Reliable genetic identification of burnt human remains

Quantitative color analysis of burned bone to predict DNA quantity, quality, and genotyping success

Badly burned skeletal remains are commonly submitted to forensic laboratories for victim identification via DNA analysis methods. Burned skeletal remains present many challenges for DNA analysis as they can contain low amounts of DNA which can also be damaged and degraded, resulting in partial or no STR profiles. Therefore, a simple, but effective screening method that identifies which samples may provide the most successful STR or mtDNA typing results for identification would enable forensic laboratories to save time, money, and resources. One metric that can be used and a screening method is the color of burned bone, as bone color changes with exposure to fire as temperature and length of exposure increase. This research developed a quantitative screening method based on the surface color of burned bone. The different visual bone colors (light brown, dark brown, black, gray, and white) were quantified using the Commission on Illumination L*a*b color space. These values were then compared to DNA yield, STR, and mtDNA profile completeness to identify whether the L*a*b values can predict genotyping success. A Bayesian network was constructed to determine the probability of STR typing success, given a set of L*a*b values. Results demonstrated that samples with an a* value greater than or equal to one and b* value greater than eight (light brown and dark brown burned samples) were the most predictive of STR typing success and mtDNA typing success. A decision tree for processing burned bones was constructed based on the color value thresholds.

An overview of the heat-induced changes of the chemical composition of bone from fresh to calcined

When bone is exposed to thermal stress, the chemical composition changes. This affects bone tissue regeneration after surgery, and these changes can also aid in reconstructing ante-, peri-, and post-mortem events in forensic investigations and past activities on cremation practices in archaeology. However, to date, no complete overview exists on the chemical composition of both fresh and thermally altered bone. Therefore, we aimed (i) to present the chemical composition of fresh bone and (ii) to present an overview of heat-induced chemical changes in bone under both reducing and oxidizing conditions. From the overview, it became clear that some chemical changes occur at a consistent temperature, independent of exposure duration, meaning there is a temperature threshold. However, the occurrence of other chemical changes appeared to be more inter-experimentally variable, and therefore, it is recommended to further investigate these changes.

Targeted enrichment of whole-genome SNPs from highly burned skeletal remains

Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.

Understanding the burden of unidentified bodies: a systematic review

While human identification is a crucial aspect of medico-legal investigations, many individuals remain unidentified each year across the world. The burden of unidentified bodies is often referred to when motivating for improved methods of identification, and anatomical teaching, yet the actual burden is somewhat unclear. A systematic literature review was undertaken to identify articles that empirically investigate the number of unidentified bodies experienced. Despite the large number of articles returned, an alarmingly low number (24 articles) provided specific and empirical details on the number of unidentified bodies, demographics and trends thereof. It is possible that this lack of data is due to the variable definition of 'unidentified' bodies and the use of alternative terminology such as 'homelessness' or 'unclaimed' bodies. Nevertheless, the 24 articles provided data for 15 forensic facilities across ten countries of both developed and developing statuses. On average, developing countries experienced more than double (9.56%) the number of unidentified bodies when compared to developed nations (4.40%). While facilities were mandated under different legislations and infrastructures available varied greatly, the most common issue faced is the lack of standardised procedures for forensic human identification. Further to this, the need for investigative databases was highlighted. Through addressing the standardisation of identification procedures and terminology, alongside the appropriate utilisation of existing infrastructure and database creation, the number of unidentified bodies could be significantly reduced globally.

Kinship analysis of skeletal remains from the Middle Ages

Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.

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.

Proteins, possibly human, found in World War II concentration camp artifact

Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.

The intervertebral discs' fibrocartilage as a DNA source for genetic identification in severely charred cadavers

Identifying charred human remains poses a challenge to forensic laboratories. High temperature completely incinerates the superficial tissues and partially destroys bones, forcing the forensics to seek an alternative, for bones and teeth, forensic material that should quickly and cheaply deliver DNA of sufficient quantity and quality. We sought, other than rib cartilage, types of cartilages that could serve as a DNA source. DNA was isolated from the fibrous cartilage of a fibrous ring of intervertebral L1-L2 discs sampled from charred cadavers or charred body fragments: 5 victims of car fires, 1 victim of combustion during a residential house gas explosion, and 3 victims of nitroglycerin explosion. DNA was isolated by the column method. DNA quality and concentration were assessed by RT-PCR and multiplex PCR for 23 autosomal and 17 Y chromosome STR loci. STR polymorphism results obtained by capillary electrophoresis served for likelihood ratio (LR) calculations. DNA concentration in relation to the cadaver's age and post-mortem interval (PMI) were analyzed. All samples (n = 9) yielded good-quality DNA in quantities (0.57-17.51 ng/µL for T. Large autosomal sequence) suitable for STR-based amplification. The isolated DNA characterized a low degradation index (0.80-1.99), and we were able to obtain complete genetic profiles. In each of the nine cases, the genotyping results allowed identifying the victims based on comparative material from the immediate family. The results demonstrate the usefulness of human intervertebral disc fibrocartilage as an alternative DNA source for the genetic identification of charred bodies or charred torso fragments.

Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth

The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.

The impact of moderate heating on human bones: an infrared and neutron spectroscopy study

This study aims to analyse human bones exposed to low/medium temperatures (200-650°C) under experimentally controlled conditions, both oxidizing and reducing, using complementary optical and neutron vibrational spectroscopy techniques. Clear differences were observed between the aerobically and anaerobically heated bones. The organic constituents disappeared at lower temperatures for the former (ca 300°C), while they lingered for higher temperatures in anaerobic environments (ca 450-550°C). Unsaturated non-graphitizing carbon species (chars) were detected mainly for anaerobically heated samples, and cyanamide formation occurred only at 650°C in reducing settings. Overall, the main changes were observed from 300 to 400°C in anaerobic conditions and from 450 to 500°C in aerobic environments. The present results enabled the identification of specific spectroscopic biomarkers of the effect of moderate temperatures (less than or equal to 650°C) on human bone, thus contributing to a better characterization of forensic and archaeological skeletal remains subject to heating under distinct environmental settings. In particular, these data may provide information regarding cannibalism or ancient bone boiling and defleshing rituals.

Sweet tooth: DNA profiling of a cranium from an isolated retained root fragment

Sampling of healthy multi‐rooted teeth is recommended for the genetic identification of human skeletal remains. However, this may not always be possible, as in the reported case consisting of an isolated human cranium found in an aggregate crushing and processing plant in Piedmont, Northwest Italy. The cranium displayed significant weathering, suggesting a post‐mortem interval of several years, and was edentulous with the exception of the apical root fragment of the upper left canine, consequence of an antemortem horizontal fracture. Prolonged decalcification of the root fragment followed by powder‐free DNA extraction from ~10 mg of root tip tissue led to the recovery of >10 ng of high molecular weight human DNA, in comparison with ~0.01 ng of DNA per mg of bone powder obtained from the petrous portion of the temporal bone. Quantity and quality of DNA isolated from apical tooth tissue enabled multiple genotyping, including a reportable female STR profile, mitochondrial DNA analysis, and ancestry‐informative insertion/deletion polymorphisms. Although the cranium remained unidentified after DNA comparisons, our findings confirm that apical tooth tissue is a promising source of DNA, easily obtained through a powder‐free extraction protocol. Results also indicate that root tips should not be overlooked in challenging identification cases, even in the presence of compromised tooth specimens.

DNA degradation in human teeth exposed to thermal stress

Human identification from burned remains poses a challenge to forensic laboratories, and DNA profiling is widely used for this purpose. Our aim was to evaluate the effect of temperature on DNA degradation in human teeth. Thirty teeth were exposed to temperatures of 100, 200, or 400 °C for 60 min. DNA was quantified by Real-Time qPCR (Quantifiler Human DNA Quantification Kit) and fluorescence spectroscopy (Qubit 3.0 Fluorometer). DNA degradation was evaluated by using STR markers (AmpFLSTR Identifiler Plus PCR Amplification Kit) to determine the allele and locus dropout, inter-locus balance, and degradation slope (observed (Oa) to expected (Ea) locus peak height ratio against the molecular weight). Most of the genomic DNA was degraded between 100 °C and 200 °C. At 100 °C, locus dropout ratios showed significant differences between the largest loci (FGA, D7S820, D18S51, D16S539, D2S1338 and CSF1PO) and amelogenin. Inter-locus balance values significantly differed between all dye channels except between NED and PET. The dropout ratio between D18S51 (NED) and amelogenin (PET) can be recommended for the evaluation of DNA degradation. The Oa/Ea regression model can predict locus peak heights in DNA degradation (R2 = 0.7881). These findings may be useful to assess the reliability of DNA typing for human identification in teeth subjected to prolonged incineration.

