Forensic DNA typing of human nails at various stages of decomposition

Age determination through DNA methylation patterns in fingernails and toenails

Over the past decade, age prediction based on DNA methylation has become a vastly investigated topic; many age prediction models have been developed based on different DNAm markers and using various tissues. However, the potential of using nails to this end has not yet been explored. Their inherent resistance to decay and ease of sampling would offer an advantage in cases where post-mortem degradation poses challenges concerning sample collection and DNA-extraction. In the current study, clippings from both fingernails and toenails were collected from 108 living test subjects (age range: 0-96 years). The methylation status of 15 CpGs located in 4 previously established age-related markers (ASPA, EDARADD, PDE4C, ELOVL2) was investigated through pyrosequencing of bisulphite converted DNA. Significant dissimilarities in methylation levels were observed between all four limbs, hence both limb-specific age prediction models and prediction models combining multiple sampling locations were developed. When applied to their respective test sets, these models yielded a mean absolute deviation between predicted and chronological age ranging from 5.48 to 9.36 years when using ordinary least squares regression. In addition, the assay was tested on methylation data derived from 5 nail samples collected from deceased individuals, demonstrating its feasibility for application in post-mortem cases. In conclusion, this study provides the first proof that chronological age can be assessed through DNA methylation patterns in nails.

Recommendations for the successful identification of altered human remains using standard and emerging technologies: Results of a systematic approach

Successful DNA-based identification of altered human remains relies on the condition of the corpses and varies between tissue types. Therefore, the aim of this prospective multicenter study was to generate evidence-based recommendations for the successful identification of altered remains. For this, 19 commonly used soft and hard tissues from 102 altered human bodies were investigated. The corpses' condition was categorized into three anatomical regions using a practical scoring system. Besides other data, DNA yields, degradation indices, and short tandem repeat (STR) profile completeness were determined in 949 tissue samples. Additionally, varying degrees of alteration and tissue-specific differences were evaluated using the Next Generation Sequencing (NGS) platform MiSeq FGx™. Selected challenging samples were sequenced in parallel with the Ion S5™ platform to assess platform-specific performances in the prediction of the deceased's phenotype and the biogeographic ancestry. Differences between tissue types and DNA extraction methods were found, revealing, for example, the lowest degradation for vertebral disc samples from corpses with initiating, advanced and high degrees of decomposition. With respect to STR profile completeness, blood samples outperformed all other tissues including even profoundly degraded corpses. NGS results revealed higher profile completeness compared to standard capillary electrophoresis (CE) genotyping. Per sample, material and degradation degree, a probability for its genotyping success, including the "extended" European Standard Set (eESS) loci, was provided for the forensic community. Based on the observations, recommendations for the alteration-specific optimal tissue types were made to improve the first-attempt identification success of altered human remains for forensic casework.

Validation and beyond: Next generation sequencing of forensic casework samples including challenging tissue samples from altered human corpses using the MiSeq FGx system

The proceeding developments in next generation sequencing (NGS) technologies enable increasing discrimination power for short tandem repeat (STR) analyses and provide new possibilities for human identification. Therefore, the growing relevance and demand in forensic casework display the need for reliable validation studies and experiences with challenging DNA samples. The presented validation of the MiSeq FGx system and the ForenSeq™ DNA Signature Prep Kit (1) investigated sensitivity, repeatability, reproducibility, concordance, pooling variations, DNA extraction method variances, DNA mixtures, degraded, and casework samples and (2) optimized the sequencing workflow for challenging samples from human corpses by testing additional PCR purification, pooling adjustments, and adapter volume reductions. Overall results indicate the system's reliability in concordance to traditional capillary electrophoresis (CE)‐based genotyping and reproducibility of sequencing data. Genotyping success rates of 100% were obtained down to 62.5 pg DNA input concentrations. Autosomal STR (aSTR) profiles of artificially degraded samples revealed significantly lower numbers of locus and allelic dropouts than CE. However, it was observed that the system still exposed drawbacks when sequencing highly degraded and inhibited samples from human remains. Due to the lack of studies evaluating the sequencing success of samples from decomposed or skeletonised corpses, the presented optimisation studies provide valuable recommendations such as an additional PCR purification, an increase in library pooling volumes, and a reduction of adapter volumes for samples with concentrations ≥31.2 pg. Thus, this research highlights the importance of all‐encompassing validation studies for implementing novel technologies in forensic casework and presents recommendations for challenging samples.

Which tissue to take? A retrospective study of the identification success of altered human remains

In forensic medicine, deceased are usually identified by comparing ante- and post-mortem dental or radiological features. However, in severe putrefaction, burning or absent reference data, the remaining tool for identifying human remains is DNA genotyping. But even a DNA-based identification can be challenging when confronted with a high post-mortem interval or heat impacts because it can lead to undesirable degradation of the DNA that varies among tissue types. This retrospective study investigated the identification success in 402 altered human corpses over seven years by comparing the examined tissue types from decomposed, skeletonised and burnt corpses as well as bodies found in water. For each tissue, the STR genotyping results and the number of additional or parallel genetic analyses were evaluated. By comparing the amplification success in samples from altered and unaltered remains, condition-based and tissue-specific differences were observed. With a mean number of 1.6 additional amplifications in cases with well-preserved corpses and 4.5 in altered corpses, the results showed significantly more DNA analyses for altered remains. In 83% of the cases, extra amplifications were performed to identify the corpse. The tissue-specific differences revealed an uncertainty in choosing suitable material from altered corpses for a successful DNA profile. Especially for bone and muscle samples, the genotyping success was the most unpredictable. Furthermore, comparing the retrospective outcome with other research findings, a remarkable variety of recommendations for the "best tissue choice" exists in the forensic community. Thus, our survey highlights the advantages of a broader and systematic approach on hard and soft tissues for successful DNA-based identification of altered human remains at first attempt.

