STR Profiles Research Articles

Assessment of the efficiency of DNA isolation and profiling applying a temperature-driven method in human remains.

The identification of human remains is of utmost importance in a variety of scenarios. One of the primary identification methods is DNA. DNA extraction from human remains could be difficult, particularly in situations where the remains have been exposed to environmental conditions and other insults. Several studies tried to improve extraction by applying different approaches. ForensicGEM Universal (MicroGem) is a single-tube approach to DNA extraction and a temperature-driven method that could have some advantages with respect to previous techniques, among them, reducing the risk of contamination, not requiring specialized equipment, or several steps to perform. The aim of this study was to assess, for the first time, the efficiency of DNA extraction and quality of STR profiles applying the MicroGem protocol and modifications of this protocol from tooth samples in comparison with automatic extraction (AE). Our results indicated that AE and MicroGem performed similar, though with variability depending on the MicroGem modifications, increasing the DNA yield and STR profile quality when DNA is concentrated with Microcon. These findings demonstrated the efficiency of this methodology for DNA extraction from human remains while also providing a simple and quick technique suitable to apply in a variety of forensic scenarios.

Using cluster analysis for grouping partial autosomal haplotypes derived from single sperm STR profiling

Abstract Background and objective The use of single cell STR profiling for mixture deconvolution is increasingly being discussed in forensics; however, studies regarding STR profiling of single sperm are relatively rare. Considering that each sperm cell exclusively contains a haploid genome, STR profiling as well as grouping profiles from each single contributor to derive consensus profiles seems to be difficult. Thus, so far, the information obtained from gonosomal markers partially combined with previously performed whole genome amplification was used. For this study, we wanted to determine the quality of individual sperm analysis using our routine workflow and, assuming the results provided sufficient profiles, to establish means to cluster them. Material and methods In terms of a feasibility study, STR profiles of single sperm cells were examined using different multiplex kits and amplification conditions. Based on this database, a cluster analysis for grouping partial haploid autosomal profiles was successfully developed. Simulations were carried out to increase the database. Furthermore, the correlation between successful cluster analysis and the number of sperm, the quality of the profiles obtained and the number of contributors was investigated. Results and conclusion From a pool of partial haploid profiles of 2–5 individuals, generally reliable grouping can be obtained by cluster analysis and diploid profiles can be derived for each contributor. When examining 40 sperm per contributor, in 92.2% (2 person mixture) and 71.6% (5 person mixture) complete and correct profiles could be deconvoluted; however, the fewer sperm per person are available for analysis, the more the completeness of the haploid profile affects the quality of the cluster analysis and therefore the correctness of the deconvoluted profile.

Optimisation of a DNA extraction protocol from fingerprints for the analysis of nuclear STR and mitochondrial DNA genetic profiles

Abstract Most of the cells found in fingerprints belong to the cornified barrier of the epidermis (stratum corneum), lack nuclei and cytoplasmic organelles, and are filled with keratin. Nuclear and mitochondrial DNA is degraded and embedded in the keratin mesh, a very resistant protein that is difficult to remove during DNA extraction. In this work, we studied the possible negative effect of keratin on PCR reactions and the influence of keratinase and proteinase K on the extraction of DNA from fingerprints. The role of glycogen in the DNA yield during the precipitation step and the importance of washing the obtained DNA with 70% ethanol were also studied. DNA was extracted from 96 fingerprints corresponding to recent prints and stored for 1, 5, and 18 months from 6 individuals. No differences were observed in the concentration of extracted DNA or in the number of nuclear STR alleles in the genetic profiles of fingerprints stored during different times. However, sex differences were observed in both the concentration of DNA obtained and the number of nuclear STR alleles detected, being lower in females than in males. In 80% of the fingerprints genetic profiles were obtained with at least half of the STR nuclear markers and, in 50% of the fingerprints genetic profiles were obtained with more than 90% of the markers, which would allow an unambiguous identification of the donor. In all fingerprints where mtDNA was analysed, complete sequencing of the HV1 and HV2 regions was possible, which increases the accuracy of the results obtained. The optimised protocol allowed obtaining a complete STR nuclear genetic profile of a 20-year-old palmprint. Key Points

