Developmental validation of GlobalFiler™ PCR amplification kit: a 6-dye multiplex assay designed for amplification of casework samples

Development of a multiplex recombinase amplification assay for the rapid and concurrent detection of human DNA and sex identification

In forensic practice, it is essential to identify human DNA and determine the sex of individuals from biological samples collected at crime scenes. Currently, the common detection methods mainly focus on targeted DNA analysis based on PCR technology, which is time-consuming and relies on laboratory equipment. In recent years, recombinase polymerase amplification (RPA), as one of ubiquitous isothermal amplification technology, has gained popularity across various diagnostic fields due to its advantages of rapid processing and minimal temperature control requirements. This study has developed a multiplex RPA assay suitable for human and sex components identification. The assay has good sensitivity (as low as 25 pg) and strong tolerance to inhibitors (in the presence of 200 ng/μL humic acid, 400 ng/μL tannic acid, and 8000 ng/μL collagen). Furthermore, we combined the alkaline lysis and RPA detection to construct a rapid detection scheme, which can shorten detection time to half an hour. We also conducted a preliminary exploration of the visualization scheme for the constructed RPA assay. The above research demonstrates simultaneous and rapid detection of human and sex components, offering an accurate and sensitive detection scheme.

Developmental validation of the AGCU EX-38 typing system: a comprehensive forensic tool for enhanced genetic identification

The necessity for developing the AGCU EX-38 typing system arises from the ever-increasing demand for more accurate and comprehensive forensic tools. Traditional kits with fewer STRs often fall short in complex cases requiring higher resolution. The AGCU EX-38 typing system incorporates 35 autosomal STRs, including extended CODIS loci as well as additional non-CODIS loci (D6S1043, D19S3045, D3S3045, D7S3048, D11S2368, D4S2366, D8S1132, D15S659, Penta D, Penta E, D6S447, D3S1744, D14S608, D18S535). This combination of CODIS and non-CODIS markers provides a significant advantage, particularly in complex kinship analyses such as half-sibship cases. This six-dye kit encompasses 38 loci, with a maximum amplicon size of 550 base pairs (bp), and features nine STRs within 200 bp and 14 STRs within 300 bp, offering unparalleled coverage and sensitivity. The AGCU EX-38 typing system is the only available kit on the market containing 35 autosomal STRs with six-dye chemistry, making it a unique and invaluable resource for forensic laboratories. This configuration allows for higher resolution and superior performance in cases with degraded or mixed DNA samples. In this study, we report the results of the developmental validation study, which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines. The data includes PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design and demonstrate the kit's robustness, reliability, and suitability for genetic identification and population studies.

Cancellation of Spectral and Spatial Crosstalk in Spectral Imaging for High-Dynamic-Range Electrophoretic Analysis of STR-PCR Products

In spectral imaging, an optical system generates two mutually dependent kinds of crosstalk on an image sensor: spectral crosstalk (i.e., spectral mixing) between fluorescences of different dyes and spatial crosstalk (i.e., image artifacts) between fluorescences from different emission points in the field of view of the sensor. Therefore, an algorithm to cancel both kinds of crosstalk simultaneously (i.e., simultaneous spectral unmixing and image-artifact reduction) is proposed. The algorithm is based on the assumption that a crosstalk matrix (i.e., point-spread functions, PSFs) consisting of all crosstalk ratios is constant regardless of the causes of both kinds of crosstalk. By applying the algorithm to a nine-wavelength-band measurement of four-capillary electrophoretic separation of STR-PCR (short tandem repeat-polymerase chain reaction) products labeled with six dyes, true peaks of each of the dyes were obtained, while false peaks due to spatial crosstalk were reduced below the lower limit of detection in electropherograms. As a result, effective sensitivity and effective dynamic range were improved by 2 orders of magnitude. Moreover, it became possible to perform robust human identification of on-site-collected trace samples containing template DNA at any concentration in a 3-order concentration range by a single STR-PCR and a single electrophoretic separation.

Comprehensive investigation of the Applied Biosystems™ SeqStudio™ Genetic Analyzer platform for forensic DNA typing

Capillary electrophoresis (CE) is the conventional method for separating and detecting amplified DNA fragments for forensic human identification (HID). The Applied Biosystems™ SeqStudio™ Genetic Analyzer, referred to herein as the SeqStudio™, is the most recent CE platform introduced for forensic purposes. The SeqStudio™ includes an all-in-one reagent cartridge containing four capillaries. Validating a CE platform requires consideration of injection time, sensitivity and reproducibility, and mixture performance. The evaluation of the SeqStudio™ was performed using a standard polymerase chain reaction (PCR)-CE workflow. Injection time, sensitivity, and mixture studies were performed to determine the optimal parameters for reproducible and reliable data. The injection time study yielded a general decline in the relative florescence units (RFU) as injection time decreased from ten to one second. The sensitivity study showed no locus or allelic dropout from one nanogram (ng) to 250 picogram (pg) DNA input at the one second injection time, however, when not considering the TH01 locus, the sensitivity was further reduced to 62.5pg. The two-person and three-person mixture studies demonstrated that the SeqStudio™ is capable of detecting a large range of DNA mixture ratios. The evaluation serves as a model for best practices and supports the use of the SeqStudio™ for HID.