Rechtsmedizinische Begutachtung von Knochenfunden am Gießener Institut für Rechtsmedizin

Einleitung

Funde von Knochen(fragmenten) können von Interesse für Strafverfolgungs- oder Denkmalbehörden sein. Die forensisch-osteologische Begutachtung kann zur Einordnung der Bedeutung des Fundes beitragen. Ziel der Studie war, durch eine Auswertung von am Institut für Rechtsmedizin Gießen begutachteten Knochenfunden einen Überblick über Umstände und Art der Funde sowie Umfang und Ergebnisse der Begutachtungen zu erhalten.

Material und Methoden

Für den Zeitraum von 2005 bis 2019 wurden im Institut archivierte osteologische Gutachten analysiert und Daten zu Fundort, -umständen, Humanspezifität, postmortalem Intervall, Spuren von Gewalteinwirkungen und die Ergebnisse weiterführender Untersuchungen ausgewertet.

Ergebnisse

Von 172 begutachteten Knochenfunden wurden 40 % in Wald- und Wiesengebieten aufgefunden. In 58 % enthielten die Funde menschliche Knochen, davon wurde in 32 % eine forensisch relevante Liegezeit nicht ausgeschlossen. Zeichen perimortaler Gewalteinwirkung fanden sich in 6 % menschlicher Knochenfunde. Ergänzende DNA-Untersuchungen wurden in 20 % aller Funde durchgeführt; davon verlief in 62 % die Typisierung humaner STR erfolgreich, und in 41 % gelang die Zuordnung zu einem antemortalen Profil. Bei den zur Begutachtung übersandten nichtmenschlichen Knochen handelte es sich am häufigsten um Knochen von Hirsch bzw. Reh (32 %), Schwein (29 %) und Rind (14 %).

Diskussion

Die Begutachtung von Knochenfunden soll Behörden ermöglichen, die (straf-)rechtliche Relevanz eines Fundes einzuordnen. Die makroskopische Untersuchung ist dafür von großer Bedeutung. Für die Identifizierung menschlicher Knochen besitzen DNA-Vergleichsuntersuchungen einen großen Stellenwert. Sie waren für 81 % der erfolgreichen Identifizierungen der Fälle mit menschlichen Knochen verantwortlich.

A review of the current understanding of burned bone as a source of DNA for human identification

Identification of incinerated human remains may rely on genetic analysis of burned bone which can prove far more challenging than fresh tissues. Severe thermal insult results in the destruction or denaturation of DNA in soft tissues, however genetic material may be preserved in the skeletal tissues. Considerations for DNA retrieval from these samples include low levels of exogenous DNA, the dense, mineralised nature of bone, and the presence of contamination, and qPCR inhibitors. This review collates current knowledge in three areas relating to optimising DNA recovery from burned bone: 1) impact of burning on bone and subsequent effects on sample collection, 2) difficulties of preparing burned samples for DNA extraction, and 3) protocols for bone decalcification and DNA extraction. Bone decalcification and various DNA extraction protocols have been tested and optimised for ancient bone, suggesting that prolonged EDTA (Ethylenediaminetetraacetic acid) demineralisation followed by solid-phased silica-based extraction techniques provide the greatest DNA yield. However, there is significantly less literature exploring the optimal protocol for incinerated bones. Although burned bone, like ancient and diagenetic bone, can be considered "low-copy", the taphonomic processes occurring are likely different. As techniques developed for ancient samples are tailored to deal with bone that has been altered in a particular way, it is important to understand if burned bone undergoes similar or different changes. Currently the effects of burning on bone and the DNA within it is not fully understood. Future research should focus on increasing our understanding of the effects of heat on bone and on comparing the outcome of various DNA extraction protocols for these tissues.