Unraveling the Impact of Pre-analytical and Analytical Factors on the Quality of Biological Evidence: A Comprehensive Systematic Review

Background:: Ensuring the quality of biological evidence is key and has become a routine requirement in forensic laboratories. The quality of biological evidence is determined by the pre-analytical and analytical phase that encompasses all procedures, starting with the crime scene to laboratory investigation of biological evidence. This is the most vulnerable part of the total testing process and a major component of the reliability and validity of results. Therefore, to generate a quality report, every biological evidence resource should be collected, maintained, and disseminated to the highest quality, based on the intended forensic use. Methods:: Pre-analytical errors can happen at any stage prior to the testing process due to the use of insufficient or improper order of evidence collection, packaging, labelling, prolonged environmental exposure, failure to find the proper storage, the collection of evidence that is unsuitable for quality or quantity, inappropriate mixing of a sample, etc. Such circumstances during transportation, preparation, and storage can change the outcome of forensic evidence. While analytical errors may arise in the laboratory during the processing of evidence due to mishandling, crosscontamination, and a lack of standardised procedures. Result:: Thus, employing advanced analytical methodologies, strict quality control measures, ad-herence to ethical guidelines, and appropriate data interpretation during PCR, STR profiling, and DNA sequencing are of utmost importance. The validation of quality assurance in forensic biol-ogy has been guided by a "fit-for-purpose" approach, emphasizing the suitability of methods and procedures for forensic requirements and intended applications. Pre-analytical and analytical fac-tors play a critical role in determining the success of DNA analysis and its admissibility in a court of law. Conclusion:: To address this, this review aimed at summarizing recommendations about the pre-analytical and analytical phases and provides some guidance to reduce the effects of such factors that can have a significant impact on biological evidence.

DNA analysis of partial hydatidiform mole revealing triandric monogynic tetraploidy.

The authors present a case of a partial hydatidiform mole where DNA analysis (STR - short tandem repeat genotyping) showed a triandric monogynic tetraploid genome composition with a XXXY gonosomal complement. This genetic finding clinicopathologically correlates with a partial hydatidiform mole, although it is rare in comparison with the typical, diandric monogynic triploid partial moles. The genetic analysis definitively confirmed the suspected diagnosis of a partial mole. To exclude the possibility that molar pregnancy represented retained products of conception after elective pregnancy termination, STR profiles from molar pregnancy and previous products of conception were compared. Short tandem repeats genotyping is a useful molecular genetic method in the differential diagnosis of partial hydatidiform moles, where clinical-pathological findings are frequently ambiguous.

Generation of iPSC line from a Joubert syndrome patient with compound heterozygous mutations in CPLANE1 gene

We generated iPSC line using skin fibroblasts obtained from a female patient affected by Joubert syndrome, caused by two compound heterozygous variants (c.143G > A; p.Gly48Glu and c.1784 T > G; p.Leu595Ter) in CPLANE1. We used Sendai-virus-based technique for reprogramming and then we applied karyotype analysis, to exclude possible acquired big rearrangements. We verified the presence of the same STR profile as fibroblasts, the stem cell state (by immunofluorescence and qPCR) and, finally, the pluripotency state (by in vitro trilineage differentiation).

Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry

DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AimTo evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. Material & methodsBiological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. ResultsAfter DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016–50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. ConclusionWe demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.

