Identification of skeletal remains of Communist Armed Forces victims during and after World War II: combined Y-chromosome (STR) and MiniSTR approach

Evaluating the efficacy of three Y-STRs commercial kits in degraded skeletal remains

Y chromosome short tandem repeats (Y-STRs) typing is a useful tool in scenarios such as mass graves analysis or disaster victim identification and has become a routine analysis in many laboratories. Not many comparisons have been performed with the currently available commercial kits, much less with degraded skeletal remains. This research aims to evaluate the performance of three commercial Y-STR kits: Yfiler™ Plus, PowerPlex® Y23, and Investigator® Argus Y-28 in 63 degraded skeletal remains from mass graves. PowerPlex® Y23 yields more reportable markers and twice the RFU on average, while Yfiler™ Plus and Investigator® Argus Y-28 exhibited a similar behaviour. Additionally, Argus Y-28, which has not been tested with this kind of samples in literature before, showed a good performance. Finally, a predictive model was attempted to be developed from quantification and autosomal STR data. However, no acceptable model could be obtained. Nevertheless, good Y-STR typing results may be expected if at least 50 pg DNA input is used or 13 autosomal markers were previously obtained.

Identification of skeletal remains in Croatia and Bosnia and Herzegovina, including the homeland war - a 30-year review

Over the past 30 years, forensic experts from Croatia and Bosnia and Herzegovina have embraced advanced technologies and innovations to enable great efficacy and proficiency in the identification of war victims. The wartime events in the countries of former Yugoslavia greatly influenced the application of the selected DNA analyses as routine tools for the identification of skeletal remains, especially those from mass graves. Initially, the work was challenging because of the magnitude of the events, technical aspects, and political aspects. Collaboration with reputable foreign forensic experts helped tremendously in the efforts to start applying DNA analysis routinely and with increasing success. In this article, we reviewed the most significant achievements related to the application of DNA analysis in identifying skeletal remains in situations where standard identification methods were insufficient.

The last flight of F/O Tadeusz Stabrowski. Identification of the polish pilot

The paper presents the process of identifying an unnamed soldier of the Polish armed forces in the west, whose remains were found in a nameless grave at the municipal cemetery in Le Crotoy in France. The Polish Genetic Database of Victims of Totalitarianism team carried out the research in cooperation with the Ministry of Culture and National Heritage. A comprehensive analysis of autosomal and Y-STR markers was performed. Historical, anthropological, and forensic examinations of the remains were also carried out. The items found with the remains were also examined. Identification based on DNA analysis made it possible to restore the identity of the Polish pilot who died on 11 March 1943 near the French coast, F/O Tadeusz Stabrowski. The airman regained his name in 2018, he was about 26 years old at the time of his death and left behind a grieving wife and son in the United Kingdom. The success of identifying the NN remains was guaranteed by the appointment of an interdisciplinary team consisting of specialists in archaeology, anthropology, history, forensic medicine and forensic genetics. The analysis of historical sources allowed to determine 4 missing airmen whose remains could have been buried in the cemetery in Le Crotoy. An interesting aspect of the research was the cooperation with history enthusiasts and fans of Polish aviation, thanks to which it was finally possible to narrow down the group of pilots sought and reach the family of Tadeusz Stabrowski, who submitted comparative material for research. This is the first case of establishing the identity of a Polish pilot killed in France. Many institutions have been involved in the project, including Polish Ministry of Culture and National Heritage (MDiKN), which partially funded the research.

Direct STR typing from human bones

Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.

Separating forensic, WWII, and archaeological human skeletal remains using ATR-FTIR spectra

ATR-FTIR spectroscopy is a fast and accessible, minimally or non-destructive technique which provides information on physiochemical characteristics of analyzed materials. In forensic and archaeological sciences, it is commonly used for answering numerous questions, including the archaeological or forensic context of the human skeletal remains. In this research, the accuracy of ATR-FTIR-obtained spectra for separation between forensic, WWII, and archaeological human skeletal remains was investigated. Building from the previously proposed methodological procedures, various ratio-based and whole spectra separation procedures were applied, carefully analyzed, and evaluated. Results showed that employing whole spectral domains works best for the separation of archaeological, WWII, and forensic samples, even with samples of highly variable origin. Principal component analysis (PCA) further highlighted the necessity of acknowledging all the major components in the remains: amides, phosphates, and carbonates for the separation. Most influential proved to be amide I, namely its secondary structure, which presented well-preserved and organized collagen structure in forensic and WWII samples, while highly degraded in archaeological samples. Using the whole spectral domain for separation between samples from different contexts proved to be fast and simple, with no manipulation beyond baseline correction and normalization of spectra necessary. However, a dataset with samples of known origin is required for the learning model and predictions. A less accurate alternative is separation based on combining ratios of peaks correlating to organics and minerals in the bone, which eliminated overlapping and managed to classify the majority of the samples correctly as archaeological, WWII, or forensic.

