A novel, 4-h DNA extraction method for STR typing of casework bone samples

African and Asian elephant ivory discrimination using a portable strip test

Currently, the global elephant population has significantly declined due to the poaching of elephants for their ivory, and this is the reason why elephants are listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). However, Thailand allows the legal trade of ivory from registered, domesticated Asian elephants, leading to the smuggling of African elephant ivory, and passing them off as Asian elephant ivory. Therefore, this research aims to develop and validate a portable strip test to discriminate between Asian and African elephants DNA, using Recombinase Polymerase Amplification (RPA) and Lateral Flow Dipstick assay (LFD) according to international standards. The results showed that the strip test can be successfully developed with 100% accuracy (n = 105). This kit is specific to elephants, has a detection limit of 0.125 ng of DNA, and can effectively discriminate a variety of elephant ivory, including raw ivory, ivory products, and aged ivory over 25 years old, which had been damaged by fire, all with 100% accuracy (n = 117). Additionally, the developed strip test is designed to be portable and cost-effective. It does not require expensive laboratory equipment and provides a faster analysis process compared with conventional PCR-based methods. This will expedite the legal process and enforcement of laws related to elephant conservation, reducing the opportunities for illegal activities, and enabling timely prosecution under relevant wildlife conservation laws in Thailand and internationally.

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.

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.

Comparative study of Rapid DNA versus conventional methods on compromised bones

Equivalent amounts of compromised bones were used to directly compare STR success of conventional and Rapid DNA methods. Conventional DNA extraction methods, including manual full demineralization and semi-automated PrepFiler BTA/ AutoMate Express (ThermoFisher Scientific), provided insights regarding the DNA quantity and extent of degradation of each compromised bone analyzed with ANDE 6C (ANDE Corp) and RapidHIT ID (ThermoFisher Scientific) Rapid systems. Full demineralization provided higher DNA yields than extraction with the AutoMate Express for quality control (QC) and environmentally challenged bones. The degradation indices ranged from ∼1.8 to 73. Both demineralization and AutoMate Express extracts benefited from additional clean-up with NucleoSpin XS devices, which usually resulted in more alleles being detected than without further clean-up. Complete "CODIS 20″ profiles could be obtained with bone QC1 with all methods. However, among the 14 compromised bones with low DNA content, complete CODIS 20 profiles were detected for 7, 4, and 0 bones analyzed with demineralization, AutoMate Express and ANDE methods, respectively. The RapidHIT ID was the least sensitive method, providing the fewest detectable alleles for the bones tested. Whereas extracted DNA of approximately 0.1 ng can yield complete GlobalFiler STR profiles, at least 30 ng was required for complete FlexPlex 27 profiles using the ANDE 6C Rapid DNA system. In addition to being less sensitive than conventional methods, the tested Rapid DNA approaches were less predictable when attempting to improve STR success and proved to be less reliable in genotyping accuracy.

Forensic DNA extraction methods for human hard tissue: A systematic literature review and meta-analysis of technologies and sample type

DNA identification of human remains has a valuable role in the field of forensic science and wider. Although DNA is vital in identification of unknown human remains, post-mortem environmental factors can lead to poor molecular preservation. In this respect, focus has been placed on DNA extraction methodologies for hard tissue samples, as these are the longest surviving. Despite decades of research being conducted on DNA extraction methods for bone and teeth, little consensus has been reached as to the best performing. Therefore, the aim of this study was to conduct a thorough systematic literature review to identify potential DNA extraction technique(s) which perform optimally for forensic DNA profiling from hard tissue samples. PRISMA guidelines were used, by which a search strategy was developed. This included identifying databases and discipline specific journals, keywords, and exclusion and inclusion criteria. In total, 175 articles were identified that detailed over 50 different DNA extraction methodologies. Results of the meta-analysis conducted on 41 articles - meeting further inclusion criteria - showed that statistically significant higher DNA profiling success was associated with solid-phase magnetic bead/resin methods. In addition, incorporating a demineralisation pre-step resulted in significantly higher profiling successes. For hard tissue type, bone outperformed teeth, and even though dense cortical femur samples were more frequently used across the studies, profiling success was comparable, and in some cases, higher in cancellous bone samples. Notably, incomplete data sharing resulted in many studies being excluded, thus an emphasis for minimum reporting standards is made. In conclusion, this study identifies strategies that may improve success rates of forensic DNA profiling from hard tissue samples. Finally, continued improvements to current methods can ensure faster times to resolution and restoring the identity of those who died in obscurity.