Effectiveness of various methods of DNA isolation from bones and teeth of animals exposed to high temperature

In the event of fires, natural disasters, and other events associated with high temperature, bones and teeth are the only source of genetic material for identifying human or animal carcasses. To obtain reliable final results of identification tests, the use of appropriate nucleic acid extraction methods is crucial. Therefore, the main objective of this research was to evaluate the effectiveness of selected methods of DNA isolation from animal burnt bones and teeth. In addition, the effect of the duration of high temperature on the stability of nuclear and mitochondrial DNA in these tissues was determined, as well as the possibility of using the genetic material obtained for species identification of remains of unknown origin. Bones and teeth collected during necropsy of dogs were burnt in a laboratory oven at 400 °C (752 °F; 673.15 K) for 5, 10, 15, 30, 45 and 60 min. DNA was isolated according to four different protocols, using three commercial kits, i.e. the PrepFiler® Forensic DNA Extraction Kit from Applied Biosystems, the QIAamp® DNA Investigator Kit from QIAGEN, and the DNA Mini Kit from Syngen, as well as a classic organic method. The effectiveness of these methods was compared by assessing the amount of isolated DNA using Real-Time PCR and its purity using a NanoDrop™ spectrophotometer. Each isolate was also subjected to PCR with primers designed to amplify fragments of dog mitochondrial DNA. The effectiveness of species identification was assessed for the method showing the best DNA recovery and for the organic method, considered the gold standard for analysis of difficult material. The QIAamp® DNA Investigator Kit showed the highest efficiency of DNA isolation from bones and teeth burnt for 15 min (the longest burning time for which DNA could still be recovered from bones and teeth). The results of the experiment clearly indicate that DNA stability in hard tissues depends on how long they burn. In the case of exposure to 400 °C, reliable genetic testing, including species identification, is possible when the burning time does not exceed 15 min. Among the hard tissues examined, bones proved more suitable than teeth for identification purposes. It was also concluded that identification of bone remains with extreme heat damage should be based on mitochondrial DNA analysis.

Comparison of bone demineralisation procedures for DNA recovery from burned remains

Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.

A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling

Standard protocols for extracting DNA from bone are variable and are largely dependent on the state of preservation. In archaic samples, endogenous DNA is believed to be tightly bound to crystal aggregates in the Hydroxyapatite (HAp) matrix requiring prolonged demineralisation to allow its release. By comparison, fresh bone contains abundant cellular material, discounting the need for demineralisation. Recommendations for incinerated bone, specifically how viable sampling sites should be selected and the ideal techniques for DNA recovery are unclear, and the protocol used is often selected based on macroscopic sample appearance. It has been postulated that like archaic bone, burned bone is 'highly degraded' and therefore aDNA techniques may present better results for DNA recovery than using fresh protocols. However, little research has been undertaken comparing the crystal structure of burnt, fresh and archaic bone. This study uses a combination of XRPD and SEM analysis to compare the crystalline profile and microscopic appearance of burned bone subjected to temperatures ranging from 100-1000°C, with archaic and fresh samples. Although macroscopically visually different, fresh samples and samples heated up to 500°C showed no microscopic differences or significant changes in crystallinity. By comparison, samples heated above 500°C became significantly more crystalline, with HAp crystal size increasing dramatically. Archaic samples were different again, more closely resembling the amorphous fresh samples than the highly crystalline incinerated samples. These results suggests that, potentially, samples burned at 500°C or lower can be treated as fresh samples, whilst samples exposed to higher temperatures may require adapted protocols. Whether or not these highly burned samples require demineralisation needs to be investigated.

Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques

Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.

Variations in mitochondrial DNA control region among Malay and Chinese subpopulations (sequence 16000-16200)

DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000-16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.

Cytoskeletal and extracellular matrix proteins resist the burning of bones

Due the proteins from bone remains are highly resistant to pass of time and environmental conditions, they could tell us about the events that probably happened in the past. In the forensic and physical anthropology context, burnt bone remains are one of the most common pieces of recovered evidence and, generally, they are associated with funerary practices, criminal scenes or massive catastrophic events. In the present study, bone pieces of pigs were calcined at different calcination temperatures, and proteins were searched using biochemical, immunochemical and ultrastructure visualization under these experimentally conditions. For this purpose, it was successfully developed a non-demineralizing protein extraction method from burnt bone remains and the use of specific antibodies permitted the identification of different extracellular matrix and intracellular proteins. While collagen proteins type I and IV were identified and detected under middle and high calcination temperatures (300°C and 600°C); cytoskeletal proteins as actin, tubulin and, the microtubule associated protein Tau, were found under calcination process, even up high calcination temperatures. Under ultrastructural analysis, fibrous materials with a classical disposition of collagens were observed even at high calcination temperatures of the burnt bone remains. The protein identification and characterization in burnt bones as performed in present studies, is clearly demonstrating that using specific strategies for protein characterizations it is possible to found protein biomarkers in burnt bone remains and this strategy could be useful for forensic and anthropological purposes.