Identification of the skeletal remains of the Czech communist regime crime victim, priest Josef Toufar

Parish priest Josef Toufar died as a direct consequence of torture committed by Communist State Security Service agents, forcing him to confess that "miraculous" movement of crucifix above the main altar during the Holy Mass held in the Roman-Catholic church in Číhošť was staged by using a technical equipment. Josef Toufar was presumably buried in a mass grave at the cemetery in Prague-Ďáblice under a false name Josef Zouhar. In 2013 the Czech Bishops' Conference grant an approval to begin the process of his beatification. However, the beatification required the exhumation and identification of the remains. In this case report, we describe the process of searching, exhumation, and the combined A-STR/Y-STR DNA analysis of remains of Pater Josef Toufar. His identification was feasible due to kinship analysis: buccal swabs of three family members (niece, grand-niece, and grand-nephew) were available for testing.

DNA Identification of Commingled Human Remains from the Cemetery Relocated by Flooding in Central Bosnia and Herzegovina

The floods in Bosnia and Herzegovina in May 2014 caused landslides all over the country. In the small village of Šerići, near the town of Zenica, a landslide destroyed the local cemetery, relocated graves, and commingled skeletal remains. As the use of other physical methods of identification (facial recognition, fingerprint analysis, dental analysis, etc.) was not possible, DNA analysis was applied. DNA was isolated from 20 skeletal remains (bone and tooth samples) and six reference samples (blood from living relatives) and amplified using PowerPlex^® Fusion and PowerPlex^® Y23 kits. DNA profiles were generated for all reference samples and 17 skeletal remains. A statistical analysis (calculation of paternity, maternity, and sibling indexes and matching probabilities) resulted in 10 positive identifications. In this study, 5 individuals were identified based on one reference sample. This has once again demonstrated the significance of DNA analysis in resolving the most complicated cases, such as the identification of commingled human skeletal remains.

Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina

Aim

To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina.

Methods

Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. Quantifiler^TM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach.

Results

A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications.

Conclusion

DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons’ relatives and collect referent samples from them.

STR-typing of ancient skeletal remains: which multiplex-PCR kit is the best?

Aim

To comparatively test nine commercially available short tandem repeat (STR)-multiplex kits (PowerPlex 16, 16HS, ES, ESI17, ESX17, S5 [all Promega]; AmpFiSTR Identifiler, NGM and SEfiler [all Applied Biosystems]) for their efficiency and applicability to analyze ancient and thus highly degraded DNA samples.

Methods

Fifteen human skeletal remains from the late medieval age were obtained and analyzed using the nine polymerase chain reaction assays with slightly modified protocols. Data were systematically compared to find the most meaningful and sensitive assay.

Results

The ESI, ESX, and NGM kits showed the best overall results regarding amplification success, detection rate, identification of heterozygous alleles, sex determination, and reproducibility of the obtained data.

Conclusion

Since application of these three kits enables the employment of different primer sequences for all the investigated amplicons, a combined application is recommended for best possible and – most importantly – reliable genetic analysis of ancient skeletal material or otherwise highly degraded samples, eg, from forensic cases.

Non-invasive examination of a skull fragment recovered from a World War Two aircraft crash site

The discovery of human remains dating to the time of the Second World War is a common occurrence in Europe and the Pacific regions. This case report demonstrates the analysis of a bone fragment recovered from a Luftwaffe crash site in Austria during the summer of 2007. Eye-witness statements and official reports were used to reconstruct the historical background of the case. A recovered German military identity tag helped to identify the pilot. Aircraft parts, also discovered at the crash site in 2007, aided the identification of the aircraft type and corroborated the eye-witness reports of the final moments before and during the crash. The bone was analyzed chiefly to establish its human or non-human origin and to identify from which anatomic region the fragment could have arisen. It was identified as part of a human adult skull which exhibited peri-mortem fractures and heat damage as well as post-mortem vegetation staining. The historical background information in connection with the morphological analysis led to the presumptive identification of the cranial fragment as belonging to a downed German pilot.

