Routine Forensic Analysis Research Articles

Investigating the capability of UA-DLLME and DART-HRMS in the analysis of benzodiazepines in whole human blood

Benzodiazepine (BZD) misuse has increased in the last decade, making its occurrence in criminal cases more commonplace. The detection of BZD in complex biological samples is challenging since they are usually found in small concentrations, requiring the development of sensitive and fast-to-execute methods. In this study, the application of direct analysis in real time – high-resolution mass spectrometry (DART-HRMS) was evaluated in the detection of 10 benzodiazepines (diazepam, oxazepam, chlordiazepoxide, temazepam, alprazolam, flunitrazepam, bromazepam, clonazepam, lorazepam, and midazolam) in ante and postmortem blood samples. Moreover, an ultrasound-assisted dispersive liquid–liquid microextraction (UA-DLLME) approach was developed by full factorial design as a clean-up step before the DART-HRMS analysis. DART-HRMS was capable of qualitative detection of all evaluated BZD in raw antemortem blood samples at concentrations as low as 10 µg mL−1. The UA-DLLME DART-HRMS approach was linear for the 10 BZD in the range of 1 to 10 µg mL−1, with recoveries ranging from 78.5 to 119.5 %, a precision lower than 36 % at 1 µg mL−1, and limits of detection varying between 0.25 and 0.50 µg mL−1. Moreover, the UA-DLLME DART-HRMS method was efficiently applied to postmortem blood samples from criminal cases, enabling the detection of BZD. The developed method facilitated the analysis of 10 BZD in ante and postmortem blood samples, offering a quick sample extraction that linked to the DART-HRMS can be used as a fast and reliable triage method for regulatory screening purposes and could be readily integrated into routine forensic analysis workflows in a high throughput manner.

Practical benzylation of N,N-substituted ethanolamines related to chemical warfare agents for analysis and detection by electron ionization gas chromatography-mass spectrometry.

The benzylation of three low molecular weight N,N-disubstituted ethanolamines related to chemical warfare agents (CWAs) to furnish derivatives with improved gas chromatography-mass spectrometry (GC-MS) profiles is described. Due to their low molecular weight and polar nature, N,N-disubstituted ethanolamines are notoriously difficult to detect by routine GC-MS analyses during Organisation for the Prohibition of Chemical Weapons (OPCW) proficiency tests (PTs), particularly in scenarios when they are present at low levels (~1-10 ppm) amidst more abundant interferences. Our studies revealed that the optimal derivatization conditions involved the treatment of the ethanolamine with benzyl bromide in the presence of an inorganic base (e.g., Na2 CO3 ) in dichloromethane at 55°C for 2 h. This optimized set of conditions was then successfully applied to the derivatization of N,N-dimethylethanolamine, N,N-diethylethanolamine and N,N-diisopropylethanolamine present separately at 1 and 10 μg/mL concentrations in a glycerol-rich matrix sample featured in the 48th OPCW PT. The benzylated derivatives of the three ethanolamines possessed retention times long enough to clear the massive glycerol-containing matrix interferences. The protocol herein is introduced as an alternative method for derivatization of these CWA and pharmaceutically important species and should find broad applicability in laboratories where routine forensic analysis is carried out.

Changes in methamphetamine impurity profiles induced by tert-butoxycarbonylation.