Colourimetric analysis of thermally altered human bone samples

At this moment, no method is available to objectively estimate the temperature to which skeletal remains have been exposed during a fire. Estimating this temperature can provide crucial information in a legal investigation. Exposure of bone to heat results in observable and measurable changes, including a change in colour. To determine the exposure temperature of experimental bone samples, heat related changes in colour were systemically studied by means of image analysis. In total 1138 samples of fresh human long bone diaphysis and epiphysis, varying in size, were subjected to heat ranging from room temperature to 900 °C for various durations and in different media. The samples were scanned with a calibrated flatbed scanner and photographed with a Digital Single Lens Reflex camera. Red, Green, Blue values and Lightness, A-, and B-coordinates were collected for statistical analysis. Cluster analysis showed that discriminating thresholds for Lightness and B-coordinate could be defined and used to construct a model of decision rules. This model enables the user to differentiate between seven different temperature clusters with relatively high precision and accuracy. The proposed decision model provides an objective, robust and non-destructive method for estimating the exposure temperature of heated bone samples.

Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases

The acquisition of biological information and assessment of the most probable geographic origin of unidentified individuals for obtaining positive identification is central in forensic sciences. Identification based on forensic DNA, however, varies greatly in relation to degradation of DNA. Our primary aim is to assess the applicability of a petrous bone sampling method in combination with Next Generation Sequencing to evaluate the quality and quantity of DNA in taphonomically degraded petrous bones from forensic and cemetery cases. A related aim is to analyse the genomic data to obtain the molecular sex of each individual, and their most probable geographic origin. Six of seven subjects were previously identified and used for comparison with the results. To analyse their probable geographic origin, samples were genotyped for the 627.719 SNP positions. Results show that the inner ear cochlear region of the petrous bone provides good percentages of endogenous DNA (14.61–66.89%), even in the case of burnt bodies. All comparisons between forensic records and genetic results agree (sex) and are compatible (geographic origin). The application of the proposed methodology may be a powerful tool for use in forensic scenarios, ranging from missing persons to unidentified migrants who perish when crossing borders.

Scientific evidence for the identification of an Aboriginal massacre at the Sturt Creek sites on the Kimberley frontier of north-western Australia

Archival research into episodes of frontier violence in the Kimberley region of Western Australia indicate that the bodies of Aboriginal victims of massacres were frequently incinerated following the event. This paper presents the results of a scientific investigation of a reported massacre at Sturt Creek where burnt bone fragments were identified in two adjacent sites and documents the archaeological signatures associated with the sites. The methodology used to undertake the project brought together three systems of knowledge: the oral testimonies of the descent group originating from a sole adult survivor of the massacre; archival, historical and scientific research. An archaeological survey defined the two distinct sites containing hundreds of fragile bone fragments; a third site was found to be highly disturbed. Scientific investigations included macroscopic and microscopic examination of selected bone fragments by an anatomical pathologist and a zooarchaeologist and X-ray diffraction analysis of sixteen bone fragments. The anatomical pathologist and zooarchaeologist undertook macroscopic and microscopic examinations of selected bone samples to identify morphological evidence for human origin. It was concluded that three bone fragments examined may have been human, and two of the fragments may have been from the vault of a skull. It was concluded that the likelihood of them being human would be strengthened if it was found that the three samples had been subjected to high temperatures. X-ray diffraction analysis of 16 bone fragments provided this evidence. All fragments showed sharp hydroxylapatite peaks (crystallite sizes 9882nm and 597nm respectively) and all had been subjected to extreme temperatures of either 600°C for more than 80h, 650°C for more than 20h, 700°C for more than 4h or 800°C for more than 1h. XRD analyses were also done on bone samples collected from three cooking hearths at three different archaeological sites. It was found that two of the three samples had been exposed to substantially lower temperatures for a short time period. It was concluded that there was strong pathological and archaeological evidence that the bone fragments were human in origin, but that the evidence was not conclusive. This research also identified archaeological signatures for the identification of massacre sites in similar Australian environments and circumstances.

Alteration of STR profiles in ovarian carcinoma cells during primary culture

PURPOSE

Cell authentication is a necessary procedure to avoid scientific data from cell culture experiments with cross-contamination or false classification. A genetic fingerprint pattern of a specimen by short tandem repeats (STR) is self-evident. Due to high amount of chromosomal rearrangements, known in epithelia ovary cancer cells and the instable STR pattern described in other tumour entities like leukaemia, this study explores the suitability of STR profiling for primary cultured epithelial ovary cancer cells.