Suitability of specific soft tissue swabs for the forensic identification of highly decomposed bodies

When decomposition of a recovered body is fairly advanced, identification based on common morphologic features is often impossible. In these cases, short tandem repeat (STR) marker genotyping has established itself as a convenient and reliable alternative. However, at very progressed stages of decomposition, postmortem tissue putrefaction processes can decrease DNA yields considerably. Hence, not all types of tissue are equally suitable for successful STR marker-based postmortem identification. Bone or dental material is often analysed in corpses with advanced decompositional changes. However, processing of these materials is very elaborate and time and resource consuming. We have therefore focused on the suitableness of various types of soft tissue swabs, where DNA extraction is easier and faster. By sampling 28 bodies at various stages of decomposition, we evaluated the suitability of different tissues for genotyping at varying degrees of physical decay. This was achieved by a systematic classification of the sampled bodies by morphological scoring and subsequent analysis of multiple tissue swabs of the aortic wall, urinary bladder wall, brain, liver, oral mucosa and skeletal muscle. In summary, we found variable degrees of suitability of different types of soft tissue swabs for DNA-based identification. Swabs of the aortic wall, the urinary bladder wall and brain tissue yielded the best results - in descending order - even at advanced levels of decay.

Comparative analysis of DNA extraction processes for DNA-based identification from putrefied bodies in forensic routine work

Identification of putrefied bodies is an important and common task in forensic routine. Usually, the identification of deceased is done by visual recognition, fingerprints, physical distinguishing marks (e.g. tattoos, scars and surgical implants) and/or dental examination. However, if morphologic characteristics are not recognizable, due to advanced putrefaction of the corpse, or recent medical records are not available, the DNA-based identification is favored. Thus, in order to find another reliable procedure for DNA extraction of putrefied samples regarding tissue selection, costs and time, two commercial forensic kits were compared: DNeasy® Blood & Tissue kit and SwabSolution™ kit. Both kits were used for DNA extraction from five soft tissues (brain, aorta, liver, kidney and psoas major muscle) and nails (finger- and toenail) obtained during the medicolegal autopsy of 20 putrefied corpses. DNeasy® Blood & Tissue kit was by quantitative comparison mostly superior to SwabSolution™ kit: it yielded more DNA of better quality (i.e. less degraded and inhibited). However, the qualitative results (DNA profiles) of both extraction procedures were similar. Among the analyzed tissue types, nails were proved as the most suitable for DNA-based identification of putrefied bodies.

Nails as a primary sample type for molecular genetic identification of highly decomposed human remains

For identification of badly preserved cadavers, only a few tissues can be used as a source of DNA, mostly bones and teeth, from which sampling and DNA extraction are difficult and time-consuming. In most highly decomposed remains, the nails are preserved. The aim of this study was to evaluate nails as an alternative source of DNA instead of bones and teeth in demanding routine identification cases. An automated extraction method was optimized on nails obtained from 33 cadavers with a post-mortem interval (PMI) up to 5 years. The commercially available EZ1 Investigator Kit (Qiagen) was used for extraction, and the G2 buffer included in the kit was replaced with TN_Ca buffer, and DTT was added for digestion of 5 mg of nail. The DNA was purified in a Biorobot EZ1 device (Qiagen), quantified using the PowerQuant System (Promega), and STR typing was performed with the NGM kit (TFS). From 0.3 to 270 μg DNA/g of nail was obtained from the samples analyzed, with an average yield of 36 μg DNA/g of nail. Full STR profiles were obtained from all nails except one. The optimized extraction method proved to be fast and highly efficient in the removal of PCR inhibitors, and it yields high amounts of DNA for successful STR typing. Nails were implemented as the primary sample type for obtaining DNA from highly decomposed and partially skeletonized cadavers in routine forensic identification cases in our laboratory.

Detection of short tandem repeat polymorphisms from human nails using direct polymerase chain reaction method

Human nail is an important forensic material for parental testing and individual identification in large-scale disasters. Detection of STR polymorphism from hard tissues generally requires DNA purification, which is technically complicated and time consuming. In the present study, we attempted to detect STR polymorphisms from untreated human nail samples by direct PCR amplification method using the primer mixture supplied with the GenePrint® SilverSTR® III System or the AmpFℓSTR® Identifiler® PCR Amplification Kit, and Tks Gflex DNA polymerase known to be effective for amplification from crude samples. A nail fragment measuring approximately 1.5 mm in breadth and 0.5 mm in length was placed directly into a PCR tube, and various PCR conditions were tested. The PCR products were analyzed by denaturing acrylamide gel electrophoresis or CE. Multiple STR polymorphisms were detected successfully. This method that detects STR polymorphisms not only from fresh human fingernails, but also from old nail fragments stored at room temperature for up to 10 years is expected to become a novel DNA analytical method in forensic medicine and genetic studies.