Biological and genetic characterization of a newly established human external auditory canal carcinoma cell line, SCEACono2

Squamous cell carcinoma of the external auditory canal (EACSCC) is an extraordinarily rare and aggressive malignant disease. Establishment of EACSCC cell line with robust molecular characteristics is essential for the basic and translational research of EACSCC. Here, we show the newly established EACSCC cell line SCEACono2, derived from a patient with well-to-moderately differentiated EACSCC. We analyzed histologic and genetic features of SCEACono2 hiring multiple experiments, including next-generation sequencing (NGS). Immunocytochemical staining of SCEACono2 showed positivity of p53 and SCC1/2. Furthermore, SCEACono2 exhibited a unique characteristic that cytokeratin, vimentin as well as cancer stem cell markers (CD44, CD133, ALP and Oct3/4) were positive. SCEACono2 had an ability to form tumors at the temporal lesion xenograft nude mice model. NGS revealed that SCEACono2 harbored the somatic mutations of TP53 (p.G245S) and NOTCH1 (p.A465T). RNA-seq and downstream bioinformatics analysis revealed significant enrichment of genes involved in inflammation and cell adhesion in SCEACono2 compared to SCC-9 and HSC-4. STR profiling indicated no evidence of cross-contamination. In conclusion, SCEACono2 could serves as a promising and robust research resource of EACSCC in vitro and in vivo.

Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells.

While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25-200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.

A comparison of six adhesive tapes as tape lifts for efficient trace DNA recovery without the transfer of PCR inhibitors

Tape-lifting is a non-destructive method employed in the laboratory to recover and collect trace DNA evidence from crime scene exhibits with porous surfaces. The success of tape-lifting is a balance between capturing the biological material and compatibility with downstream DNA extraction processes to ensure efficient release of the tape-lifted material during DNA extraction. In this study, six commercially available low-, regular- and high-tack adhesive tapes were evaluated. The low-tack S183 tape and the highly adhesive S-Hold tape were compared for DNA recovery efficiency from different materials commonly encountered in casework. All tape-lifts were processed using PrepFiler Express™ BTA and AutoMate Express™ Forensic DNA extraction systems, DNA samples quantitated by Quantifiler TRIO, amplified using Powerplex® 21 and VeriFiler™ PLUS (VFP), and analysed on a 3500xl genetic analyser to evaluate the quality of the resultant STR profiles obtained.The more adhesive S-Hold tape recovered comparable or more DNA than the low-tack S183 tape from the majority of materials tested. However, STR profiles obtained from S183 tape-lifts were of markedly higher quality compared to S-Hold tape-lifts. This was most evident for towel, denim and printed chiffon, where S-Hold samples exhibited severe PCR inhibition, with VFP internal quality markers confirming the presence of inhibitors. The findings suggest that strong adhesion is not necessarily beneficial for tape-lifting, as the low tack S183 tape was able to efficiently recover cellular material from the surface of porous substrates commonly encountered in casework, while avoiding the co-transfer of PCR-inhibitory substances from the sampled material.

Droplet-based optical trapping for cell separation in mock forensic samples.

Optical tweezers have a wide range of uses for mechanical manipulation of objects in the microscopic range. This includes both living and static cells in a variety of biomedical and research applications. Single-focus optical tweezers, formed by focusing a laser beam through a high numerical aperture immersion objective, create a significant force, which enables controlled transport of a variety of different cell types and morphologies in three dimensions. Optical tweezers have been previously reported to capture and separate spermatozoa from a reconstituted simulated postcoital sample. We report herein the development of a simplified, more efficient cell transfer protocol that can separate and isolate both spermatozoa as well as leukocytes, with similar efficiencies as those previously reported. The new cell transfer method was used to separate sperm cells from a reconstituted mixture of spermatozoa and vaginal epithelial cells, with complete STR profiles developed from 50 cells with little evidence of contribution from the female contributor to the mixture. This modified protocol was then used to separate 21 samples of enriched leukocytes, with trapped cells ranging from 5 to 22 cells. Complete STR profiles were developed from as few as 10 leukocytes. Thus, with minimal sample preparation and a short trapping time, this method has the potential to provide an alternative to traditional differential extraction methods for separation of sperm:nonsperm mixtures while also providing versatility for separation of cells with differing morphologies.