Characterizing stutter in single cells and the impact on multi-cell analysis

Short tandem repeat analysis is a robust and reliable DNA analysis technique that aids in source identification of a biological sample. However, the interpretation, particularly when DNA mixtures are present at low levels, can be complicated by the presence of PCR artifacts most commonly referred to as stutter. The presence of stutter products can increase the difficulty of interpretation in DNA mixtures as well as low-level DNA samples down to a single cell. Stutter product formation is stochastic in nature and although methods exist that can estimate the magnitude of stutter product formation, it still is not well understood. With the increased sensitivity of forensic DNA analyses, it has become possible to obtain interpretable DNA profiles from as low as 6.6 pg of DNA, or a single human diploid cell. However, this presents an interpretational challenge because the stutter in these low-level DNA samples might stray from the expected patterns observed in high-level DNA samples. Therefore, this project focuses on characterizing stutter in single cell samples to help generate a deeper understanding of stutter and provide a guide for detecting and evaluating stutter in low-level samples. Stutter analysis was performed using data generated from 180 single cells isolated with the DEPArrayTM NxT, amplified using the PowerPlex Fusion 6 C amplification kit at 29 or 30 cycles. Stutter was successfully characterized in single cells and stutter percentages were highly elevated compared to high-level samples where the variance increased as the number of cells being analyzed decreased leading to potential high stutter at low DNA levels. Using empirical and simulated (resampled) data, this study also reinforces historically relevant patterns in stutter product formation and demonstrates the relative differences in stutter in n-1, n-2 and n + 1 stutter product formation in simple, complex and compound repeats.

Massively parallel sequencing of a forensic combined panel of 107-plex STR loci and 292-plex SNP loci in the Han Chinese population

Massively parallel sequencing (MPS), a well-established strategy for forensic DNA profiling, enables the simultaneous sequencing of multiple targeted loci of multiple samples at a single-base resolution with high coverage. In this study, we developed a novel typing system by combining solution-based hybrid capture methods with MPS to target as many as 107 short tandem repeats (STRs) and 292 single nucleotide polymorphisms (SNPs) in the Han Chinese population. Completely accurate and concordant STR genotypes were obtained when compared to typing results generated from conventional capillary electrophoresis analysis, with six loci exhibiting inferior performance due to allele dropout or even locus dropout. The locus detection success reached 85.2 % for STRs at a DNA input of 10 ng and 95.61 % for SNPs at a DNA input of 5 ng. Mixture studies substantiated the considerable potential of our system in identifying minor contributor alleles at both STR and SNP loci. Additionally, the system demonstrated full inferential abilities in distinguishing first-degree kinship from unrelated individual pairs and achieved significant effectiveness of 99.78 % and 80.2 % for the identification of second- and third-degree kinship, respectively. These findings indicated that our novel typing system is highly discriminative and informative when used in the Han Chinese population and would be highly efficient for use in paternity testing and complex kinship analysis.

Characterization of challenging forensic DNA traces using advanced molecular technologies

The majority of crime scenes contain DNA that is either present in small amounts or degraded, making it difficult to obtain usable DNA profiles using conventional technologies. The current standard for analyzing casework samples is the specific amplification of short tandem repeats (STR), which is limited by DNA quality and quantity. Since the goal of forensic science is to identify a suspect or victim regardless of trace quality, we evaluated three technological approaches to better characterize and exploit these traces: (i) ultra-sensitive pulse-field electrophoresis on a Femto Pulse System (FPS) to visualize DNA content, (ii) real-time quantitative PCR based on Alu repeats to quantify human DNA and analyze its integrity, and (iii) 16S ribosomal RNA gene (16S rRNA) amplicon sequencing to identify microbiota. We optimized FPS analysis using DNA from model traces (blood, saliva, semen, touch DNA, and vaginal swabs) and applied the protocol to 100 casework samples. We found differences between the FPS profiles of model and casework samples, showing a variation in fragment size and distribution, suggesting the presence of non-human DNA. Using Alu-qPCR and 16S rRNA amplicon sequencing, we determined the amount and proportion of human and non-human DNA. Human DNA was detected in 84% of traces with an average of 70 pg per trace, while 16S rRNA revealed microbial DNA as the most abundant DNA in traces. These analyses provide new insights into forensic trace composition, allowing better sorting and profiling of traces.

The (in)dependence of single-cell data inferences on model constructs

Recent developments in single-cell analysis have revolutionized basic research and have garnered the attention of the forensic domain. Though single-cell analysis is not new to forensics, the ways in which these data can be generated and interpreted are. Modern interpretation strategies report likelihood ratios that rely on a model of the world that is a simplification of it. It is, therefore, plausible that different reasonable models will assign noticeably different weights of evidence (WoEs) to some of these data, resulting in inconsistent reports and protracted reviews of that evidence, potentially across years. With one goal of research being to identify and understand sources of inconsistencies during early stages, we undertake a study that evaluates WoE at the limit of one single-cell electropherogram (scEPG) across three architecturally distinct probabilistic models. The three are named EESCIt (Evidentiary Evaluation of Single Cells), TD (Top-Down), and DCM (Discrete Cell Model). To do this, we performance test the three models on a set of 996 individual scEPGs and conduct one H1-true, i.e., true contributor, and 201 H2-true, i.e., false contributor, tests, per scEPG. With the 201,192 outcomes per model, we confirm that scEPGs well resolve the hypotheses, regardless of what model was applied. We also observe that WoEs increase, on average, by 1 for every 1000 RFU of total intensity added until a plateau near the logarithm of the inverse of the random match probability is reached at ca. 22,000 RFU. By querying WoE calibration for each model, we determine if the evidence is over- or under-stated for any one of them. We find that for WoE ≥ -1 hardly any calibration discrepancy is observed. There were rare instances, however, for which WoEs that were ≤ -1 too strongly pointed in the negative direction, though H1 was true. This was the result of five scEPGs that not only exhibited extreme signal in stutter positions, but also carried little information in other loci. These findings show that all three models appropriately stated WoEs for scEPGs when reporting positive WoE, and the two continuous model's WoE reasonably represented the findings when WoE < -1 for most loci. To further explore, we continued with paired analyses that evaluated the agreement in WoE, per scEPG, across models. Unlike unpaired analyses, this evaluation determines if well performing models return equivalent results for the same scEPG. The paired analysis was summarized by way of intraclass correlations, which were at least 0.99997. Further, we found that 762 of 996 WoEs were within a range of 3 orders of magnitude of each other, though many of these were associated with WoEs that were large, i.e., > 9, in the first instance. When we more closely focus on scEPGs giving ranges ≥ 3, but whose WoE ≤ 9 for at least one of the models, we find there are 21 of them. When we perform a locus-by-locus investigation of these 21 and of the five scEPGs returning too strong negative WoE for true contributors we find that extreme stutter is usually the cause of the challenges. To ameliorate differences in predicting rare, though impactful, events we proffer interpretive adaptions that extend beyond manually addressing the phenomena. With the WoE being calibrated within their relevant regions across EESCIt, TD and DCM, we categorize each as meeting the pillar of legitimacy for single-cell data within their intended WoE ranges.