Analysis of impurities in methamphetamine (MA) can be used to characterize MA seizures, investigate the relationship among MA seizures, and provide information on their synthetic routes. Recently, chemically derivatized MA, such as tert-butoxycarbonyl (t-Boc) MA, has been seized and attracted attention because routine forensic analysis methods may fail to correctly identify them. Chemical derivatization is a simple method for protection and deprotection of a compound, and protection of MA using t-Boc can be used to mask the MA. Although t-Boc derivatization might alter the impurity profile of MA, the actual changes in the impurity profile have not been investigated. In this study, changes in the MA impurity profile with tert-butoxycarbonylation were explored. MA and some typical impurities were derivatized using di-tert-butyl dicarbonate and water. Analysis of the impurities in five MA samples by gas chromatography showed that peaks both appeared and disappeared for the deprotected MA compared with the original MA. However, typical impurities important for characterizing MA seizures were conserved after derivatization and deprotection. Most of the new peaks were speculated to be contaminants introduced during derivatization and deprotection. A peak giving a mass spectrum similar to that of t-Boc MA was detected in the chromatograms of t-Boc MA and deprotected MA. Although the origin of this peak was not determined, it might be a marker for the MA involving tert-butoxycarbonylation. These results indicate that tert-butoxycarbonylation can alter the MA impurity profile; therefore, care is needed when interpreting results for derivatized MA.

A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples

An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen’s biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method—for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible—is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.

Validation of a novel fluorescent probe-based real-time PCR assay to detect saliva-specific unmethylated CpG sites for saliva identification

The identification of saliva from forensic samples is often important to establish what happened at a crime scene, especially in sexual assault cases. Recently, CpG sites that are specifically methylated or unmethylated in saliva have been reported as markers for saliva identification. In this study, we designed a fluorescent probe-based real-time polymerase chain reaction (PCR) assay for analyzing the methylation status of two neighboring CpG sites, which we previously found were saliva-specifically unmethylated. Specificity analysis using various types of body fluid/tissue samples demonstrated a probe detecting the unmethylation of the two CpG sites reacted only to saliva DNA, indicating this probe as an all-or-nothing marker for the presence of saliva DNA. Sensitivity analysis demonstrated that the detection limit was 0.5 ng saliva DNA as input for bisulfite conversion, while we confirmed a negative effect of larger amounts of non-saliva DNA on sensitivity in the analysis of saliva–vaginal DNA mixtures. We finally validated the applicability of this test to swabs from licked skin and bottles after drinking as mock forensic samples in comparison with other saliva-specific markers. We confirmed the potential usefulness of this test for skin samples, from which a saliva-specific mRNA was not detected reliably, while the ingredients in several beverages might affect methylation analysis. Given the simplicity of real-time PCR as well as the high specificity and sensitivity of the test, we believe the developed method is suitable for routine forensic analysis and can play an important role in saliva identification.

Evaluation of face masks as a valuable forensic DNA evidence in the post-COVID era.

After the onset of COVID-19 pandemic, a sharp surge in the usage of the face-masks throughout the globe has been observed. Pre-experiment survey of 252 individuals indicated a higher use of cotton-make masks (41%), followed by N-95 make (31%), and surgical disposable masks (26%). It was also further revealed that a higher fraction of individuals wear a face-mask more than 3 times (37%) before its disposal. In order to assess the potential usability of different mask types as forensic DNA evidence, a study was conducted on 50 healthy individuals. DNA content of different fractions such as the portion of mask covering the mouth region and the ear-piece showed a good source of host DNA. Though no statistically significant difference (P < 0.05) was found in the DNA quantity obtained from different face mask types, an increasing trend was obtained in the order: cloth make type (7.031 ± 0.31ng), N-95 make (4.711 ± 0.15ng), and surgical disposable type (2.17 ± 0.13ng). The time of wearing of a face-mask showed a positive correlation with the yield of DNA irrespective of the face-mask type used. Samples retrieved from both the portions covering the mouth area and the ear-piece showed a good source of genomic DNA yielding an average of 4.82 ± 0.11ng and 4.44 ± 0.10ng of DNA, respectively. Irrespective of the face-mask types, number of reuse, and the portion of the mask, 66.66-96.11% of samples showed a complete autosomal STR DNA profile. This suggests that if a face-mask is found at the crime scene, it should be collected and preserved as a potential source of DNA evidence for routine forensic DNA analysis.

