DNA analysis of Second World War skeletal remains is challenging because of the limited yield of DNA that is usually recovered. Recent forensic research has focused on determining which skeletal ...elements are superior in their preservation of DNA, and little focus has been placed on measuring intra-bone variability. Metatarsals and metacarpals outperformed all the other bones in DNA yield when analyzing all representative skeletal elements of three Second World War victims, and intra-bone variability was not studied. Soft-tissue remnants were found to contribute to higher DNA yield in trabecular bone tissue. Because metatarsals and metacarpals are composed of trabecular epiphyses and a dense diaphysis, the goal of this study was to explore intra-bone variability in DNA content by measuring nuclear DNA quantity and quality using the PowerQuant System (Promega). A total of 193 bones from a single Second World War mass grave were examined. From each bone, DNA was extracted from the compact diaphysis and from both spongy epiphyses combined. This study confirms higher DNA quantity in epiphyses than diaphyses among all the bones analyzed, and more DNA was obtained from metacarpal epiphyses than from metatarsal epiphyses. Therefore, whenever the possibility for sampling both metacarpals and metatarsals from skeletal remains exists, collecting metacarpals is recommended. In cases in which the hands are missing, metatarsals should be sampled. In any case, epiphyses are a richer source of DNA than diaphyses.
For identification of badly preserved cadavers, only a few tissues can be used as a source of DNA, mostly bones and teeth, from which sampling and DNA extraction are difficult and time-consuming. In ...most highly decomposed remains, the nails are preserved. The aim of this study was to evaluate nails as an alternative source of DNA instead of bones and teeth in demanding routine identification cases. An automated extraction method was optimized on nails obtained from 33 cadavers with a post-mortem interval (PMI) up to 5 years. The commercially available EZ1 Investigator Kit (Qiagen) was used for extraction, and the G2 buffer included in the kit was replaced with TN
Ca
buffer, and DTT was added for digestion of 5 mg of nail. The DNA was purified in a Biorobot EZ1 device (Qiagen), quantified using the PowerQuant System (Promega), and STR typing was performed with the NGM kit (TFS). From 0.3 to 270 μg DNA/g of nail was obtained from the samples analyzed, with an average yield of 36 μg DNA/g of nail. Full STR profiles were obtained from all nails except one. The optimized extraction method proved to be fast and highly efficient in the removal of PCR inhibitors, and it yields high amounts of DNA for successful STR typing. Nails were implemented as the primary sample type for obtaining DNA from highly decomposed and partially skeletonized cadavers in routine forensic identification cases in our laboratory.
DNA sampling and typing are used for identifying missing persons or war victims. In recent forensic studies, little focus has been placed on determining intra-bone variability within a single ...skeletal element. When dealing with aged human bones, complete skeletal remains are rarely present. In cases in which only the torso is available, studies have shown that ribs are one of the most appropriate samples, but intra-bone variability has not yet been studied. A higher degree of remodeling was found to contribute to higher DNA yield in the parts of the skeletal element where the most strain is concentrated. This study explores intra-bone variability in proximal, middle, and distal parts of the first human rib by determining the quantity and quality of DNA using the PowerQuant System (Promega) and autosomal STR typing success using the PowerPlex ESI 17 Fast System (Promega). Thirty first ribs from a single Second World War mass grave were sampled. No variation in DNA degradation was observed across the individual rib. The highest quantity of DNA was measured in the proximal part of the first rib, and in all ribs except three, full or almost full genetic profiles were obtained. Thus, when only the torso is present in archaeological or medico-legal cases, first ribs are recommended to be collected if possible, and the proximal or vertebral ends should be sampled for genetic analysis.
•DNA quantity and STR typing success of 48 bone types in three WWII skeletons differed by anatomical region but not by skeleton.•Metatarsals, metacarpals, and petrous bones outperformed all other ...bone types in DNA quantity and quality.•The ten highest-yielding bone types differed from skeleton to skeleton.•The third metacarpal yielding the highest DNA concentration in all three skeletons.•The data obtained have implications for skeletal sampling from old and highly degraded skeletal remains.
DNA yield varies by anatomical region, and the selection of bone types that yield maximum recovery of DNA is important to maximize the success of human identification of skeletal remains. The goal of our study was to explore inter- and intra-individual variation in DNA content by measuring nuclear DNA quantity and quality and autosomal STR typing success to determine the most promising skeletal elements for bone sampling. To exclude the influence of taphonomic issues as much as possible, three complete male skeletons from a single Second World War mass grave were examined and all representative skeletal element types of the human body were analyzed. Forty-eight different types of bones from the head, torso, arm, leg, hand, and foot were sampled from each skeleton, 144 bones altogether. The samples were cleaned, and half a gram of bone powder was decalcified using a full demineralization extraction method. The DNA was purified in a Biorobot EZ1 (Qiagen). DNA content and rates of DNA degradation were determined with the PowerQuant (Promega), and the Investigator ESSplex SE QS (Qiagen) was used for STR typing. The highest-yielding bones mostly produced the most complete STR profiles. Among the skeletal elements containing on average the most DNA and producing the most complete profiles in all three skeletons examined were metacarpals, metatarsals, and the petrous portion of the temporal bone. Metatarsals and metacarpals can easily be sampled without using a saw, thus reducing potential DNA contamination. Skeletons from the Second World War can be used as a model for poorly preserved skeletal remains, and the results of the investigation can be applied for genetic identification of highly degraded skeletal remains in routine forensic casework. Although the research was limited to only three skeletons found in a unique mass grave, the data obtained could contribute to sampling strategies for identifying old skeletal remains. More Second World War skeletons will be analyzed in the future to investigate inter-bone variation in the preservation of DNA.