Enhancing trace DNA profile recovery in forensic casework using the amplicon RX post-PCR clean-up kit

This study evaluated the effectiveness of the amplicon RX post-PCR clean-up kit in enhancing trace DNA profile recovery from forensic casework samples amplified using the GlobalFiler PCR amplification kit. The impact of post-PCR clean-up on allele recovery and signal intensity was assessed in both trace casework samples and control samples across a range of DNA concentrations. The results showed that the amplicon RX method significantly improved allele recovery compared to the 29-cycle protocol (p = 8.30 × 10-12) and achieved slightly better results than the 30-cycle protocol (p = 0.019). Additionally, the Amplicon RX method demonstrated a significant increase in signal intensity (p = 2.70 × 10-4), reflecting improved sensitivity in detecting trace DNA profiles compared to the 30-cycle protocol. In the evaluation of control samples, the amplicon RX method consistently outperformed both the 29- and 30-cycle protocols, especially at lower DNA concentrations (D3: 0.001 ng/µL). While the performance of all methods declined at the lowest concentration (D4: 0.0001 ng/µL), the Amplicon RX method still demonstrated superior allele recovery (p = 0.014 compared to 29 cycles; p = 0.011 compared to 30 cycles). Therefore, the Amplicon RX method should be widely adopted in forensic laboratories to enhance the analysis of extremely low-template and compromised samples. These findings highlight the potential of the amplicon RX post-PCR clean-up kit to improve trace DNA analysis in forensic casework. Further research is recommended to validate these results and explore its broader application in forensic DNA analysis, particularly in complex DNA mixtures and extremely low-template samples.

Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples

The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 102 copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.IMPORTANCEPrevious studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.

Advancements in differentiation between sperm cells and epithelial cells for efficient forensic DNA analysis in sexual assault cases

Most of the sexual assault casework samples are of mixed sources. Forensic DNA laboratories are always in the requirement of a precise technique for the efficient separation of sperm and non-sperm DNA from mixed samples. Since the introduction of the differential extraction technique in 1985, it has seen significant advancements in the form of either chemicals used or modification of incubation times. Several automated and semi-automated techniques have also adopted the fundamentals of conventional differential extraction techniques. However, lengthy incubation, several manual steps, and carryover over non-sperm material in sperm fraction are some of the major limitations of this technique. Advanced cell separation techniques have shown huge promise in separating sperm cells from a mixture based on their size, shape, composition, and membrane structure and antigens present on sperm membranes. Such advanced techniques such as DEParray, ADE, FACS, LCM, HOT and their respective pros and cons have been discussed in this article. As current-day forensic techniques should be as per the line of Olympic slogan i.e., faster, higher, stronger, the advanced cell separation techniques show a huge potential to be implemented in the casework samples.

Developmental Validation of the Microreader 23HS Plex ID System: A Novel Supplementary Non-CODIS STR Multiplex Assay for Forensic Application

A novel supplementary non-CODIS STR multiplex assay designated as the "Microreader 23HS Plex ID System" was developed. The Microreader 23HS Plex ID System enables simultaneous profiling of 23 STR loci and the amelogenin locus. The majority of these loci are non-CODIS STRs (D4S2408, D9S2157, D20S161, D3S2459, D18S1364, D13S305, D1S2142, D19S400, D6S1017, D7S1517, D2S1776, D2S1360, D3S1744, D16S3391, D3S1545, D11S4463, D20S85, D1S549, D10S2325, D21S2055), with the exception of three CODIS STRs (D2S441, D12S391, and D22S1045). Followed the recommendations of Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese validation standards, a comprehensive set of validation studies were conducted, encompassing PCR conditions, stutter ratio and peak height balance, sensitivity, precision and accuracy, reproducibility, species specificity, inhibition, as well as mixture testing. The results demonstrated that the Microreader 23HS Plex ID System is a reliable and robust assay, with well-balanced peak heights, high precision and accuracy, species specificity, and resistance to common inhibitors. The sensitivity of the assay was determined to be 0.125 ng of template DNA. In mixture study, all minor alleles were detected in two-sample mixtures across various ratios (1:19, 1:9, 1:4, 3:7, 2:3, 1:1, 3:2, 4:1, 9:1, and 19:1). In population study, a total of 500 unrelated individuals of Han ethnicity from East China were genotyped. The allele frequencies and forensic population genetic parameters were calculated, with a cumulative random match probability of 7.757 × 10-27, and a total power of discrimination exceeding 0.999,999,999,999,999,999,999,999,99. In conclusion, the Microreader 23HS Plex ID System shows promise as a valuable supplementary tool for forensic applications, particularly in addressing complex kinship testing and challenges posed by STR mutation.