Direct STR typing from human bones

Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.

Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types

BACKGROUND

Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples.

METHODS

The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses.

RESULTS

The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities.

CONCLUSIONS

This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.

The influence of sample quantity and lysis parameters on the success of ancient DNA extraction from skeletal remains

DNA extraction is of utmost importance in archaeobiology, as it determines the success of further DNA analyses. This study concentrates on the success of ancient DNA extraction using silica spin columns and PCR-based analysis from archaeological skeletal material and investigates the influence of sample quantity, lysis time and lysis temperature during sample preparation. The results show that lysis times ranging from 2 to 48 h are suitable, and that lysis should be carried out at a constant temperature of 56°C. Concerning sample quantity, 10 mg for mitochondrial DNA and 50 mg for chromosomal DNA are sufficient for high quality analyses. Thus invaluable sample material can be saved, and time of sample preparation can be reduced considerably.

Factors influencing DNA extraction from human skeletal remains: bone characteristic and total demineralization process

Background

The extraction of DNA from skeletal remains with good quality and quantity is often challenging for the ability to generate DNA typing. Previous studies demonstrated the DNA extraction with total demineralization from fresh teeth and bones; however, the application in old skeletal remains has been less performed. To obtain good quality and high yield of DNA amount extracted from skeletal remains, the objective of this study was focused on exploring the factors influencing the total demineralization process to obtain developing effective methods.

Results

The concentration of EDTA was found to significantly enhance calcium chelation from the bone while pH of EDTA solution, incubation temperature, incubation time, and volume of EDTA solution were not significant. The optimal condition of total demineralization obtained from Placket-Burmann results represented good-quality DNA and the highest concentration of extracted DNA yield. Subsequently, the STR typing in some bone specimens processed by total demineralization process prior to DNA extraction was improved.

Conclusions

EDTA concentration was a key influencing factor on the total demineralization process to chelate calcium from human skeletal remains. The total demineralization process in old bone specimens probably improved the STR profiles.

Discrimination of highly degraded, aged Asian and African elephant ivory using denaturing gradient gel electrophoresis (DGGE)

BACKGROUND

Elephant populations have greatly reduced mainly due to illegal poaching for their ivory. The trade in elephant products is protected by national laws and CITES agreements to prevent them from further decline. For instance, in Thailand, it is illegal to trade ivory from African elephants; however, the law allows possession of ivory from Asian elephants if permission has been obtained from the authorities. As such, means of enforcement of legislation are needed to classify the legal status of seized ivory products. Many DNA-based techniques have been previously reported for this purpose, although all have a limit of detection not suitable for extremely degraded samples.

AIM

We report an assay based on nested PCR followed by DGGE to confirm the legal or illegal status of seized ivory samples where it is assumed that the DNA will be highly degraded.

METHOD AND RESULTS

The assay was tested on aged ivory from which the assay was tested for reproducibility, specificity, and, importantly, sensitivity. Blind testing showed 100% identification accuracy. Correct assignment in all 304 samples tested was achieved including confirmation of the legal status of 227 highly degraded, aged ivories, thus underlining the high sensitivity of the assay.

CONCLUSION AND RECOMMENDATION

The research output will be beneficial to analyze ivory casework samples in wildlife forensic laboratories.