, T.; Branicki, W.; Xavier, C.; Parson, W.
• Is Part Of: Forensic science international. Volume 56(2022)
• Publication Date: 2022-01
• Subjects: DNA methylation -- Age prediction -- Forensic DNA phenotyping -- Bisulfite sequencing -- Massively parallel sequencing -- Semen; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2021.102596
• Languages: English
• ISSNs: 1872-4973

Abstract

Abstract: The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool. Highlights: Development of new targeted bisulfite MPS assays for age estimation from semen. Bisulfite multiplex PCR design targeting 13 or 5 age markers. Inter-laboratory validation showed stable and accurate DNA methylation quantification. Robust results with 50 ng DNA input at bisulfite conversion level.