Sample collection and assessment of decomposition
Buccal swabs were collected from 73 deceased individuals (age 0–90, mean: 51.2 years; 68.5% male) in different stages of decomposition and a postmortem interval (precisely known in 42 of the 73 cases) of 1–42 days. An additional 142 samples were taken from healthy living individuals (age 0–89 years, mean: 41.6 years; 41.5% male).
In cases of deceased individuals, macroscopically visible external changes of decomposition were described and the cases subsequently classified based on the proposed scorings by Megyesi et al. [20] (Table 1). Decomposition scores of the heads were used to group samples into the following categories with respect to their degree of decomposition: score 1 for no signs of decomposition (n = 21), score 2–3 for early signs of decomposition (n = 18), score 4–5 for signs of advanced decomposition (n = 22) and a score > 6 for severe signs of decomposition (n = 12).
Table 1 Scoring sheet for assessment of decomposition (Megyesi et al. [20]) DNA isolation and pyrosequencing
For genomic DNA isolation, NuceloSpin® Tissue Kit by Macherey-Nagel was used according to the manufacturer’s standard protocol for human tissue with overnight lysis. Extracted genomic DNA was stored at − 20 °C until further analysis. DNA quantity and quality were measured using the Investigator Quantiplex Pro Kit (Qiagen) via real-time PCR (Applied Biosystems™ 7500 Real-Time PCR Systems) following manufacturer’s instructions with default settings. For bisulfite conversion, the EZ DNA Methylation-Gold™ Kit (Zymo Research) was used following manufacturer’s instructions. When possible, the recommended amount of 200–500 ng of input DNA was applied. In some samples, the input was lower due to low original DNA amounts (Table 2). Bisulfite-converted DNA was amplified using the primers described by Weidner et al. [4] using the following thermal cycler conditions: 95 °C, 15 min; 45× cycles (95 °C, 30 s; 52 °C, 30 s; 72 °C, 30 s); 72 °C, 5 min; 4 °C, hold. The length of the subsequent product was 155 bp.
Table 2 Postmortem samples: DNA concentrations (ng/μl) and degradation indices (*: samples with DNA quantities too low for further application (≤ 3 ng/μl); score 1, no signs of decomposition, n = 21; score 2 + 3, early signs of decomposition, n = 18; scores 4 + 5, advanced decomposition, n = 22; score > 6, severe signs of decomposition, n = 12) Subsequently, the converted and amplified DNA was immobilized to 1 μl Streptavidin Sepharose™ HP beads (GE Healthcare). For pyrosequencing, the Pyromark Q24 and Pyromark Q24 Advanced Systems (Qiagen) were used. Sequencing primers were described in Weidner et al. [4]. All samples were measured at least in duplicate. Single values did not differ by more than 3% within one sample; this was also true for comparative measurements using both pyrosequencing systems (Q24, Q24 Advanced).
Data analysis
The relationship between chronological age and the methylation status of the highly age-associated CpG-1 site of PDE4C (upstream of cg17861230; see Weidner et al. [4]) was tested by linear regression and the corresponding correlation coefficients were determined. The samples of living individuals were split into two groups. One group was used as training set (n = 71, ages 0–89, mean age: 42 years), the other as validation set n = 71, ages 0–85, mean age: 42 years). Corpses with sufficient DNA yields (see Table 2) were treated as a second (postmortem) validation set (n = 52, ages 0–88, mean age: 49.5 years). The MADs (mean absolute deviations) of age estimates were calculated as mean of deviations of estimated from chronological ages.
Cytology of buccal swabs
Buccal swabs were taken from corpses in different stages of decomposition (scores 1, 5, and 7) and smears were prepared on specimen slides. The smears were stained with the Pappenheim method: after drying, the slides were immersed in undiluted May-Grünwald stain for 5 min, rinsed with distilled water, immersed in Giemsa stain diluted with distilled water in a ratio of 1:9 for 15 min before being rinsed again with distilled water. After staining, images of the smears were taken with the Nikon C-TEP3 system with a 100-fold magnification.