Frequency of Newborn Fentanyl Exposure and Coexposure to Other Drugs of Abuse

Prenatal exposure to fentanyl may lead to neonatal abstinence syndrome (NAS), a constellation of symptoms observed when newborns begin withdrawing from addictive substances such as opioids. The use of umbilical cord (UC) tissue segments for newborn toxicology has been increasing due to its apparent long detection window, sensitivity, and ease of collection. However, very little has been reported in the literature concerning the prevalence of in utero exposure to fentanyl and coexposure to other commonly abused substances. The specific aims of this retrospective study are twofold. We will report prevalence of neonatal exposure to fentanyl for a nationwide high-risk population using UC submitted to a national reference laboratory for routine forensic toxicology analysis and the coexposure patterns observed for these fentanyl-exposed neonates.

Independent development and validation of a novel six-color fluorescence multiplex panel including 61 diallelic DIPs and 2 miniSTRs for forensic degradation sample.

Current forensic DNA profiles are obtained based on analyses of PCR product sizes or DNA sequence polymorphisms. Sometimes routine forensic analysis using short tandem repeat (STR) generates unsuccessful DNA testing result if the biological sample encountered is excessively degraded and low-template DNA. Herein, a new six-color fluorescence labeling system, including 59 autosomal diallelic deletion or insertion polymorphisms (DIPs), 2 miniSTRs, 2 Y-chromosome DIPs, and 1 Amelogenin gene with the amplicon sizes of less than 200bp, was self-developed. According to the validation guidelines for DNA analysis methods formulated by the Scientific Working Group on DNA Analysis Methods, the validation studies have also been carried out for the multiplex system. This novel panel possessed the features of strong stability, high sensitivity, and good specificity, which was especially suitable for the forensic degraded and mixed sample detections. The cumulative power of exclusion and cumulative matching probability of the system were 0.9999978 and 9.833E-28, respectively, in Han Chinese in Hunan, China. Moreover, this system will be an effective new tool that can be independently applied to forensic personal identification and paternity testing in the populations from the East Asia region, even from the South Asia, America, and Europe regions. The system can also contribute to population phylogenetic affinity and genetic structure analyses among different populations.

Effect of ozone disinfection on forensic STR profiling

While good laboratory practice in a forensic lab minimises the chance of infection of laboratory personnel, in certain cases, possible contamination of pieces of evidence with highly contagious pathogens might call for additional precautions. The number of potential disinfection methods that might be suitable for forensic genetics are surprisingly limited. First and foremost, the ideal technique should not inhibit DNA amplification, it should be effective against a host of pathogens, and it should be applicable on porous surfaces.We examined ozone treatment on extracted DNA samples and mock casework samples. Ozone-treated and control specimens were amplified with Qiagen Investigator ESSplex SE QS kit. Detected allele counts were compared between the treated and untreated sample groups.Following disinfection, concentration of ozone-treated DNA was about half of the control samples, but full STR profiles were recovered. In the case of mock casework samples (disposable surgical masks), there was no significant difference (p = 0.513) between the detected allele counts of control and ozone-treated samples. Sampling location of surgical masks (earloop, nosepiece) showed a statistically significant difference (p = 0.011), though. Comparing the effect of contributors on STR profiling, a significant difference (p = 0.001) was observed, which could be explained with the differences between individuals including shedding capacity, head size or shape.According to our pilot study, ozone treatment does not encumber the routine forensic DNA analysis, the sampling position or the contributor affected the allele counts more than the ozone treatment.

