Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones

An optimal skeletal element for DNA testing: Evaluation of DNA quantity and quality from various bone types in routine forensic practice

For human identification, the quality and quantity of DNA must be sufficient for amplification and analysis. When DNA extraction from bone tissues and teeth is required, the optimal skeletal elements should be selected as samples for DNA extraction because DNA yield differs among elements. Recently, some studies have reported that a high quantity of high-quality DNA can be extracted from the small cancellous bones of the hands and feet. In this study, we evaluated the effectiveness of small cancellous bones in the human identification of skeletal remains in routine forensic genetic casework. Cancellous bones [phalanges, (meta)carpal bones, and (meta)tarsal bones)] and the cortical bones (femur and petrous bones) and teeth, which have generally been recommended as samples, were collected from the same individuals that needed identifying using DNA analysis in our laboratory. The quantity of DNA from small cancellous bones tended to be higher than that from cortical bones, and the quality from the former was as high as that from the latter. This study showed that in routine forensic casework, the small cancellous bones of the hands and feet should be actively selected as samples for DNA testing.

Comparison of the optimal and suboptimal quantity of mitotype libraries using next-generation sequencing

Optimizing analysis parameters and sample input is crucial in forensic genetics methods to generate reliable results, and even more so when working with muti-copy mitochondrial DNA (mtDNA) and low-quality samples. This study compared mitotypes based on next-generation sequencing (NGS) results derived from the same samples at two different sequencing library concentrations-30 pM and 0.3 pM. Thirty femur samples from the Second World War were used as a model for poorly preserved DNA. Quantitative PCR (qPCR) method targeting 113 bp long fragment was employed to assess the quantity of mitogenomes. HID Ion Chef™ Instrument with Precision ID mtDNA Control Region Panel was used for library preparation and templating. Sequencing was performed with Ion GeneStudio™ S5 System. Reference haplotypes were determined from sequencing samples at 30 pM library input. Haplotypes were compared between optimal (30 pM) and suboptimal (0.3 pM) library inputs. Often the difference in haplotypes was length heteroplasmy, which in line with other studies shows that this type of variant is not reliable for interpretation in forensics. Excluding length variants at positions 573, 309, and 16,193, 56.7% of the samples matched, and in two samples, no sequence was obtained at suboptimal library input. The rest of the samples differed between optimal and suboptimal library input. To conclude, genotyping and analyzing low-quantity libraries derived from low-quality aged skeletonized human remains therefore must be done with caution in forensic genetics casework.

Measure quantity of mitochondrial DNA in aged bones or calculate it from nuclear DNA quantitative PCR results?

Mitochondrial DNA (mtDNA) is of great value in forensics to procure information about a person when a next of kin, personal belongings, or other sources of nuclear DNA (nDNA) are unavailable, or nDNA is lacking in quality and quantity. The quality and reliability of the results depend greatly on ensuring optimal conditions for the given method, for instance, the optimal input of the copy number (CN) in next-generation sequencing (NGS) methods. The unavailability of commercial quantitative PCR (qPCR) methods to determine mtDNA CN creates the necessity to rely on recommendations to infer mtDNA CN from nDNA yield. Because nDNA yield varies between individuals, tissues, parts of the same tissue, and because mtDNA CN varies between tissues, such assumptions must be examined for a specific context, rather than be generalized. This study compares mtDNA CN calculated from nDNA yield and qPCR measured mtDNA CN. Seventy-five femurs from the Second World War victims were used as samples; they were cut below the greater trochanter, surface contaminants were removed by mechanical and chemical cleaning, samples were fully demineralized, and DNA was isolated. PowerQuant® Kit (Promega) was used to analyze DNA yield. An in-house method was used to determine mtDNA CN. Comparison of mtDNA CN from nDNA derived calculations and measured mtDNA CN highlighted vast differences. The results emphasize the need to perform qPCR to assess mtDNA CN before NGS analyses of aged bones' mitogenomes rather than estimating mtDNA CN from nDNA yield to ensure the quality and reliability of the results of NGS analysis.

Comparison of DNA preservation and ATR-FTIR spectroscopy indices of cortical and trabecular bone of metacarpals and metatarsals

Shape, size, composition, and function of the bones in the human body vary on the macro, micro and nanoscale. This can influence changes caused by taphonomy and post-mortem preservation, including DNA. Highly mineralised compact bone is less susceptible to taphonomic factors than porous trabecular bone. Some studies imply that DNA can be better preserved in trabecular bone, due to remnants of the soft tissue or bacteria better digesting organic matter while not digesting DNA. The aim of this study was to understand the differences between compact (diaphyses) and trabecular (epiphyses) bone on a molecular level and thus the reasons for the better preservation of the DNA in the trabecular bone. The powder obtained from epiphyses and diaphyses of metacarpals and metatarsals was analysed using ATR-FTIR spectroscopy and compared. Samples with poorest DNA preservation originated from diaphyses, predominantly of metatarsals. They were characterised by higher concentrations of phosphates and crystallinity, while lower collagen quality in comparison to samples with the best DNA preservation. Epiphyses presented higher concentrations of better-preserved collagen while diaphyses had higher concentrations of carbonates and phosphates and higher crystallinity. Due to better-preserved collagen in the epiphyses, the soft tissue remnants hypothesis seems more likely than the bacteria hypothesis.