METHODS

STR profiles of epithelial ovary cancers of 16 patients were compared with corresponding blood and corresponding primary cell cultures. The primary cell cultures of epithelial ovary tumours were passaged up to 28 times. In between, cultures were cryo conserved and recultured again, two to five times per patient.

RESULTS

In two cases, the STR pattern of tumour lost alleles (1/16 and 3/16) in comparison of corresponding STR-pattern from blood. In comparison to blood, cell culture of a third case, lost four alleles (4/16) accompanied with morphologic changes after 14th passage. It is equal after cryo conservation of the seventh passage from the same patient. The only changes in STR profiles we recognized are losses of alleles. Remaining STR markers allow authentication.

CONCLUSIONS

Very likely, the allelic drop-outs beyond passage 14 assume complex genetic losses of heterozygosis resulting in changed growth behaviour of cells. All other STR-profiles of remaining 15 patients analysed in this study are stable over all passages and freeze-thaw processes. Thus, ovary cancer cell cultures in research should be authenticated by STR-profile in general.

[The molecular genetic analysis of chromosomal DNA in burned bones]

The objective of the present study was a demonstrative consideration of the debatable problem concerning the possibility of obtaining reliable genetic information by the investigation of burned bones. The bone fragments with the identifiable external features of different degree of ignition (i.e. in the carbonized, grey- and white-burnt states) were placed in the muffle furnace for the controlled thermal treatment. The analytical suitability of these burned bone objects for genotyping was estimated with the use of standard chromosomal STR-loci multiplex genotyping panels. The results of the study cast serious doubts as regards the possibility of genotyping of chromosomal DNA extracted from the burned bones. It was shown that the exposure of the bone tissue to a temperature of 150 degrees Celsius during 2 hours can turn it into a material absolutely unsuitable for genotyping due to the loss of all individual genotypic traits. Characteristically the burned bone objects are externally indistinguishable from the native bone. At the same time, the material with the signs of the high-temperature impact visible by the unaided eye (e.g. in the carbonized, pronounced black as well as grey and white-burnt states) is altogether unsuitable for the reliable identification of the genetic profile of chromosomal DNA.

Post-mortem interval estimation of human skeletal remains by micro-computed tomography, mid-infrared microscopic imaging and energy dispersive X-ray mapping

In this study different state-of-the-art visualization methods such as micro-computed tomography (micro-CT), mid-infrared (MIR) microscopic imaging and energy dispersive X-ray (EDS) mapping were evaluated to study human skeletal remains for the determination of the post-mortem interval (PMI). PMI specific features were identified and visualized by overlaying molecular imaging data and morphological tissue structures generated by radiological techniques and microscopic images gained from confocal microscopy (Infinite Focus (IFM)). In this way, a more distinct picture concerning processes during the PMI as well as a more realistic approximation of the PMI were achieved. It could be demonstrated that the gained result in combination with multivariate data analysis can be used to predict the Ca/C ratio and bone volume (BV) over total volume (TV) for PMI estimation. Statistical limitation of this study is the small sample size, and future work will be based on more specimens to develop a screening tool for PMI based on the outcome of this multidimensional approach.

DNA survival and physical and histological properties of heat-induced alterations in burnt bones

During forensic casework, it is vital to be able to obtain valuable information from burnt bone fragments to ascertain the identity of the victim. Here, we report the findings of an experimental study on burnt bovine compact bone segments. Compact bones were cut to size and heated in an electric furnace at a temperature range of 100–1,100 °C with 100 °C increments. Heat-induced alterations to the bone color,weight, volume, and density were monitored using gross morphology and micro-focus X-ray computed tomography.We found that the increase in temperature caused the color of the compact bones to change in order of yellow, brown, gray,and white. In contrast to the weight reduction that occurred immediately after burning, we measured no significant reduction in volume even at 600 °C; however, volume reduced drastically once the temperature reached 700 °C. Light microscopic histological observations of burnt bone revealed heat induced alterations such as cracking and separation of the osteons at higher temperatures. In addition to these findings,we sought to examine the survival of DNA in the burnt bones using polymerase chain reaction of mitochondrial DNA. No amplification was found in the specimens burnt at 250 °C or higher, indicating the likely difficulty in testing the DNA of burnt bones from forensic casework. The results of this study will enable an estimation of the burning temperatures of burnt bones found in forensic cases and will provide an important framework with which to interpret data obtained during anthropological testing and DNA typing.