Capillary electrophoresis of miniSTR markers to genotype highly degraded DNA samples

The amplification of short tandem repeat (STR) markers throughout the human nuclear DNA genome are used to associate crime scene evidence to the perpetrator's profile in criminal investigations. For highly challenged or compromised materials such as stains exposed to the elements, skeletal remains from missing persons cases, or fragmented and degraded samples from mass disasters, obtaining a full STR profile may be difficult if not impossible. With the introduction of short amplicon STR or "miniSTR" typing, it is possible to obtain STR genetic information from highly challenged samples without the need to sequence the hypervariable regions of the mitochondrial DNA (mtDNA) genome. Non-Combined DNA Index System (CODIS) STR markers have been developed to obtain information beyond the core CODIS loci. This chapter will focus on the steps necessary to prepare and use one of the non-CODIS (NC) multiplexes, NC01 (Coble and Butler 2005), for analysis on capillary electrophoresis instrumentation.

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations.

Positive identification by a skull with multiple epigenetic traits and abnormal structure of the neurocranium, viscerocranium, and the skeleton

Wormian bones are small ossicles appearing within the cranial sutures in more than 40% of skulls, most commonly at the lambdoid suture and pterion. During the skeletal analysis of an unidentified male war victim, we observed multiple wormian bones and a patent metopic suture. Additionally, the right elbow was deformed, probably as a consequence of an old trauma. The skull was analyzed by cranial measurements and computerized tomography, revealing the presence of cranial deformities including hyperbrachicrania, localized reduction in hemispheral widths, increased cranial capacity, and sclerosis of the viscerocranium. Besides unique anatomical features and their anthropological value, such skeletal abnormalities also have a forensic value as the evidence to support the final identification of the victim.

The strategies to DVI challenges in Typhoon Morakot

Small village populations in which there is a high amount of kinship can cause complications in cases of disaster victim identification. This problem was highlighted by the loss of life after Typhoon Morakot struck Taiwan where over 500 people from small isolated communities lost their lives. Most of the victims were buried by landslides in the remote mountainous areas of southern Taiwan. Only 146 pieces of human remains were recovered after searching for 4 months. Most of the human remains were received for examination as severely damaged fragments prevented possible identification by morphological features. DNA testing using the traditional duo parent/child or sibling screening by STR data opens the possibility of including not only the actual victim but also false positives. Variable likelihood ratios were obtained when comparing DNA types from human remains to those from potential relatives; however, with the DNA typing of numerous members of the same living family, multiple matches to potential families were avoided. Of the 146 samples obtained and collapsed to 130 victims, they were linked to 124 individuals resulting in their identification when compared to a pool of 588 potential relatives. Six of the human remains could not be linked to any living relative and remain unknown.

Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia

This paper describes molecular genetic identification of one third of the skeletal remains of 88 victims of postwar (June 1945) killings found in the Konfin I mass grave in Slovenia. Living relatives were traced for 36 victims. We analyzed 84 right femurs and compared their genetic profiles to the genetic material of living relatives. We cleaned the bones, removed surface contamination, and ground the bones into powder. Prior to DNA isolation using Biorobot EZ1 (Qiagen), the powder was decalcified. The nuclear DNA of the samples was quantified using the real-time polymerase chain reaction method. We extracted 0.8 to 100 ng DNA/g of bone powder from 82 bones. Autosomal genetic profiles and Y-chromosome haplotypes were obtained from 98% of the bones, and mitochondrial DNA (mtDNA) haplotypes from 95% of the bones for the HVI region and from 98% of the bones for the HVII region. Genetic profiles of the nuclear and mtDNA were determined for reference persons. For traceability in the event of contamination, we created an elimination database including genetic profiles of the nuclear and mtDNA of all persons that had been in contact with the skeletal remains. When comparing genetic profiles, we matched 28 of the 84 bones analyzed with living relatives (brothers, sisters, sons, daughters, nephews, or cousins). The statistical analyses showed a high confidence of correct identification for all 28 victims in the Konfin I mass grave (posterior probability ranged from 99.9% to more than 99.999999%).