PCR combined with lateral flow immunochromatographic assay to differentiate the narcotic Mitragyna speciosa from related species and detect it in forensic evidence

Plants in the genus Mitragyna (Rubiaceae) are used in traditional medicine because of their broad therapeutic activity. Four Mitragyna species, M. speciosa (Roxb.) Korth. (MS), M. rotundifolia (Roxb.) Kuntze (MR), M. diversifolia (Wall. ex G. Don) Havil. (MD), and M. hirsuta Havil. (MH), occur in Thailand. M. speciosa, commonly known as ‘Kratom’ in Thai, is the only narcotic species for which buying, selling, importing or possessing has been prohibited by law in Thailand and some other countries. Mitragynine and 7-hydroxymitragynine, the major psychoactive compounds, are important in the treatment of opioid withdrawal. However, this species is used in traditional medicine to relieve pain and inflammation. Consequently, a rapid and easy technique for differentiating M. speciosa from closely related species is needed for routine forensic analysis. In this study, polymerase chain reaction coupled with lateral flow immunochromatographic assay (PCR-LFA) based on matK was developed for the detection of M. speciosa in forensic specimens. Duplex primers (MS-F-FAM, Ctrl-F-DIG and Ctrl-R-Biotin) were designed based on species-specific nucleotide indels observed exclusively in the matK sequences of M. speciosa. Positive results for M. speciosa are indicated by the clear presence of three black lines on the lateral flow cassette. Forensic samples were investigated, and the three black test lines indicating M. speciosa were observed for seven of eight specimens. PCR-LFA has been proven to be fast, easy and efficient for detecting the narcotic M. speciosa and could be developed as a rapid forensic diagnostic technique for other plants.

GC-MS – Still standing for clinical and forensic analysis: validation of a multidrug method to detect and quantify illicit drugs

ABSTRACT An SPE-GC-MS analytical method using whole blood samples has been developed and validated to detect and quantify nineteen compounds belonging to the Drugs of Abuse (DA) groups of cocaine and metabolites, opiates and new psychoactive substances (NPS). The method detailed here is necessary because the recreational consumption of these DA has increased considerably in recent years and poly-drug-consumption is now very common. The method developed was both specific and selective. Three different working ranges have been defined due to the differences between therapeutic, toxic and lethal concentrations of DA. Linearity was confirmed for the defined working ranges of all DA, except pseudoephedrine, ephedrine, norephedrine, and TFMPP. Since the remaining nineteen substances showed heteroscedasticity, six ponderation factors were studied to find the best fit for each compound. Limits of Detection and Lower Limits of Quantification have been studied and defined. No carryover was noted, with acceptable extraction recoveries. The achievement of all validation criteria according to international guidelines allows the application of the proposed method in routine forensic analysis. Using this method can also significantly reduce response times and GC-MS analysis costs.

Mitochondrial DNA in forensic use.

Genetic analysis of mitochondrial DNA (mtDNA) has always been a useful tool for forensic geneticists, mainly because of its ubiquitous presence in biological material, even in the absence of nuclear DNA. Sequencing, however, is not a skill that is part of the routine forensic analysis because of the relative rarity of requests, and the need for retention of necessary skill sets and associated accreditation issues. While standard Sanger sequencing may be relatively simple, many requests are made in the face of compromised biological samples. Newer technologies, provided through massively parallel sequencing (MPS), will increase the opportunity for scientists to include this tool in their routine, particularly for missing person investigations. MPS has also enabled a different approach to sequencing that can increase sensitivity in a more targeted approach. In these circumstances it is likely that only a laboratory that specialises in undertaking forensic mtDNA analysis will be able to take these difficult cases forward, more so because reviews of the literature have revealed significantly high levels of typing errors in publications reporting mtDNA sequences. The forensic community has set out important guidelines, not only in the practical aspects of analysis, but also in the interpretation of that sequence to ensure that accurate comparisons can be made. Analysis of low-level, compromised and ancient DNA is not easy, however, as contamination is extremely difficult to eliminate and circumstances leading to sequencing errors are all too easily introduced. These problems, and solutions, are discussed in the article in relation to several historic cases.