Genomic Multicopy Loci Targeted by Current Forensic Quantitative PCR Assays

Modern forensic DNA quantitation assays provide information on the suitability of a DNA extract for a particular type of analysis, on the amount of sample to put into the analysis in order to yield an optimal (or best possible) result, and on the requirement for optional steps to improve the analysis. To achieve a high sensitivity and specificity, these assays are based on quantitative PCR (qPCR) and analyze target DNA loci that are present in multiple copies distributed across the genome. These target loci allow the determination of the amount of DNA, the degree of DNA degradation, and the proportion of DNA from male contributors. In addition, internal control DNA of a known amount is analyzed in order to inform about the presence of PCR inhibitors. These assays are nowadays provided as commercial kits that have been technically validated and are compatible with common qPCR instruments. In this review, the principles of forensic qPCR assays will be explained, followed by information on the nature of DNA loci targeted by modern forensic qPCR assays. Finally, we critically draw attention to the current trend of manufacturers not to disclose the exact nature of the target loci of their commercial kits.

Developing a Machine Learning 'Smart' Polymerase Chain Reaction Thermocycler Part 2: Putting the Theoretical Framework into Practice

The introduction of PCR into forensic science and the rapid increases in the sensitivity, specificity and discrimination power of DNA profiling that followed have been fundamental in shaping the field of forensic biology. Despite these developments, the challenges associated with the DNA profiling of trace, inhibited and degraded samples remain. Thus, any improvement to the performance of sub-optimal samples in DNA profiling would be of great value to the forensic community. The potential exists to optimise the PCR performance of samples by altering the cycling conditions used. If the effects of changing cycling conditions upon the quality of a DNA profile can be well understood, then the PCR process can be manipulated to achieve a specific goal. This work is a proof-of-concept study for the development of a smart PCR system, the theoretical foundations of which are outlined in part 1 of this publication. The first steps needed to demonstrate the performance of our smart PCR goal involved the manual alteration of cycling conditions and assessment of the DNA profiles produced. In this study, the timing and temperature of the denaturation and annealing stages of the PCR were manually altered to achieve the goal of reducing PCR runtime while maintaining an acceptable quality and quantity of DNA product. A real-time feedback system was also trialled using an STR PCR and qPCR reaction mix, and the DNA profiles generated were compared to profiles produced using the standard STR PCR kits. The aim of this work was to leverage machine learning to enable real-time adjustments during a PCR, allowing optimisation of cycling conditions towards predefined user goals. A set of parameters was found that yielded similar results to the standard endpoint PCR methodology but was completed 30 min faster. The development of an intelligent system would have significant implications for the various biological disciplines that are reliant on PCR technology.

Performance comparison of a previously validated microhaplotype panel and a forensic STR panel for DNA mixture analysis

Short Tandem Repeats (STRs) are the most widespread markers in forensic genetics. However, STR stutter peaks can mask alleles from a minor contributor when analysing mixtures, hindering the interpretation of complex profiles. In this study we compared the performance of a previously described panel of microhaplotypes (MHs), an alternative type of forensic marker, against a standard STR kit. The parameters evaluated included: capability of determining the minimum number of contributors in the mixture; percentages of allele drop-outs and drop-ins; retrieval of alleles belonging to the minor contributor, and estimation of likelihood ratio (LR) values. In addition, the capacity of EuroForMix software to estimate each donor's percentage of contribution was tested, as well as the impact on results when using manually, or automatically prepared libraries. The MH panel showed better performance than STRs for the detection of 2-contributor mixtures, but the lower degree of polymorphism per MH marker hindered the task of deconvolution with multiple contributors. MHs presented higher drop-in rates and lower drop-out rates, a higher capability to recover the minor contributor's alleles and provided higher LR values than STRs, likely due to the much higher number of loci combined in the panel. Estimations of contributor ratios using EuroForMix showed promising results and marginal differences were found in these values between manually and automatically prepared libraries. Overall, results showed that the mixture detection performance of the MH panel was better or equal to the standard forensic autosomal STR panel, indicating microhaplotypes are informative markers for this purpose.

NSPlex: an efficient method to analyze non-specific peaks amplified using commercial STR kits

Commercial short tandem repeat (STR) kits exclusively contain human-specific primers; however, various non-human organisms with high homology to the STR kit's primer sequences can cause cross-reactivity. Owing to the proprietary nature of the primers in STR kits, the origins and sequences of most non-specific peaks (NSPs) remain unclear. Such NSPs can complicate data interpretation between the casework and reference samples; thus, we developed "NSPlex", an efficient method to discover the biological origins of NSPs. We used leftover STR kit amplicons after capillary electrophoresis and performed advanced bioinformatics analyses using next-generation sequencing followed by BLAST nucleotide searches. Using our method, we could successfully identify NSP generated from PCR amplicons of a sample mixture of human DNA and DNA extracted from matcha powder (finely ground powder of green tea leaves and previously known as a potential source of NSP). Our results showed our method is efficient for NSP analysis without the need for the primer information as in commercial STR kits.

Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics

Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results.

Novel buffer for long-term preservation of DNA in biological material at room temperature

The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.

Cross-species amplification from non-human primate DNAs in commercial human DNA assay kits

Species specificity of commercial human DNA quantification kits and short tandem repeat (STR) profiling kits was examined using primate DNA samples. These samples comprised 33 individuals from eight primate species, each with gender and kinship data, including human (Homo sapiens), chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus) of Hominidae family, and Japanese macaque (Macaca fuscata), long-tailed macaque (Macaca fascicularis), hamadryas baboon (Papio hamadryas), and savannah monkey (Chlorocebus sp.) of Cercopithecidae family. The findings revealed varying levels of cross-species amplifications in all non-human DNA samples that correlated with their evolutionary proximity to humans, both kit types. Moreover, cross-species amplification, including female DNA samples, was observed in a Y-chromosomal STR profiling kit. Additionally, species specificity differed among the commercial kits examined. The cross-species amplification data presented in this study offer valuable assistance in interpreting the results of individual human identification in forensic cases involving non-human primates.

Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles

The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.

Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis

Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.

RNA-based short tandem repeat analysis on the D18S51 locus

DNA typing based on short tandem repeat (STR) analysis is an effective forensic method for human identification. Some STRs are contained within the introns of protein-coding genes and are transcribed as pre-mRNAs. However, the possibility of using RNA for STR analysis is yet to be fully explored. Considering that RNA in forensic samples is relatively stable, especially under dry- and low-temperature conditions, we hypothesized that STR information could be obtained from RNA. Here, we investigated the possibility of conducting RNA-based STR analysis using the D18S51 locus as a model.

PCR in Forensic Science: A Critical Review

The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.

Single-cell investigative genetics: Single-cell data produces genotype distributions concentrated at the true genotype across all mixture complexities

In the absence of a suspect the forensic aim is investigative, and the focus is one of discerning what genotypes best explain the evidence. In traditional systems, the list of candidate genotypes may become vast if the sample contains DNA from many donors or the information from a minor contributor is swamped by that of major contributors, leading to lower evidential value for a true donor's contribution and, as a result, possibly overlooked or inefficient investigative leads. Recent developments in single-cell analysis offer a way forward, by producing data capable of discriminating genotypes. This is accomplished by first clustering single-cell data by similarity without reference to a known genotype. With good clustering it is reasonable to assume that the scEPGs in a cluster are of a single contributor. With that assumption we determine the probability of a cluster's content given each possible genotype at each locus, which is then used to determine the posterior probability mass distribution for all genotypes by application of Bayes' rule. A decision criterion is then applied such that the sum of the ranked probabilities of all genotypes falling in the set is at least 1-α. This is the credible genotype set and is used to inform database search criteria. Within this work we demonstrate the salience of single-cell analysis by performance testing a set of 630 previously constructed admixtures containing up to 5 donors of balanced and unbalanced contributions. We use scEPGs that were generated by isolating single cells, employing a direct-to-PCR extraction treatment, amplifying STRs that are compliant with existing national databases and applying post-PCR treatments that elicit a detection limit of one DNA copy. We determined that, for these test data, 99.3% of the true genotypes are included in the 99.8% credible set, regardless of the number of donors that comprised the mixture. We also determined that the most probable genotype was the true genotype for 97% of the loci when the number of cells in a cluster was at least two. Since efficient investigative leads will be borne by posterior mass distributions that are narrow and concentrated at the true genotype, we report that, for this test set, 47,900 (86%) loci returned only one credible genotype and of these 47,551 (99%) were the true genotype. When determining the LR for true contributors, 91% of the clusters rendered LR>1018, showing the potential of single-cell data to positively affect investigative reporting.

Evaluation of Storage Conditions and the Effect on DNA from Forensic Evidence Objects Retrieved from Lake Water

DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, method for recovery, transport and storage routines of the objects before the objects arrive in the laboratory. The present study evaluated the effect of four storage conditions on the DNA retrieved from bloodstains, touch DNA, fingerprints and hairs, initially deposited on knives, smartphones, packing tapes, duct tapes and garbage bags, and submerged in lake water for three time periods. After retrieval, the objects were stored either through air-drying at room temperature, freezing at -30 °C, in nitrogen gas or in lake water. The results showed that the submersion time strongly influenced the amount and degradation of DNA, especially after the longest submersion time (21 days). A significant variation was observed in success for STR profiling, while mtDNA profiling was less affected by the submersion time interval and storage conditions. This study illustrates that retrieval from water as soon as possible and immediate storage through air-drying or freezing before DNA analysis is beneficial for the outcome of DNA profiling in crime scene investigations.

DNA identification from dental pulp and cementum

Teeth are one of the body tissues remaining after severe decomposition from which a DNA profile can be obtained to aid in human identification. Currently, the standard approach to isolate DNA from teeth requires pulverizing the entire tooth. This destructive approach compromises any further morphological or anthropological study. We report on two methods of DNA isolation that minimizes destruction of the tooth when accessing the DNA within pulp and cementum. Forty-nine teeth, removed as part of normal dental procedures, were buried for up to 92 days, with a further nine teeth acting as unburied controls. Additionally, four teeth samples collected during a forensic examination were included in this study. The two processes were: using a fine drill to access the pulp from the crown and then using endodontic files to collect the biological material; and using a sterile blade to scrape the cementum. It was found that the samples collected from the cementum had greater DNA quality compared to those samples obtained from the pulp. Microbial activity was found to play a role in the degradation of the nuclear material, reducing DNA yields from pulp. DNA profiling data from 24 loci, including 22 STR markers, indicated that multi-rooted teeth provided better DNA quantity and quality than those with a single root. The DNA quantity obtained from pulp samples of teeth which exhibited cavities was adversely affected, although this DNA loss was not from samples collected from the cementum of teeth in similar condition. Obtaining samples from DNA profiling from the cementum was found to be ideal if the morphological preservation of the tooth is required. Obtaining pathogen DNA is of interest when an occlusal approach to retrieve pulp may serve as a good alternative to prepare DNA without destruction of the tooth structure.

