Evaluation of a new experimental kit for the extraction of DNA from bones and teeth using a non-powder method

12 real forensic cases solved by the DNA STR-typing of skeletal remains exposed to extreme environment conditions, without the conventional bone pulverization step

DNA identification of human skeletal remains play a valuable role in the forensic field, especially in missing persons and mass disasters investigation. Hard tissues, such as bones and teeth, represent a very common kind of samples analyzed in forensic laboratories because often they are the only biological materials remaining. However, the major limitation in using these compact samples rely on time consuming and labor-intensive treatment of grinding them into powder before proceeding with the conventional DNA purification and extraction step. In this context, a novel DNA extraction assay, called the TBone Ex kit (DNA Chip Research Inc.), was developed to digests bone chips without powdering "as reported by Kitayama (JAMA 12:84-89, 2010)." Here, we simultaneously analyzed bone and tooth samples obtained by our police laboratory that belonged to 15 different forensic cases from Sardinia (Italy). The total of 27 samples were recovered from different scenarios and were exposed to extreme environmental factors, including sunlight, seawater, soil, fauna, vegetation and high temperature and humidity. The TBone Ex kit was used prior to the EZ2 DNA extraction kit on the EZ2 Connect Fx instrument (Qiagen), and high quality autosomal and Y-chromosome STRs profiles were obtained for the 80% of the cases, in a relatively short time frame. This study provides additional support for the use of the TBone Ex kit for digesting bone fragments/whole teeth as an effective alternative to pulverization protocols. We empirically demonstrated the effectiveness of the kit in processing multiple bone samples simultaneously, largely simplifying the DNA extraction procedure, and the good yield of recovered DNA for downstream genetic typing in highly compromised forensic real specimens. In conclusion, the results of this study appear useful for forensic laboratories, to which the various actors of the criminal justice system - such as potential jury members, judges, defense attorneys and prosecutors - require immediate feedback.

Effect of postmortem interval and conditions of teeth on STR based DNA profiling from unidentified dead bodies

Teeth are important exhibits to establish the identity of unidentified dead bodies by DNA profiling. Tooth acts as a cage to protect DNA from harsh environmental conditions. Unidentified bodies are sometimes found many years after death causing loss of valuable soft tissues which can be used for DNA extraction. Skeletal remains and dental evidence provide the best alternative when decomposed or burnt bodies are examined to establish the identity. In this study, the powder-free method was used to extract DNA from ninety-five teeth of unidentified dead bodies across seven years (2014-2020). Intact and broken dental remains were analyzed majorly from decomposed remains. The present study reports successful STR profiles obtained from dental evidence using powder free method. Complete DNA profiles were obtained from intact teeth while damaged teeth either gave partial profiles or no results. This data suggest that intact teeth are excellent samples for DNA profiling from decomposed unidentified dead bodies even with greater post mortem interval. Findings from this study can hence be useful in establishing the identity in forensic and archeological casework.

Large fragment demineralization: an alternative pretreatment for forensic DNA typing of bones

In forensic genetics, the analysis of postmortem bones is one of the most challenging due to the low quantity of degraded endogenous DNA. The most widely used approach for sample preparation, in those cases, is pulverizing the bone. However, processing pulverized bone is extremely delicate, requiring strict laboratory conditions and operating procedures. In fact, several recent publications have focused on non-powder approaches. The objectives of this study were, thus, to validate a non-powder protocol for DNA extraction from forensic bones and an alternative pretreatment, large fragment demineralization (LFD). Thirty human femurs and tibiae received by the Legal Medicine Institute of Brescia, Italy, were included in the study. Bone powder and one transversal section of the diaphysis were sampled from each bone. DNA extraction from the powder was carried out using PrepFiler BTA (BTA), while the transversal section was submitted to the alternative demineralizing pretreatment (LFD) followed by DNA extraction using the QIAamp DNA Investigator. DNA extracts were assessed for human DNA quantity and degradation by means of a validated in-house qPCR assay and amplified with commercial kits. Inhibition assessment was carried out through Quality Sensor analysis using 24plex QS Kit. The differences in quantity, quality of human DNA, and number of alleles detected between both methods were comparable and not statistically significant. We propose the use of the LFD protocol as a complementary approach capable of confirming the genotypes or detect alleles not observed using BTA, without the need for pulverization.