Development and Validation of a Gas Chromatographic Method for the Quantification of Minor Alkaloids in Cocaine

The quantification of minor alkaloids in seized cocaine can provide information for drug profiling and law enforcement initiatives. This work presents the development and validation of an analytical method to quantitate minor alkaloids in cocaine samples using gas chromatography with flame ionization detector, after derivatization. The method was validated in accordance with the ISO/IEC 17.025:2017 requirements. The calibration was linear (determination coefficient (R2) ≥ 0.998), ranging from 1.0 to 3,500 mg L-1 for all target analytes with suitable selectivity and precision (relative standard deviation lower than 10%). The method showed stability and robustness with respect to analytical parameter variations and presented good accuracy (recovery ranging from 90 to 108%). The method was considered adequate to routine forensic analysis in simultaneous quantification of anhydroecgonine methyl ester, anhydroecgonine, methylecgonine, tropacocaine, norcocaine, N-formylcocaine, trimethoxycocaine, ecgonine, benzoylecgonine, trans- and cis-cinnamoylcocaine. Eleven cocaine samples seized in different Brazilian regions were analyzed and their relative amounts of tropacocaine and trimethoxycocaine with respect to cocaine indicate both the possible varieties of coca leaf used for cocaine production and the likely origin of drug samples (Bolivia/Peru or Colombia). The contents of other minor alkaloids depict aspects of sample history such as purification by oxidation, hydrolysis and dehydration by thermal processes.

Optimization of QuEChERS extraction for detection and quantification of 20 antidepressants in postmortem blood samples by LC-MS/MS

In this study, a comprehensively optimization of QuEChERS (quick, easy, cheap, effective, rugged and safe) method using design of experiments (DOE) was conducted to evaluate the best conditions to obtain the most effective extraction. Liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) analysis was performed to identify and quantify the antidepressants, with electrospray ionization acquired in positive mode. The method was validated for all analytes; the calibration curves were linear from 10–1000ng/mL, with R2>0.98, and with LOD and LOQ defined as 10ng/mL. Method imprecision and bias were less than 14.3% and 18.9%, respectively. Neither carryover nor interferences were observed. Overall, the optimized method was applied in postmortem real sample analysis to quantify the antidepressants. This study showed a viable method that can be applied for routine forensic analysis, with a quick and easy sample preparation and a rapid total run time of 8min for each analysis.

Evaluation and applicability of Alere iCup DX 14 for rapid postmortem urine drug screening at autopsy

Performing point-of-care urine drug screen testing at autopsy by a forensic pathologist may provide an early indication of the presence of analytes of interest during autopsy. An evaluation for the screening of 14 classes of common drugs of abuse in postmortem urine by the point-of-care screening device, Alere iCup DX 14, is presented. One hundred ninety postmortem urine samples were screened with the iCup occurring at autopsy by the forensic pathologist. Positive and negative results obtained from the screening kit were evaluated against confirmatory test results obtained using routine forensic toxicology analyses that employed LC-MS/MS and GC-MS to detect a combination of over 85 common drugs of abuse and medications. Sensitivity for each respective iCup drug class ranged from 66% (buprenorphine) to 100% (methadone, tricyclic antidepressants). Specificity for each respective iCup drug class ranged from 89% (benzodiazepines) to 100% (amphetamines, barbiturates, buprenorphine, 3,4-methylenedioxymethamphetamine, methadone). Positive predictive values ranged from 44% (benzodiazepines) to 100% (amphetamines, barbiturates, buprenorphine, methylenedioxymethamphetamine, methadone), while negative predictive values ranged from 96% (methamphetamine) to 100% (barbiturates, methadone, tricyclic antidepressants). A high false-positive rate was yielded by the benzodiazepine class. The lack of fentanyl screening in the point-of-care device is a significant limitation considering its prolific prevalence in forensic casework. The results obtained in the study should be acknowledged when considering the use of the Alere iCup DX 14 in the context of postmortem casework to help indicate potential drug use contemporaneously with autopsy and when requiring such preliminary results prior to the release of a final forensic toxicology report.

