Intra-bone nuclear DNA variability and STR typing success in Second World War 12th thoracic vertebrae

DNA preservation in compact and trabecular bone

Significant variation exists in the molecular structure of compact and trabecular bone. In compact bone full dissolution of the bone powder is required to efficiently release the DNA from hydroxyapatite. In trabecular bone where soft tissues are preserved, we assume that full dissolution of the bone powder is not required to release the DNA from collagen. To investigate this issue, research was performed on 45 Second World War diaphysis (compact bone)-epiphysis (trabecular bone) femur pairs, each processed with a full dissolution (FD) and partial dissolution (PD) extraction method. DNA quality and quantity were assessed using qPCR PowerQuant analyses, and autosomal STRs were typed to confirm the authenticity of isolated DNA. Our results support different mechanisms of DNA preservation in compact and trabecular bone because FD method was more efficient than PD method only in compact bone, and no difference in DNA yield was observed in trabecular bone, showing no need for full dissolution of the bone powder when trabecular bone tissue is processed. In addition, a significant difference in DNA yield was observed between compact and trabecular bone when PD was applied, with more DNA extracted from trabecular bone than compact bone. High suitability of trabecular bone processed with PD method is also supported by the similar quantities of DNA isolated by FD method when applied to both compact and trabecular bone. Additionally similar quantities of DNA were isolated when compact bone was extracted with FD method and trabecular bone was extracted with PD method. Processing trabecular bone with PD method in routine identification of skeletonized human remains shortens the extraction procedure and simplifies the grinding process.

Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave

Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell® FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.

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.

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.

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 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.

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.