Comparison of DNA yield and STR profiles from the diaphysis, mid-diaphysis, and metaphysis regions of femur and tibia long bones

DNA testing of human bones is performed for identification when there is no remaining soft tissue, which often means the samples are old or environmentally compromised. Under these circumstances, it can be difficult to obtain a STR DNA profile. It is important to recover the highest quantity and quality of DNA for STR typing. This study compared the DNA recovery and STR profiles from five anatomical locations in five femora and five tibiae. These locations include the proximal metaphysis, proximal diaphysis, mid-diaphysis, distal diaphysis, and distal metaphysis. Twenty-five femur samples and 25 tibia samples were analyzed using the Qiagen Investigator Quantiplex Pro RGQ Kit for quantitating the extracted DNA and the Qiagen Investigator 24plex QS Kit for STR DNA typing. The highest DNA recovery of the five regions tested in both the femur and the tibia was from the midshaft diaphysis. The femur samples resulted in a significantly higher DNA recovery than the tibia samples as analyzed using a Kruskal-Wallis test (P = 0.002103). The midshaft diaphysis and distal diaphysis yielded the most complete STR DNA profiles in the femora, while the distal and proximal diaphysis yielded the most complete STR DNA profiles in the tibiae. There was no correlation between the amount of DNA recovered and the completeness of the STR DNA profile produced with low template extracts in this study.

A newly developed age estimation method based on CpG methylation of teeth-derived DNA using real-time methylation-specific PCR

Age estimation of unidentified bodies is important in forensic medicine and crime scenes. There is accumulating evidence that DNA methylation in the human genome isolated from body fluids changes with age. Most of the data have been obtained by pyrosequencing. In the forensic field, a simple, quick, and economical method is required to evaluate the age of various types of samples. In this study, an age estimation method based on methylation levels of DNA extracted from teeth using real-time methylation-specific PCR (MSP) was developed. The CpG island in the upstream region of ELOVL2, which is known as a validated biomarker in blood samples, was selected as a target site. The CpG methylation levels highly correlated with age (r = 0.843, n = 29). Age-related increase in DNA methylation levels was not affected by sex differences. In addition, the simple regression model based on methylation status of the CpG island exhibited moderate accuracy with a mean absolute deviation between chronological age and predicted age of 8.94 years. The results imply that real-time MSP can be a new tool to perform age prediction of unidentified bodies in forensic scenes.

A Powder-free DNA Extraction Workflow for Skeletal Samples

The processing of skeletal material poses several challenges for forensic laboratories. Current methods can be laborious, time-consuming, require dedicated equipment, and are vulnerable to contamination. In this study, various sample mass (1 × 50 mg, 3 × 50 mg, and 1 × 150 mg chip(s)) and incubation times (2, 4, and 16 h) were tested using the PrepFiler^® BTA™ Forensic DNA Extraction Kit to digest whole bone chips in lieu of powdering. The most effective method was then applied to bones and tooth fragments collected from contemporary human cadavers exposed to various environmental conditions using an automated platform. Over a third of the samples tested generated full DNA profiles without having to powder the bone/tooth fragment or further alter the manufacturer's protocol. However, for most samples resulting in incomplete STR profiles due to low amounts of DNA, slightly better results were achieved with powdered tissue. Overall, this work demonstrates the potential use of a faster, nonpowdering DNA extraction method for processing skeletal samples as an effective first-pass screening tool.

Detection of nucleic acids and other low abundance components in native bone and osteosarcoma extracellular matrix by isotope enrichment and DNP-enhanced NMR

Sensitivity enhancement by isotope enrichment and DNP NMR enables detection of minor but biologically relevant species in native intact bone, including nucleic acids, choline from phospholipid headgroups, and histidinyl and hydroxylysyl groups. Labelled matrix from the aggressive osteosarcoma K7M2 cell line confirms the assignments of nucleic acid signals arising from purine, pyrimidine, ribose, and deoxyribose species. Detection of these species is an important and necessary step in elucidating the atomic level structural basis of their functions in intact tissue.