Development of specific and rapid detection of human DNA by recombinase polymerase amplification assay for forensic analysis

The determination of human-derived samples is very important in forensic investigations and case investigation in order to determine vital information on the suspect and the case. In this study, we established a recombinase polymerase amplification (RPA) assay for rapid identification of human-derived components. The sensitivity of the assay was 0.003125 ng, with excellent species specificity, and human-derived DNA could be detected in the presence of non-human-derived components at a ratio of 1:1000. Moreover, the RPA assay had a strong tolerance to inhibitors, in the presence of 800 ng/μL humic acid, 400 ng/μL tannic acid, and 8000 ng/μL collagen. In forensic investigation, common body fluids (blood, saliva, semen, vaginal secretions) are all applicable, and the presence of DNA can be detected from samples after simple alkaline lysis, which greatly shortens the detection time. Four simulation and case samples (aged bones, aged bloodstains, hair, touch DNA) were also successfully applied. The above research results show that the RPA assay constructed in this study can be fully applied to forensic medicine to provide high sensitivity and applicability detection methods.

The Revolution of Animal Genomics in Forensic Sciences

Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.

Development of Improved DNA Collection and Extraction Methods for Handled Documents

Handwritten documents may contain probative DNA, but most crime laboratories do not process this evidence. DNA recovery should not impair other evidence processing such as latent prints or indented writing. In this study, single fingermarks on paper were sampled with flocked swabs, cutting, and dry vacuuming. In addition, two extraction methods were compared for the sample type. DNA yields were low across all methods; however, this work confirms the ability to recover DNA from paper and the usefulness of the vacuum sampling method combined with the Chelex-Tween method. Stability of touch DNA deposits were compared over an 11-month period to better understand degradation that may occur over time. No significant difference in DNA recovery was observed, suggesting DNA deposits on paper are stable over an 11-month span.

One-step endpoint RT-PCR assays for confirmatory body fluid identification

Messenger RNA (mRNA) expression analysis is increasingly used in casework, in the form of multiplex two-step reverse transcriptase PCR (RT-PCR) assays such as CellTyper 2 (CT2), developed by the Institute of Environmental Science and Research (ESR). This paper presents the development of a one-step endpoint RT-PCR workflow to improve the efficiency and precision of confirmatory body fluid identification. A comparative study of commercial one-step RT-PCR kits was undertaken, with the highest performing kit (RNA to C_T) retained for further development. Sensitivity, specificity across body fluids, and precision was assessed simultaneously using receiver operating characteristic (ROC) curves. An optimal RFU cut-off value which maximised sensitivity and specificity was determined for each marker. All assays performed significantly better when compared to the equivalent of a completely uninformative test (area under the curve of 0.5) for their target body fluid. Sensitivity varied between different donors, but the limit of detectionss were estimated as follows; saliva markers HTN3: 1 in 100 dilution of a whole buccal swab and FDCSP: 1 in 10 dilution of a whole buccal swab, circulatory blood marker SLC4A1: 0.1 µL blood, menstrual fluid markers STC1, MMP10: 1 in 10 dilution of a whole menstrual swab, spermatozoa markers PRM1, TNP1: 0.1 µL semen, seminal fluid markers KLK2: 0.1 µL semen and MSMB: 0.01 µL semen, and vaginal material marker CYP2B7P: 1 in 1000 dilution of a whole vaginal swab. The method successfully detected most body fluids in a range of simple mixtures with 77 out of 80 markers observed when expected. The developed one-step endpoint RT-PCR assays lack the sensitivity and precision required for forensic casework and provide little benefit when compared with standard two-step endpoint RT-PCR, other than minimal time and cost savings, similar sensitivity, and improved precision for some markers. As both methods utilise endpoint RT-PCR, they have the same narrow linear dynamic range. The novel method is therefore similarly susceptible to varied RNA input, a major disadvantage of this approach. The limited sensitivity and precision consistently encountered with endpoint RT-PCR - regardless of cDNA synthesis strategy - could be addressed by a real-time PCR approach.

Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software

For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.

Identification and characterization of novel DIP-STRs from whole-genome sequencing data

In an attempt to enhance forensic DNA mixture deconvolution several alternative DNA typing approaches have been developed. Among these, DIP-STR compound markers can resolve extremely unbalanced two-source DNA mixtures of same-or-opposite sex donors, up to a 1:1000 minor:major DNA ratio. A forensic set of 10 markers was validated for casework and a larger set of 23 DIP-STRs has proven suitable to biogeographic ancestry inference and for prenatal paternity testing. Yet, to promote the widespread use of this original approach, more markers and multiplex panels need to be developed. To this end, here we describe an extended set of forensic DIP-STRs identified using currently available whole-genome sequencing datasets. Complete lists of Indels and STRs were obtained from reported frequencies of genetic variants of 76,156 genomes. About 3000 identified DIP-STRs candidates were shorter than 200 bp and 500 showed high haplotype variability estimated using the genotypes of individuals homozygous for the DIP or the STR. Here, we present 23 additional DIP-STRs validated for sensitivity, specificity and Swiss population variability. Finally, a set of 30 markers comprising seven previously validated ones is proposed for the prospective development of a forensic DIP-STR multiplex panel.

Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples

Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts.

Comprehensive analysis of microsatellite polymorphisms in human populations

Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, and genotyping methods for MS have yet to be established. Here, we analyzed approximately 8.5 million MS regions using a previously developed MS caller for short reads (MIVcall method) for three large publicly available human genome sequencing data sets: the Korean Personal Genome Project, Simons Genome Diversity Project, and Human Genome Diversity Project. Our analysis identified 253,114 polymorphic MS. A comparison among different populations suggests that MS in the coding region evolved by random genetic drift and natural selection. In an analysis of genetic structures, MS clearly revealed population structures as SNPs and detected clusters that were not found by SNPs in African and Oceanian populations. Based on the MS polymorphisms, we selected MS marker candidates for individual identification. Finally, we applied our method to a deep sequenced ancient DNA sample. This study provides a comprehensive picture of MS polymorphisms and application to human population studies.