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 fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples

An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.

Comparison of DNA preservation between adult and non-adult ancient skeletons

Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons.

Forensic DNA Typing From Femurs and Bones of the Foot: A Study of 3 Cases

ABSTRACT

Evidence has been accumulating in the sense that femur may not always be the best option for DNA typing of skeletal remains. Recent studies have shown that bones of the hands and feet appear to be a superior source of preserved DNA. The current study reanalyzed DNA quantitation, degradation, and short tandem repeat typing in femurs, lateral cuneiforms, and distal foot phalanges. Data from 3 human identification cases involving corpses in an advanced decomposition state were collected. We found that in the studied cases, the femur provided equal or inferior results, recovering 84.9% of true alleles. Lateral cuneiforms (99.2%) and distal foot phalanges (96.8%) yielded higher percentages. In addition, more drop-ins and drop-outs were detected in femurs than cuneiforms and phalanges. This study adds to current findings that advocate for further investigation into bone selection for use in forensic practice. The impacts of our findings are limited by the small number of individuals studied and may not apply to old and degraded bones.

Comparison of DNA preservation between ribs and vertebrae

The choice of skeletal element types and their intra-bone parts is important because of differences in DNA preservation, and this must be considered when sampling bones for DNA testing. When incomplete skeletons are found, ribs and vertebrae have been shown to be the most suitable for genetic identification of bones from the torso. This study compares the preservation of DNA between 12th thoracic vertebrae and first ribs to determine which bone type is more suitable for genetic typing. The study analyzed 35 12th thoracic vertebrae and 29 first ribs from one mass grave from the Second World War with commingled skeletal remains excavated. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation and through short tandem repeat (STR) typing success. Previous studies performed on aged skeletal remains have shown that the DNA content of the first ribs and 12th thoracic vertebrae has high intra-bone variability, and this was considered when sampling the bones. After full demineralization extraction, the PowerQuant System (Promega) was used to measure the quantity and quality of DNA, and the GlobalFiler kit (Applied Biosystems) was used for STR typing. The results showed that DNA yield and degradation and STR typing success exhibited no statistically significant difference between first ribs and 12th thoracic vertebrae, and there was no intra-individual difference when comparing only paired bones from the same individuals. Consequently, with intra-bone DNA variability considered, the first ribs or the 12th thoracic vertebrae can be selected when sampling to genetically identify the skeletal remains of highly degraded torsos. HIGHLIGHTS: The first ribs and thoracic vertebrae are the most suitable bones for sampling from the torso. The proximal part of first rib and posterior vertebral column of the 12th thoracic vertebrae yielded the most DNA. The first ribs were compared with the 12th thoracic vertebrae, and the sampling process considered intra-bone DNA variability. The quality and quantity of nuclear DNA and success of STR typing were measured. The first ribs yielded the same DNA yields as well as STR typing success as the 12th thoracic vertebrae. When only the torso is present, it is not of high importance whether the first ribs or the 12th thoracic vertebrae are collected.

Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III

DNA yield and STR typing success differ among skeletal element types and within individual bones. Consequently, it is necessary to identify the skeletal elements and their intra-skeletal parts that will most likely yield utilizable and informative endogenous DNA for human identification of skeletal remains. The petrous portion of the temporal bone has been shown to be the most suitable skeletal part for sampling archaeological skeletons, and it has also been used successfully in some forensic cases. When all representative bone types were analyzed for three complete Second World War skeletons, metatarsals and metacarpals yielded more DNA than petrous bones (which generated full profiles even if the DNA yield was lower) and, among almost 200 Second World War metatarsals and metacarpals analyzed, metacarpals III were found to be the highest-yielding bones. To further improve the sampling strategy in DNA analysis of aged skeletal remains, a comparison between 26 petrous bones and 30 metacarpals III from Second World War skeletons was made considering intra-bone DNA yield variability. In metacarpals III only epiphyses were sampled, and in petrous bones only the dense part within the otic capsule was used. To exclude the influence of taphonomic issues as much as possible, petrous bones and metacarpals III from a single Second World War mass grave were examined. The difference between petrous bones and metacarpals III was explored by measuring nuclear DNA yield and success of STR typing. After cleaning the samples, full demineralization extraction was used to decalcify 0.5 g of powdered bone. PowerQuant (Promega) was used to determine DNA content and DNA degradation rates, and STR typing was performed using the PowerPlex ESI 17 Fast System (Promega). Metacarpals III produced the same DNA yields and STR typing success as petrous bones with no intra-individual difference observed in concentration of DNA, degradation rate, percentage of successfully amplified alleles, and intensity of electrophoretic signals. Sampling and processing of metacarpal III epiphyses is consequently recommended for genetic identification of highly degraded skeletal remains in routine forensic casework and in buried non-commingled aged skeletal remains whenever metacarpals III are preserved. Metacarpals III are easy to sample and less prone to contamination with modern DNA because no saw is needed for sampling in comparison to the petrous portion of the temporal bone. The data obtained in this study further improve the sampling strategy for genetic identification of Second World War skeletal remains in Slovenia.