Towards elucidating their biological roles in intact tissue, DNP NMR reveals nucleic acids, and other important low abundance biomolecules in a complex biomaterial, bone, and in cancer extracellular matrix.

Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success

Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing. Samples were extracted using three commercial extraction kits (DNA IQ™, DNA Investigator, and PrepFiler® BTA), organic (blood and hair only), and two total demineralization protocols (bone only)). Massively parallel sequencing (MPS) was performed using two different systems: Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™. The overall results showed that all DNA extraction methods were efficient and are fully compatible with both MPS systems. Key performance indicators such as STR and SNP reportable alleles, read depth, and heterozygote balance were comparable for each extraction method. In samples where CE-based STRs yielded partial profiles (bone), MPS-based STRs generated more complete or full profiles. Moreover, MPS panels contain more STR loci than current CE-based STR kits and also include SNPs, which can further increase the power of discrimination obtained from these samples, making MPS a desirable choice for the forensic analysis of such challenging samples.

Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles

It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0-4 Japanese-specific alleles per individual, whereas the Japanese had 4-26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.

Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains

Bones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler^® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler^® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality.

Evaluation of different methods for DNA extraction from human burnt bones and the generation of genetic profiles for identification

Bone exposure to heat in the presence of moisture breaks the phosphodiester bonds of the backbone, leaving sheared DNA in bone cells. This also limits the possibility of generating a complete profile of the victim. With the increasing incidence of fire outbreaks over the past few years, a paradigm shift to establish identity has been observed, from morphological identification of victims to STR profiling. For this study, 10 bone samples were taken from burnt human bodies that were recovered from different fire outbreak scenes. The DNA from these burnt human tissues was isolated using four different extraction methods: the organic extraction method, the total demineralisation method, the Qiagen kit method, and the Chelex extraction method. STR profiles of victims were generated on a genetic analyser using an AmpFlSTR Identifiler® Plus Kit and analysed on Gene Mapper ID-X. DNA isolated from bones using the total demineralisation extraction method and organic extraction method was of the highest quality due to the efficient removal of inhibitors. DNA obtained using these two methods successfully generated the STR profiles of the victims. The quality of isolated DNA obtained through the Qiagen kit was comparatively low, but STR profiles of the victims were successfully generated. The Chelex kit failed to extract good quality DNA of high quantity from the burnt bones, encountering inhibition in all samples at varying degrees. This study concludes that total demineralisation and the Qiagen kit are sophisticated and reliable methods to obtain a good yield of DNA from burnt human bones, which can be used for the identification of victims.

An alternate method for extracting DNA from environmentally challenged teeth for improved DNA analysis

A grinding-free method to extract DNA from teeth via a direct minimal-invasive retrograde approach to the pulp cavity and dentine was compared to a standard grinding/pulverisation method. This alternate method uses endodontic dental files to access the root canals and pulp cavity for tissue and dentine harvest via the apical end of the roots and avoids mechanical damage to the crown and root morphology. In contrast, other methods require pulverisation of the whole root or tooth, transection or destruction of the occlusal surface to gain access to the DNA in the root canals and pulp chamber. This study compared two methods for preparing dentine powder from the roots of environmentally challenged teeth for forensic DNA analysis. We found that although the filing method was more laborious, and produced less dentine powder, the amount of amplifiable DNA per milligram of powder was substantially higher with the filing method compared to grinding the entire root. In addition, the number of short tandem repeat (STR) alleles detected and the peak height ratios of the STR profiles were notably higher. Although several other methods of extracting DNA-rich tissue from the pulp chamber of teeth have previously been reported, the method presented in this study is minimally invasive, thereby allowing the preservation of tooth and crown morphology.