Development of a multiplex reverse transcription qPCR assay for identification of saliva, blood, and semen

ABSTRACT The identification of body fluids can provide important information for case processing in forensic investigations. Accurate identification through messenger RNA (mRNA) is effective, especially in cases of sexual assault, where body fluids from one or more contributors are mixed. In this study, a saliva, blood, and semen simultaneous identification reverse transcription-quantitative polymerase chain reaction (SBS RT-qPCR) assay using mRNA from a DNA/RNA co-extraction method was developed. The body fluid-specific mRNA markers histatin 3 (HTN3), haemoglobin subunit beta (HBB), and protamine 1 (PRM1) were selected for identification of saliva, blood, and sperm cells, respectively. The assay accurately identified saliva, blood, and semen without cross-reaction with 10 body fluids. The limits of detection (LoD) were 1/102-, 1/105-, and 1/103-fold dilutions of total RNA in saliva, blood, and semen, respectively. Furthermore, the assay accurately identified trace amounts of body fluids in mixed samples at a 58:1:1 ratio. Finally, it was possible to analyse the origin of body fluids by obtaining an STR profile using the DNA/RNA co-extraction method. The SBS RT-qPCR assay was able to simultaneously identify each body fluid with efficiency in sample consumption. Therefore, it is advisable to use the DNA/RNA co-extraction method to identify mixed body fluids in sexual assault cases.

A spit in time: identification of saliva stains and assessment of total DNA recovery up to 180 days after deposition.

The main aim of this work was to validate the detection of saliva samples from denim, cotton, and polyester fabrics aged up to six months, applying rapid immunochromatographic tests resulting in the analysis of nuclear and mitochondrial DNA recovered. A comparison was also carried out between two saliva detection tests, Laboratory and Crime Scene. 50 μl saliva samples (three per time and test) were deposited on denim, cotton, and polyester fabrics. After 1, 3, 7, 14, 21, 30, 60, 90, 150, and 180 days of storage at room temperature, the samples were recovered by swabbing and detected by SERATEC® Amylase (Laboratory) test and SERATEC® SALIVA CS (Crime Scene) test (SERATEC®, Göttingen, Germany). DNA was isolated from the swab extraction buffer applying a silica-based methodology, and quantified based on fluorescent and human-specific quantifications. Then, it was submitted to STR profiling and mtDNA sequencing. According to our results, saliva stains up to six months after deposition remain valid specimens. The intensity of the bands varied among fabric type and time. Total DNA was successfully recovered from all tested samples, though with the limitations of obtaining partial nuclear DNA profiles from the oldest samples. In contrast, complete characterization of mtDNA was achieved from all samples. Lab and CS tests performed similar on the detection of saliva, as well as, DNA yield and profiling. Future research will be able to expand these results, analyzing the stability of other body fluids and the sensitivity of rapid immunochromatographic tests to detect them.

Record-matching of STR profiles with fragmentary genomic SNP data.

In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.

A quantifiler™ trio-based HRM screening assay for the accurate prediction of single source versus mixed biological samples.

At present, the forensic DNA workflow is not capable of providing information about the contributor status (single source vs. multiple contributors) of evidentiary samples prior to end-point analysis. This exacerbates the challenges inherent to mixtures and low-template DNA samples. If additional sample information could be provided earlier in the workflow, protocols could be implemented to mitigate these challenges. An integrated Quantiplex®- high resolution melt (HRM) assay was shown to be effective in distinguishing between single source and mixture DNA samples; however, integration of the HRM assay into a more commonly used chemistry would be beneficial to the practitioner community. Thus, the assay was redesigned as an integrated Quantifiler™ Trio-HRM assay, which included the identification of a new DNA-binding dye, an increased reaction volume, and the establishment of new data analysis and standard curve metrics for all targets. This redesigned assay produced quantification values and qualitative values that were comparable to those produced when the same samples were tested using the standard Quantifiler™ Trio chemistry and settings. Further, STR profiles generated with quantification values produced from the integrated Quantifiler™ Trio-HRM assay and standard Quantifiler™ Trio chemistry were complete and fully concordant. Most importantly, the integrated Quantifiler™ Trio-HRM assay was able to accurately predict whether a sample was single source or a mixture 79.2% of the time, demonstrating the potential of this approach. With the incorporation of an expanded training set for prediction modeling, and completion of critical developmental validation studies, this assay could prove useful to the forensic DNA practitioner community.