Applied Biosystems' GlobalFiler™ PCR Amplification Kit

The GlobalFiler™ PCR Amplification Kit is one of the most sensitive kits that exist today that makes the PCR amplification of human DNA possible. PCR amplification using this specific kit makes millions of copies of 24 specific target sequences in the DNA, called markers or loci. This kit is a 6-dye, short tandem repeat (STR) multiplex assay kit that has a synthetic mix of primers and single-stranded oligonucleotides that are combined with DNA samples and then subjected to 29 or 30 cycles of denaturing, annealing, and extension, as per laboratory protocol. Methods for instrument operation will vary depending on the thermal cycler instrument model that is used. Nevertheless, the GlobalFiler™ PCR Amplification Kit has proven to be a very useful tool to DNA analysts, amplifying extremely low quantities of DNA, making it possible to detect partial, if not full, genetic profiles from a wide range of sample types. This chapter discusses the typical preparation and PCR amplification of human forensic DNA samples, using the GlobalFiler™ PCR Amplification Kit.

Developmental Validation of the Novel Five-Dye-Labeled Multiplex Autosomal STR Panel and Its Forensic Efficiency Evaluation

Short tandem repeats (STRs) are the most frequently used genetic markers in forensic genetics due to their high genetic diversities and abundant distributions in the human genome. Currently, the combined DNA index system is commonly incorporated into various commercial kits for forensic research. Some novel STRs that are different from the combined DNA index system were not only used to assess complex paternity cases but also could provide more genetic information and higher forensic efficiency in combination with those commonly used STRs. In this study, we validated forensic performance of a novel multiplex amplification STR panel to evaluate its sensitivity, species specificity, forensic application values, and so on. Obtained results revealed that the kit showed high sensitivity, and the complete allelic profile could be observed at 0.125 ng DNA sample. In addition, the kit possessed high species specificity, good tolerance to common inhibitors, and accurate genotyping ability. More importantly, STRs out of the kit displayed high discrimination power and probability of exclusion. To sum up, the novel kit presented in this study can be viewed as a promising tool for forensic human identification and complex paternity analysis.

Comparison between various DNA sterilization procedures applied in forensic analysis

Background

The advanced sensitive STR kits applied in forensic DNA typing techniques can cause challenging issues when evidence samples are contaminated with minute quantities of DNA from another source such as forensic analysts or crime scene examiners.

Results

In this study, laboratory air and surfaces, gloves, tools, and equipment were evaluated as potential sources of contaminating DNA. Different sterilization methods were tested for their ability to efficiently eliminate DNA in a sample. Inactivation methods included 10% bleach, ethanol, UV light, and DNA-ExitusPlus IF. Exposure to the different inactivation protocols for varying periods of time was performed in two lab settings: low template DNA and DNA database labs. Surfaces were swabbed and any adhering DNA was quantified using HID real-time PCR. Results were detected using HID Real-Time PCR Analysis Software v1.2 and GeneMapper ID-X Software v1.4.

Conclusions

It was concluded that most of the DNA decontamination methods are not suitable for highly sensitive and precision STR kits such as GlobalFiler PCR Amplification Kit. The most suitable tested method was using DNA-ExitusPlus IF with the incubation time increased from 10 to 15 min.

Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene^®, for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon^® for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells.

A DNA-based method for distinction of fly artifacts from human bloodstains

Fly artifacts resulting from insect activity could act as confounding factors on a crime scene and interfere with bloodstain pattern analysis interpretation. Several techniques have been proposed to distinguish fly artifacts from human bloodstains based on morphological approach and immunological assay, but a DNA-based method has not been developed so far. Even if in forensic genetic investigations the detection of human DNA is generally the primary goal, fly artifacts can provide useful information on the dynamics of crime events. The present study provides a molecular method to detect fly DNA from artifacts deposited by Calliphora vomitoria after feeding on human blood through the analysis of the mitochondrial cytochrome oxidase gene subunit I (COI). Fly artifacts originated from digestive process and of different morphology spanning from red and brownish/light brown, circular and elliptical stains to artifacts with sperm-like tail or a tear-shaped body were collected. The COI amplification was successfully obtained in 94% of fly artifact samples. The method showed high sensitivity and reproducibility, and no human DNA contamination was observed, offering specificity for use in confirmatory test. This molecular approach permits the distinction of fly artifacts from genuine bloodstains and the identification of fly's species through the COI region sequencing by protocols usually applied in forensic genetic laboratories.

Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq

Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.

A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples

Short tandem repeats (STRs) are the most widely used genetic markers in forensic application, but they are not ideal genetic markers for the analysis of forensic challenging samples such as highly degraded or unbalanced mixed samples because of their relatively large amplicons and stutter peaks. In this study, we developed a set of short microhaplotypes based on non-binary SNPs with molecular extent sizes no longer than 60 bases and genotyped 100 unrelated individuals from northern Han groups. Our results showed this panel has similar discrimination power to STR kits, as the combined random match probability (CMP) reached 1.396 × 10^-22 and mean effective number of alleles (Ae) was 3.59. The cumulative probability of exclusion for duos (CPE-duos) was 0.999919 and the cumulative probability of exclusion for trios (CPE-trios) was 0.9999999987, suggesting this panel could be applied for forensic personal identification and parentage testing independently. Population differentiation in 26 populations from the 1000 Genomes Project indicated this panel could distinguish populations from Africa, East Asia, South Asia, America, and Europe. These microhaplotypes based on non-binary SNPs have short amplicons, good discrimination power, no stutter artifacts, and have great potential in detection of highly degraded and unbalanced mixtures for personal identification, paternity testing, and ancestry inference.