Identification of a new class of thermolabile psychoactive compounds, 4-substituted 2-(4-X-2, 5-dimethoxyphenyl)-N-[(2-hydroxyphenyl)methyl]ethanamine (25X-NBOH, X = Cl, Br, or I) by gas chromatography-mass spectrometry using chemical derivatization by heptafluorobutyric anhydride (HFBA)

4-Substituted 2-(4-X-2,5-dimethoxyphenyl)-N-[(2-hydroxyphenyl)methyl] ethanamine (25X-NBOH, X = Cl, Br, or I) are new psychoactive substances (NPS). Identification of these NBOH analogues by gas chromatography-mass spectrometry is difficult because they are found in very low concentrations in the blotting paper in which they are sold, and because of the thermolabile nature of NBOH. In the ion source of a mass spectrometer they break down to the known NPS 2,5-dimethoxy-4-Xphenethylamine (2C-X) thereby giving no indication of the initial compound present. We identify 25XNBOH by heptafluorobutyric anhydride (HFBA) derivatization and subsequent mass spectrometric analysis. The major peak is the bis-derivative where both the amine and phenol are derivatized, with a minor peak of the mono-derivative in which only the amine is derivatized. There is a small amount of degradation of 25X-NBOH to the 2C-X amine which is then derivatized to the amide in-situ. Reaction with HFBA is an efficient and simple derivatization that works well with NBOH and NBOMe analogs and is recommended for routine forensic analysis.

Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System.

The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.

Distribution pattern of common drugs of abuse, ethyl glucuronide, and benzodiazepines in hair across the scalp.

While hair analysis is important and accepted in forensic applications, fundamental knowledge gaps still exist, exacerbated by a lack of knowledge of the incorporation mechanisms of substances into hair. The influence of the hair sampling location on the head on ethyl glucuronide (EtG) and cocaine concentrations was investigated by measuring the complete scalp hair of 14 (2 EtG, 4 cocaine, 8 both EtG and cocaine) study participants in a grid pattern for EtG, drugs of abuse, and benzodiazepines. Head skin perfusion and sweating rates were investigated to rationalize the concentration differences. For EtG, ratios between maximum and minimum concentrations on the scalp ranged from 2.5 to 7.1 (mean 4.4). For cocaine, the ratios ranged from 2.8 to 105 (mean 17.6). EtG concentrations were often highest at the vertex, but the distribution was strongly participant dependent. Cocaine and its metabolites showed the lowest concentrations at the vertex and the highest on the periphery, especially at the forehead. These differences led to hair from some head parts being clearly above conventional cut-offs and others clearly below. In addition to EtG and cocaine, the distributions of 24 other drugs of abuse and benzodiazepines/z-substances and metabolites are described. No clear pattern was observed for the head skin perfusion. Sweating rate measurements revealed higher sweating rates on the periphery of the haircut. Therefore, sweat could be a main incorporation route for cocaine. Concentration differences can lead to different interpretations depending on the sampling site. Therefore, the results are highly relevant for routine forensic hair analysis.

Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods

The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods’ results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.

X-chromosome data for 12 STRs: Towards an Argentinian database of forensic haplotype frequencies

The analysis of X-chromosome STRs is useful in certain kinship cases for which autosomal markers provide insufficient statistical power. Particularly, powerful results are achieved in paternity cases with a daughter, when the alleged father is not accessible for analysis, contrarily to his unquestioned mother or daughter. However, representative haplotype frequencies for this type of markers are not available for some populations, as is the case of Argentina, which prevents the quantification of the proof in routine forensic analyses. In this work we present haplotype frequencies for the 12 X-chromosome STRs included in the Investigator Argus X-12 kit, as well as segregation data, obtained from the analysis of the genetic profiles of 457 father-daughter duos, which gave us information on 914 (unrelated) haplotypes from residents of all Argentinian provinces.