Establishment and characterization of a novel cell line (SCCOHT-CH-1) and PDX models derived from Chinese patients of small cell ovarian carcinoma of the hypercalcemic type

Small cell carcinoma of the ovary hypercalcemic type (SCCOHT) is a rare and aggressive malignancy that poses a significant clinical challenge due to its grim prognosis. Unfortunately, only three SCCOHT cell lines are currently available for scientific research. In this study, we have successfully established a novel SCCOHT cell line from a recurrent lesion of a SCCOHT patient, named SCCOHT-CH-1. We comprehensively characterized the novel cell line by employing techniques such as morphological observation, CCK-8 assay, Transwell assay, clone formation assay, short tandem repeat sequence (STR) analysis, karyotype analysis, immunohistochemical staining, western blot assay, and xenograft tumor formation assay. SCCOHT-CH-1 cells were small circular and had a unique STR profile. The population-doubling time of SCCOHT-CH-1 was 33.02 h. The cell line showed potential migratory and invasive ability. Compared with another SCCOHT cell line COV434, SCCOHT-CH-1 exhibited higher expression of AKT, VIM, and CCND1. At the same time, SCCOHT-CH-1 has the ability of tumorigenesis in vivo. We also successfully constructed three patient-derived xenograft (PDX) models of SCCOHT, which were pathologically diagnosed to be consistent with the primary tumor, accompanied by loss of SAMRCA4 protein expression. The establishment of SCCOHT-CH-1 cell line and PDX models from Chinese people represent a pivotal step toward unraveling the molecular mechanism of SCCOHT and fostering the development of targeted interventions to tackle this challenging malignancy.

Novel neoantigen peptides and tumor regression in the MC38 colorectal cancer model.

28 Background: Neoantigen vaccine is an emerging modality to treat cancer by unleashing cytotoxic T cells against tumor-specific mutant antigens. Neoantigens are de-novo changes in tumor cells and are hence more immunogenic and less susceptible to off-target toxicities. In building our own pipeline for neoantigen discovery, we used the mouse colon adenocarcinoma cell line MC38 as a validation model. Methods: We sequenced MC38 cells by whole exome and RNA sequencing to shortlist variants. Candidates were confirmed by sanger sequencing, then analyzed for binding affinity to MHC class I H2-Kb and H2-Db. We selected top 10 epitopes for facile modification to maximize immunogenicity by taking into account peptide characteristics, such as hydrophobicity. In-vivo immunogenicity was tested by subcutaneous injections of pooled peptides in C57BL/6J mice. Amongst the 10 peptides tested, we picked five that elicited greatest IFNγ secretion in re-stimulated splenocytes. Predicted binding affinity did not correlate with in-vivo immunogenicity. We inoculated MC38 cells into the left flank of C57BL/6J mice and started treatment four days later. Mice were injected twice weekly with PBS (group 1), CpG only (group 2), anti-PDL1 only (group 3), Peptide pool + CpG (group 4) and Peptide pool + CpG + anti-PDL1 (group 5) (n=8 per group). CpG ODN 1826 is a TLR9 agonist and acts as an adjuvant, while anti-PDL1 is an immune checkpoint inhibitor. We monitored tumor size, animal weights and food intake every 2-3 days. Results: In control group 1, tumor size exponentially increased by 36 folds on the 18th day of treatment. Groups 2, 3, 4 and 5 saw 16, 13, 8 and 5-fold increases in tumor size respectively, 21 days post-treatment. No tumors were found in 3/7 mice in group 5 upon sacrifice, suggesting tumor regression. Tumor control in groups 4 and 5 corroborated with significant IFNγ secretion from neoantigen re-stimulated splenocytes. We observed 38-45 fold expansion in the number of CD8+ KLRG1+ short-lived effector cells and significant increase in PD-1+ TIM3+ exhausted T cells in group 4 and 5 relative to control. Reps1 and Adpgk neoantigen peptides are widely reported and used in MC38 syngenic model. However, they were not included because both were undetected by sequencing. Cell line authentication by STR profiling confirmed that our cells matched that of MC38 from Kerafast. Conclusions: Using an in-house pipeline, we derived a set of novel neoantigen peptides that robustly controlled tumor growth in the MC38 tumor challenge model. In-silico binding predictions did not correlate with in-vivo patterns of IFNγ secretion. In-vivo tests for IFNγ induction after peptide vaccination is a better measure for potential in tumor control. Upregulation of T-cell exhaustion markers after peptide vaccination explains the improved response with anti-PDL1. Reps1 and Adpgk mutations were absent in our cells, which calls caution to researchers conducting similar research.