Genetic identification by using short tandem repeats analysis in a case of suicide by self-incineration: a case report

Suicide by self-incineration is an uncommon method of suicide in the western world in contrast with Asian countries, where this type of suicide is more common. If there is a lack of witnesses, genetic analysis for identification is mandatory, especially when anthropologic or dental identification is barely significant.The authors report a case of self-incineration of a 55-year-old white man, which occurred near Siena, Tuscany, Italy.The recovered bones were classified according to the Crow-Glassman scale and assigned to category 5 (the highest extent of combustion according to this scale). Therefore, because of the extent of the bone damage, analyzing the residual soft tissue around the pelvic bones was the only way to reach a genetic identification.The authors report this case to emphasize that even if the highest level of burn injury to human body is reached, an accurate analysis of the findings may lead to a genetic identification. In these cases, an efficient cooperation among police, fire experts, and forensics is necessary, especially because it is the only way to determine if the modality of death was accidental, suicidal, or homicidal.

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.

The effect of an enzymatic bone processing method on short tandem repeat profiling of challenged bone specimens

Forensic analysis of DNA from bone can be important in investigating a variety of cases involving violent crimes and mass fatality cases. To remove the potential presence of co-mingled remains and to eliminate contaminants that interfere with forensic DNA analysis, the outer surface of the bone fragment must be cleaned. This study evaluated two methods for processing bone specimens prior to DNA isolation. Mechanical sanding and enzymatic trypsin methods were compared in this study. The effects of these methods on the yield of DNA isolated and the quality of DNA analysis were studied. It was revealed that comparable values of DNA yields between the two methods were observed. Additionally, to evaluate the capabilities of the cleaning effect of the bone processing methods, the presence of polymerase chain reaction inhibitors in the DNA extracts was monitored using the internal positive control. Similar Ct values of the internal positive control were observed as the DNA extracts of the trypsin method compared with that of the sanding method. The characterization of the effects of the trypsin treatment on the quality of DNA profiling was also carried out. To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls and the peak-height values of alleles of the short tandem repeat profiles were compared between the two methods. A paired-sample t-test revealed no significant difference between the two methods. Our data suggested that the trypsin method can be used as an alternative cleaning method to mechanical cleaning methods. This method can be used to process multiple samples simultaneously. This can be very important for achieving high-throughput DNA isolation through potential automation, which can be extremely valuable for situations such as the forensic DNA analysis of skeletal remains from mass fatality incidents.

The SNPforID Assay as a Supplementary Method in Kinship and Trace Analysis

OBJECTIVE: Short tandem repeat (STR) analysis using commercial multiplex PCR kits is the method of choice for kinship testing and trace analysis. However, under certain circumstances (deficiency testing, mutations, minute DNA amounts), STRs alone may not suffice. METHODS: We present a 50-plex single nucleotide polymorphism (SNP) assay based on the SNPs chosen by the SNPforID consortium as an additional method for paternity and for trace analysis. The new assay was applied to selected routine paternity and trace cases from our laboratory. RESULTS AND CONCLUSIONS: Our investigation shows that the new SNP multiplex assay is a valuable method to supplement STR analysis, and is a powerful means to solve complicated genetic analyses.

Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons

The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.

Comparison of three methods of DNA extraction from human bones with different degrees of degradation

There is a necessity for deceased identification as a result of many accidents and sometimes bones are the only accessible source of DNA. So far, a universal method that allows for extraction of DNA from materials at different stages of degradation does not exist. The aims of this study were: the comparison of three methods of DNA extraction from bones with different degree of degradation and an evaluation of the usefulness of these methods in forensic genetics. The efficiency of DNA extraction, the degree of extract contamination by polymerase chain reaction (PCR) inhibitors and the possibility of determining the STR loci profile were especially being compared. Nuclear DNA from bones at different states of degradation was isolated using three methods: classical, organic phenol–chloroform extraction, DNA extraction from crystal aggregates and extraction by total demineralisation. Total demineralisation is the best method for most cases of DNA extraction from bones, although it does not provide pure DNA. DNA extraction from aggregates removes inhibitors much better and is also a good method of choice when identity determination of exhumed remains is necessary. In the case of not buried bones (remains found outside) total demineralisation or phenol–chloroform protocols are more efficient for successful DNA extraction.