•Genome-wide DNA methylation was investigated in a population with one of the world's highest suicide rate.•We obtained methylation information of regions involved in gene regulation.•Several ...differences (hypomethylation and hypermethylation) in methylation level of suicide victims were observed.•Gene ontology analysis showed enrichment in terms associated with cell structural integrity and nervous system regulation.•Gene expression analysis identified changes in two genes, ZNF714 and NRIP3.
Suicidal behavior is a multifactorial, polygenic state that affects millions worldwide. It is a result of interplay between hereditary and environmental factors, tied together by epigenetics. Despite vast knowledge on suicidality complete mechanism and factors leading to suicide are unknown. However there is an indication between changes in DNA methylation patterns and suicidal behavior.
To identify differential methylation we formed a homogenous group of male suicide victims who died by hanging and control group. Altogether our study included 18 subjects in which two brain regions, Brodmann area 9 (9 suicide victims and 9 controls)) and hippocampus (6 suicide victims and 6 controls) were investigated using next-generation sequencing (NGS).
Our results have shown several differences in methylation level between suicide victims and controls in both brain regions (>25% difference in methylation and q-value < 0.01), with gene ontology pointing towards cell structural integrity and nervous system regulation. Additional gene expression analysis identified changes in two genes, ZNF714 (p-value = 0.002) and NRIP3 (p-value = 0.046).
Major limitation is small sample size. Our analysis was conducted on brain tissue including different cell types so the results are a representation of a methylation pattern for the whole brain tissue sample.
We performed a preliminary methylation study with single base pair resolution using NGS on one of the world populations with a very high suicide risk. Obtained results offer novel insights into altered methylation patterns in suicide victims, which could provide a starting point for further studies on clinical samples with highly expressed suicide risk.
•Genetic identification of the Second World War victims of the largest family massacre in Slovenia was performed.•Incomplete, poorly preserved skeletons were exhumed and 12 bone and tooth samples ...were genetically typed.•By combining autosomal and Y-STRs three male victims were identified with PP greater than 99.9 %.•The aunt was identified using the Precision ID GlobalFiler NGS STR Panel.•Identification was successful for four out of seven victims exhumed from the hidden mass grave.
The killings during the Second World War, with nearly one hundred thousand victims, is one of the greatest losses of life in Slovenia’s modern history. This article presents the genetic identification of the victims of the largest family massacre that occurred in Slovenia, in which 10 members of the same family were killed. Seven of them were buried in a hidden mass grave and only two children survived. In 2015 and 2016, two graves were found and three incomplete female skeletons and at least three incomplete male skeletons were exhumed. A total of 12 bones and teeth were analysed and compared to two living relatives. Extracted DNA was quantified using the PowerQuant kit, and various autosomal and Y-STR kits were used for STR typing. Up to 2.7 ng DNA/g of powder was acquired from the samples analysed. We managed to obtain nuclear DNA for successful STR typing from seven bones and one molar. From the female grave, autosomal profiles were obtained only from one skeleton, and from the male grave from five out of six femurs. The relationships between the males were additionally confirmed by analyses of Y-STRs. STR profiles made possible the identification of four family members; one of the aunts from the female grave, and two uncles and the father of the surviving children, who were used as family references, from the male grave. The product rule was used to calculate a combined likelihood ratio for autosomal and Y-STRs, and statistical analyses showed high confidence of correct identification with posterior probability (PP) greater than 99.9 % for three out of four victims identified. For identifying the aunt, the PP obtained after ESI-17 and NGM STR typing was too low. To increase the PP, the next-generation sequencing Precision ID GlobalFiler NGS STR Panel was used and, after the analysis of additional STR loci, the statistical analysis showed a PP greater than 99.9 %, indicating that a sufficient number of genetic markers had been investigated in identifying the skeletal remains of the aunt. An elimination database containing the genetic profiles of all individuals that had been in contact with the bones was created to ensure traceability in case of contamination, and no matches were found. After more than 70 years, the skeletal remains were returned to the surviving children, who buried their relatives in a family grave.
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.
Epigenetic mechanisms are involved in regulation of many pathologies, including suicidal behaviour. However, the factors through which epigenetics affect suicidal behaviour are not fully understood.
...We analysed DNA methylation of eight neuropsychiatric genes (NR3C1, SLC6A4, HTR1A, TPH2, SKA2, MAOA, GABRA1, and NRIP3) in brain regions (hippocampus, insula, amygdala, Brodmann area 46) and blood of 25 male suicide victims and 28 male control subjects, using bisulphite next-generation sequencing.
Comparing mean methylation values, notable changes were observed in NR3C1 (insula p-value = 0.05), HTR1A (insula p-value < 0.001, blood p-value = 0.001), SKA2 (insula p-value = 0.03, blood p-value = 0.016), MAOA (blood p-value < 0.001), GABRA1 (insula p-value = 0.05, blood p-value = 0.024) and NRIP3 (hippocampus p-value = 0.001, insula p-value = 0.002, amygdala p-value = 0.014). Comparing methylation pattern between blood and brain, similarity was observed between blood and insula for HTR1A. Gene expression analysis in hippocampus revealed changes in expression of NR3C1 (p-value = 0.049), SLC6A4 (p-value = 0.017) and HTR1A (p-value = 0.053).
Results provide an insight into the altered state of DNA methylation in suicidal behaviour. Epigenetic differences could therefore affect suicidal behaviour in both previously known and in novel neuropsychiatric candidate genes.
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.
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