From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates

Titanium dioxide (titania, TiO2) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO2 causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO2-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated. DNA in saliva and touch samples deposited on self-cleaning glass slides exposed to indoor fluorescent light for up to seven days was more degraded than control samples indicating some degree of fluorescent light-induced photocatalytic activity of the self-cleaning surfaces. When exposed to sunlight, DNA yields from saliva and touch samples deposited on the titania-coated substrates decreased rapidly, with a corresponding increase in DNA degradation. After three days no DNA samples applied to self-cleaning glass and exposed to natural sunlight yielded STR profiles. These results suggest that the photocatalytic activation of TiO2 is the likely mechanism of action underlying the extreme DNA degradation on the Bioclean® and SaniTise™ glasses. Consequently, rapid sample collection and use may be warranted in casework scenarios involving TiO2-coated materials.

Efficacy of three methods of extracting DNA from skeletal remains obtained from three taphonomic contexts

IntroductionThe extraction techniques of deoxyribonucleic acid (DNA) from old bone samples are based on the use of complex methodologies, which deal with the degradation of the sample, the low amount of DNA, and the presence of inhibitors that can be extracted simultaneously. ObjectiveTo compare the efficiency in obtaining DNA from the methods: organic extraction, commercial kit, and previous total demineralization, to obtain STR profiles of old bone samples from 3 taphonomic processes (alkaline, acid, and moist mitotic). Materials and methods29 skeletal remains from 3 different taphonomic contexts were processed: acidic, alkaline, and wet-fungal. The amount of DNA obtained from 3 methodologies was evaluated in a comparative manner: organic extraction method (phenol–chloroform–isoamyl alcohol) (SO), extraction by silica column KIT QIAamp® DNA Investigator of QIAgen® (KC), and the methodology of extraction by previous total demineralization (DP). Finally, the obtaining of the STR profiles from the methodology of greater performance was tested. ResultsThe following quantification values were obtained: (i) alkaline medium: 0.068±0.07 ng/μL (SO), 0.021±0.01 ng/μL (KC), and 0.073±0.052 ng/μL (DP); (ii) acidic medium: 0.098±0.064 ng/μL (SO), 0.041±0.029 ng/μL (KC), and 0.068±0.042 ng/μL; (iii) wet-mitotic medium: 0.25±0.061 ng/μL (SO), 0.04±0.027 ng/μL (KC), and 0.15±0.072 ng/μL (DP). Likewise, using the DNA samples obtained by the SO method, complete profiles were obtained for the wet taphonomic context while the alkaline taphonomic process proved to be the most drastic for DNA degradation, presenting a greater number of incomplete profiles. ConclusionsThe methodology of organic extraction was optimal in obtaining DNA from the 3 taphonomic processes evaluated. On the other hand, the wet-fungal taphonomic process is the one that produces the least negative impact on the preservation of DNA from skeletal remains.

Quantitative PCR overestimation of DNA in samples contaminated with tin.

Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an "inhibition study" and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.