DNA typing from skeletal remains: evaluation of multiplex and megaplex STR systems on DNA isolated from bone and teeth samples (original) (raw)
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This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55–125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that h...
A New and Efficient Method for DNA Extraction from Human Skeletal Remains Usable in DNA Typing
In historical cases, mass disasters, missing person’s identification and ancient DNA investigations, bone and teeth samples are often the best and the only biological material available for DNA typing. This is because of the physical and chemical nature of the protein-mineral matrix of bone which is relatively resistant to the adverse environmental effects and biological attacks. Most bone extraction protocols used in the forensic laboratories involve an incubation period of bone powder in extraction buffer for proteinase digestion, followed by the collection of the supernatant, and the elimination of large quantities of undigested bone powder. Here we demonstrate an extremely effective protocol for recovery of DNA. This is performed in a method that retains and concentrates all the reagent volume for complete DNA recovery. For our study, we selected challenging bone samples of skeleton remains of the martyred individuals in Iraq’s imposed war on I.R. Iran (19801988). The bones that were extracted with our new protocol showed that this new protocol significantly enhances the quantity of DNA that can be used for amplification from degraded skeletal remains. At the same time we tested in parallel the samples by using of QIAamp DNA Investigator Kit and attained the best results by using new protocol. In fact, our new DNA extraction method is based on previous standard methods such as Chelex and salting out. We have used this technique to successfully recover authentic DNA Typing from extremely challenging samples that failed repeatedly using the standard protocols. However, the amount of recovered DNA was very small but it was possible to extract genomic DNA from these challenging bone samples. The results indicated that our procedure for DNA extraction although yielded little amount of genomic DNA; however, it was pure DNA that can be used for further analysis such as PCR amplification and DNA profiling. Since the new procedure is fast and needed less time than previously standard procedures, we have named it FDEB (Fast DNA Extraction of Bone). Keywords: Bone, DNA Extraction, PCR, STR Profiling, Identification
Inter and intra-individual variation in skeletal DNA preservation in buried remains
Forensic Science International: Genetics, 2020
Our ability to identify skeletal remains often relies on the quality and quantity of DNA extracted from bone and teeth. Current research on buried remains has been retrospective, and no study to our knowledge has comprehensively assessed both intra-individual and inter-individual variation in human skeletal DNA from all representative skeletal element types recovered from a burial. Three individuals were interred together in a single grave for four years. Following disinterment, skeletal DNA was extracted, quantified, and GlobalFiler™ results were produced from 49 bones per skeleton, representing all bone types. Multiple sites per bone were also tested to determine intra-bone variability. Co-extracted bacterial and fungal DNA were quantified to determine microbial loads in the bones. Results show that the small, cancellous bones of the feet outperformed other bones in terms of DNA yield, measured as nanograms per gram of bone powder, and short tandem repeat (STR) profile completeness. The cuneiforms, in particular, had consistently high human DNA yields for all three individuals. DNA yield varied by individual and depth within the grave, with the shallowest individual demonstrating the highest DNA yields While the feet exhibited the greatest variation in DNA yield across bone type and sampling site, they also demonstrated some of the highest DNA yields and the most complete STR profiles, evoking a re-evaluation of their use for skeletal DNA sampling and analysis.