Development of Multiple Assays using 46 SNPs for Comprehensive mtDNA Haplogrouping and Application to Highly Degraded DNA

Six multiplex PCR systems using single-base extension reactions to analyze 46 mitochondrial DNA (mtDNA)-coding region single nucleotide polymorphisms (SNPs) that define 42 haplogroups, that is, 24 major mtDNA haplogroups and 18 subclades, were devised. To improve the usefulness of the established systems for the analysis of degraded DNA samples, novel primers to render amplicons with sizes <150 bp were designed. By applying these systems to 214 Japanese individuals, 24 different haplogroups (power of discrimination = 93.4%) were found. To assess the effectiveness of our systems in grouping degraded DNA, an ancient bone sample of a Jomon skeleton was analyzed and then classified as haplogroup N9b. We conclude that the present systems are powerful screening tools for major haplogroups of mtDNA in addition to the prevalent subhaplogroups in the Japanese population and that these systems are capable of analyzing highly degraded DNA samples in forensic studies.

The effect of an enzymatic bone processing method on short tandem repeat profiling of challenged bone specimens

Forensic analysis of DNA from bone can be important in investigating a variety of cases involving violent crimes and mass fatality cases. To remove the potential presence of co-mingled remains and to eliminate contaminants that interfere with forensic DNA analysis, the outer surface of the bone fragment must be cleaned. This study evaluated two methods for processing bone specimens prior to DNA isolation. Mechanical sanding and enzymatic trypsin methods were compared in this study. The effects of these methods on the yield of DNA isolated and the quality of DNA analysis were studied. It was revealed that comparable values of DNA yields between the two methods were observed. Additionally, to evaluate the capabilities of the cleaning effect of the bone processing methods, the presence of polymerase chain reaction inhibitors in the DNA extracts was monitored using the internal positive control. Similar Ct values of the internal positive control were observed as the DNA extracts of the trypsin method compared with that of the sanding method. The characterization of the effects of the trypsin treatment on the quality of DNA profiling was also carried out. To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls and the peak-height values of alleles of the short tandem repeat profiles were compared between the two methods. A paired-sample t-test revealed no significant difference between the two methods. Our data suggested that the trypsin method can be used as an alternative cleaning method to mechanical cleaning methods. This method can be used to process multiple samples simultaneously. This can be very important for achieving high-throughput DNA isolation through potential automation, which can be extremely valuable for situations such as the forensic DNA analysis of skeletal remains from mass fatality incidents.

Estimation of the detection rate in STR analysis by determining the DNA degradation ratio using quantitative PCR

Performing short tandem repeat (STR) analysis from degraded DNA is a challenge for forensic biologists. For assessing the quality and quantity of DNA, we developed quantitative PCR assays to determine the extent of DNA degradation. Quantitative PCR assays using primers that generate two sizes of amplicons from the same region of genomic DNA were used to determine the extent of DNA degradation. These quantitative PCR assays were used with artificially degraded DNA and degraded DNA extracted from aged bloodstains. Increased DNA degradation correlated with a decrease in the number of detectable loci in STR analysis. The extent of DNA degradation and the number of loci detected by STR analysis varied depending on the method of degradation. The extent of degradation of DNA extracted from aged bloodstains correlated well with that of DNA artificially degraded by DNase I in the presence of Mn(2+). Thus, determination of the extent of DNA degradation was helpful for estimating the number of detectable loci. Furthermore, this estimation method is expected to save time and labor, and is particularly suitable when only a limited amount of DNA can be extracted from casework samples.

The tooth for molecular analysis and identification : a forensic approach

The aim of this study is to optimize laboratory preparation of teeth for DNA identification. By sectioning the tooth topographically into two different radicular portions, it was analyzed whether these portions of mineralized tissue differ in the quantity and quality of DNA they contain. 25 teeth were subject to different experimental conditions and total DNA was quantified for each individual tooth's radicular portion: apical and remaining root, according to a 2003 study by Gaytemenn and Sweet. We verified, with statistically significant figures, that the apical portion of the tooth is that which contains the greatest quantity of DNA. Different analytical procedures were studied for various polymorphic markers to evaluate the quality of the DNA. We concluded that the tooth is topographically distinct in both DNA quantity and quality. The tooth's apical portion is the preferential choice in sample preparation of dental mineralized tissue for molecular analysis and identification.