Multidisciplinary Identification of the Controversial Freedom Fighter Jörg Jenatsch, Assassinated 1639 in Chur, Switzerland

Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology

Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.

A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology

It is very important to generate phenotypic results that are reliable when processing chronological old skeletal remains for cases involving the identification of missing persons. To improve the success of pigmentation prediction in Second World War victims, three bones from each of the eight skeletons analyzed were included in the study, which makes it possible to generate a consensus profile. The PowerQuant System was used for quantification, the ESI 17 Fast System was used for STR typing, and a customized version of the HIrisPlex panel was used for PCR-MPS. The HID Ion Chef Instrument was used for library preparation and templating. Sequencing was performed with the Ion GeneStudio S5 System. Identical full profiles and identical hair and eye color predictions were achieved from three bones analyzed per skeleton. Blue eye color was predicted in five skeletons and brown in three skeletons. Blond hair color was predicted in one skeleton, blond to dark blond in three skeletons, brown to dark brown in two skeletons, and dark brown to black in two skeletons. The reproducibility and reliability of the results proved the multisample analysis method to be beneficial for phenotyping chronological old skeletons because differences in DNA yields in different bone types provide a greater possibility of obtaining a better-quality consensus profile.

Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site

The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

Perimortem Skeletal Sharp Force Trauma: Detection Reliability on CT Data, Demographics and Anatomical Patterns from a Forensic Dataset

Simple Summary

The increased use of computed tomography images in forensic anthropology is easily explained with a variety of benefits: among other reasons they are digitally stored, they can easily be shared and they are non-invasive. However, it is not clear how suitable these images are for forensic anthropologists to detect sharp force trauma. Therefore, we analyzed computed tomography images, by observing digital images of 41 forensic cases in different viewing modalities. In addition, we looked for anatomical injury patterns in the soft- and hard-tissues and any significant correlations between the manner of death (suicide or homicide) with different parameters. Our findings indicated a superiority of viewing the images in 2D, but not all bone lesions were detected. The manner of death was significantly correlated to some of the parameters, which could be extrapolated to future forensic anthropological cases. We promote the inclusion of imaging training into the anthropological curricula.

Abstract

The increasing importance of trauma analysis by means of postmortem computed tomography (PMCT) is insufficiently reflected in forensic curricula, nor are best practice manuals available. We attempt to detect sharp force bone lesions on PMCT of closed forensic cases with the aims of assessing errors and pointing out patterns in anatomical location and manner of death (MOD). We investigated 41 closed sharp force fatality cases, with available PMCT and forensic reports. Two observers with different radiological training assessed the lesions on PMCT scans (2D and 3D) for comparison with the reports. Between 3% (suicides) and 15.3% (homicides) of sharp force injuries caused visible bone lesions. While our observations were repeatable, each forensic investigation left a similar number of bone lesions undetected. Injury patterns differed between MOD, with thoracic bone lesions being most frequent overall. Soft tissue injury location varied between the MOD. Associations between MOD and age as well as number of injuries were significant. The detection of bone lesions on PMCT for untrained forensic specialists is challenging, curricula and pertinent manuals are desirable. With the low frequency of bone lesions compared to soft tissue injuries, we should be aware when analyzing decomposed bodies.

Identification of a Slovenian prewar elite couple killed in the Second World War

Genetic identification of a Slovenian prewar elite couple killed in 1944 was performed by typing autosomal and Y-chromosomal STRs, and phenotypic HIrisPlex SNPs for hair and eye color prediction were analyzed for the female skeleton using next-generation sequencing (NGS) technology. The clandestine grave containing the couple's skeletal remains was found in 2015 and only the partial remains were found. Living distant relatives could be found only for the male victim. Because of a lack of comparative reference samples, it was not possible to identify the female victim through autosomal and mitochondrial DNA typing. However, the possibility of comparison of eye and hair color with a painting exhibited in the City Museum of Ljubljana by the prominent Slovenian painter Ivana Kobilca existed. Nuclear DNA obtained from the samples was quantified using the PowerQuant System, and then STR typing was carried out with different autosomal and Y-STR kits. From 0.09-9.36 ng DNA/g of powder was obtained from teeth and bones analyzed. Complete autosomal and Y-STR profiles made it possible to identify the male skeleton via comparison with two nephews. For the female victim, predicted eye and hair color was compared to colors on the painting. Kobilca's painting confirms the genetically predicted eye and hair color. After more than seventy years, the skeletal remains of the couple were handed over to their relatives, who buried the victims with dignity in a family grave.

Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany

Ancient DNA (aDNA) analysis is a powerful tool in multidisciplinary research on human remains, potentially leading to kinship scenarios and historical identifications. In this study, we present a genetic investigation of three noble families from the 17th to 19th centuries AD entombed in burial crypts at the cloister church of Riesa (Germany). Tests were aimed at identifying anticipated and incidental genetic relationships in our sample and the implications thereof for the assumed identity of the deceased. A total of 17 individuals were investigated via morphological, radiographic and aDNA analysis, yielding complete and partial autosomal and Y-STR profiles and reliable mtDNA sequences. Biostatistics and lineage markers revealed the presence of first to third degree relationships within the cohort. The pedigrees of the families Hanisch/von Odeleben and von Welck were thereby successfully reproduced, while four previously unknown individuals could be linked to the von Felgenhauer family. However, limitations of biostatistical kinship analysis became evident when the kinship scenario went beyond simple relationships. A combined analysis with archaeological data and historical records resulted in (almost) unambiguous identification of 14 of the 17 individuals.

The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeq^TM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.

Photogrammetry vs CT Scan: Evaluation of Accuracy of a Low-Cost Three-Dimensional Acquisition Method for Forensic Facial Approximation

Photogrammetry is a three-dimensional acquisition method potentially applicable to the forensic field. This possibility requires the verification of its accuracy. In this study, 3D volumes of skulls are generated to compare the photogrammetry versus the CT scan. In order to provide eligible material to the photogrammetric software, photographs were captured at a distance of 30 cm from the skull placed on a support 1 m in height and illuminated with diffused laboratory ceiling artificial light. A Nikon Coolpix P7100 camera was used. Photographs capture common elements with the previous and the next photograph so as to allow the photogrammetric software to recognize these common points between photographs and create a 3D puzzle. The Zephyr Lite (3DFlow©) software was employed to register the 3D volume. CT-based skulls are taken as a metric reference. The photogrammetry-based skulls are then enlarged according to the measurements of some landmarks or Zygion and Zygion, the distance between end of nasal and base of nasal pyramid for frontal projection, and minimum breadth of the mandibular ramus for the right lateral projection. The accuracy of the photogrammetry is compared to that of the CT scan by measuring the 3D volumes of the skulls studied. Specific landmarks are used as reference points for the measures in both frontal and lateral views. Bland-Altman graph shows homogeneity. The mean difference (1.28 mm) indicates that the measurements taken on the photogrammetry-based skull tend to slightly overestimate compared with the measurements taken on the CT-based skull.

The Sommersdorf mummies-An interdisciplinary investigation on human remains from a 17th-19th century aristocratic crypt in southern Germany

Sommersdorf Castle (Bavaria, Germany) is a medieval castle complex which has been inhabited by the aristocratic family von Crailsheim. The deceased were entombed in a crypt located in the parapets underneath the castle’s church, resulting in mummification of the bodies. Based on the family chronicle and oral history, identities have been ascribed to the mummies. The aim of the study is therefore to test the accuracy of the historical records in comparison to archaeological, anthropological and genetic data. Today, the crypt houses eleven wooden coffins from the 17^th to 19^th century AD. In ten of these, mummified and scattered human remains were found. Archive records were studied in order to identify names, ancestry, titles, occupation, date of birth and death, and place of interment of the individuals. The coffins were visually inspected and dated by typo-chronology, and the mummified and scattered skeletal remains were subjected to a physical anthropological examination. In total, the crypt contains the remains of a minimum number of nine individuals, among them three adult males, five adult females and one infant. A detailed scientific examination, including prior conservation, ancient DNA analyses, and computed tomography (CT), was performed on five mummies. By means of the CT data age at death, sex, body height, pathologies, and anatomical variants were investigated. CT analysis further showed that the bodies were naturally mummified. Mitochondrial DNA analyses revealed that the tested individuals are not maternally related. In addition, health, living conditions and circumstances of death of the entombed individuals could be highlighted. Being confronted with the strengths, weaknesses and limitations of each methodological approach, probable identification was achieved in two cases.