Validation of the Applied Biosystems RapidHIT ID instrument and ACE GlobalFiler Express sample cartridge

Rapid DNA platforms are fully automated systems capable of processing DNA from biological samples and interpreting the results in approximately 90 minutes with minimal human intervention. With a greater reliance on the system than on the analyst, validation data are especially needed to define the performance and limitations of commercially available Rapid DNA systems. Thus, validation studies of a Rapid DNA workflow consisting of the Applied Biosystems RapidHIT ID Instrument and RapidLINK software with a focus on the ACE GlobalFiler Express Sample Cartridge and reference buccal swabs were performed in accordance with Scientific Working Group on DNA Analysis Methods Validation Guidelines. These validation studies included assessments of sensitivity, contamination, concordance, reproducibility and repeatability, stability, inhibition, mixtures, sample reprocessing, precision, and first-pass success rate. Overall, the current Applied Biosystems RapidHIT ID Instrument with the ACE GlobalFiler Express sample cartridge was found to be a reliable tool for generation of STR profiles from reference-type buccal swabs.

Development and validation of novel 8-dye short tandem repeat multiplex system for forensic applications

DNA profiling of short tandem repeats (STRs) is the primary method for genotyping forensic samples. However, degraded DNA and trace samples are still major problems for commercial 5- or 6-dye STR kits. In order to improve the performance of this method, we developed a novel 8-dye STR multiplex system containing 18 autosomal loci (D3S1358, D1S1656, TPOX, D16S539, vWA, D6S1043, D2S1338, CSF1PO, D19S433, D7S820, FGA, D8S1179, D5S818, D13S317, TH01, D21S11, D12S391, and PentaD) and the sex-determining locus Amelogenin, with all fragments smaller than 330 bases. Validation was carried out as recommended by the Scientific Working Group on DNA Analysis Methods. The results showed that complete profiles were obtainable when the input DNA was as low as 0.0625 ng. Full profiles were obtained even in the presence of inhibitors such as humic acid (< 300 ng/μl), hematin (< 100 μM), and indigo (0.01%). The 8-dye STR multiplex system also showed good performance in the detection degraded DNA samples. These results indicate that the 8-dye STR multiplex system is suitable for human DNA genotyping, including for difficult forensic materials.

OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)

Opium poppy (Papaver somniferum L.) is a versatile plant exploited by the pharmaceutical and food industries. Unfortunately, it is also infamously known as a source of highly addictive narcotics, primarily heroin. Drug abuse has devastating consequences for users and also has many direct or indirect negative impacts on human society as a whole. Therefore, developing a molecular genetic tool for the individualization of opium poppy, raw opium or heroin samples could help in the fight against the drug trade by retrieving more information about the source of narcotics and linking isolated criminal cases. Bioinformatic analysis provided insight into the distribution, density and other characteristics of roughly 150 thousand microsatellite loci within the poppy genome and indicated underrepresentation of microsatellites with the desired attributes. Despite this fact, 27 polymorphic STR markers, divided into three multiplexed assays, were developed in this work. Internal validation confirmed species-specific amplification, showed that the optimal amount of DNA is within the range of 0.625-1.25 ng per reaction, and indicate relatively well balanced assays according to the metrics used. Moreover, the stutter ratio (mean + 3 SD 2.28-15.59%) and allele-specific stutters were described. The analysis of 187 individual samples led to the identification of 158 alleles in total, with a mean of 5.85 alleles and a range of 3-14 alleles per locus. Most of the alleles (151) were sequenced by the Sanger method, which enabled us to propose standardized nomenclature and create three allelic ladders. The OpiumPlex system discriminates most of the varieties from each other and pharmaceutical varieties from the others (culinary, dual and ornamental).

Applicability of human-specific STR systems, GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee (Pan troglodytes)

OBJECTIVES

Human identification systems based on STRs are widely used in human population genetics and forensic analysis. This study aimed to validate the cross-reactivity of three widely known human-specific STR identification systems i.e. GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee.

RESULTS

The present study revealed the successful amplification of 18 loci using GlobalFiler™ PCR Amplification Kit, 18 loci using Investigator 24plex QS Kit, and 20 loci using PowerPlex® Fusion 6C system. The marker Amelogenin (AMEL) showed differential allele size between male and female revealing the gender identity of chimpanzees and thus validates their application concerning forensic examination, population estimation, and genetic analysis.

Diversification of Pakistani Amelogenin-Y-Null Male Haplotypes

Amelogenin is a common sex typing marker encountered in forensic case work. Phenotypically normal males have been reported in the literature who exhibit anomalous amelogenin allele. These males express only a single amelogenin peak representing AMEL-X and are called as AMEL-Y-null males. Gender misclassification of such individuals is an obvious consequence of this mutation, as a male sample would falsely appear to be a female sample. This study was aimed to attribute the AMEL-Y-null male DNA profiles encountered in forensic casework in the Pakistani population to appropriate phylogenetic clade based on shared ancestry. A total of 18 null AMEL-Y males were screened out of the sample pool of 5000 male individuals, reflecting mutational frequency of 0.36%. A common phylogenetic ancestor is suggested for 17 individuals, based on computational analysis of the Y-STR haplotypes, shown to be belonging to the J haplogroup while only one sample belonged to the R group. The samples in J groups showed homology with subclades J2b2a M241 and J2b2a PH1648, while R group individual showed 100% homology with R1a. Data are reported after haplotype network development of AMEL-Y-null Pakistani males using Network 10.0 for the study of evolutionary distances and emergence of nodes.