Cytochrome b based genetic differentiation of Indian wild pig (Sus scrofa cristatus) and domestic pig (Sus scrofa domestica) and its use in wildlife forensics

The Indian wild pig (Sus scrofa cristatus) is a protected species and listed in the Indian Wildlife (Protection) Act, 1972. The wild pig is often hunted illegally and sold in market as meat warranting punishment under law. To avoid confusion in identification of these two subspecies during wildlife forensic examinations, we describe genetic differentiation of Indian wild and domestic pigs using a molecular technique. Analysis of sequence generated from the partial fragment (421 bp) of mitochondrial DNA (mtDNA) cytochrome b (Cyt b) gene exhibited unambiguous (> 3%) genetic variation between Indian wild and domestic pigs. We observed nine forensically informative nucleotide sequence (FINS) variations between Indian wild and domestic pigs. The overall genetic variation described in this study is helpful in forensic identification of the biological samples of wild and domestic pigs. It also helped in differentiating the Indian wild pig from other wild pig races. This study indicates that domestic pigs in India are not descendent of the Indian wild pig, however; they are closer to the other wild pig races found in Asia and Europe.     

Are these food products fraudulent? Rapid and novel triplex-direct PCR assay for meat identification

Unintentional contamination and fraudulent labeling of food, especially in halal-certified products, breach both religious and international laws. DNA-based methods are widely employed to identify trace amount of contaminants for law enforcement. Direct PCR has proved successful in the DNA analysis from degraded samples and PCR-inhibited samples, but it has never been applied to meat identification from food products. In this study, we aimed to develop a multiplex direct PCR assay for simultaneous identification of three commonly consumed meats without the need to extract DNA. Species-specific primers were designed from the mitochondrial DNA using the alignment of sequences available on GenBank. The assay was validated for its specificity, sensitivity, and usefulness in market sample analysis. The results showed that a highly specific and sensitive multiplex direct PCR assay was developed and provided the expected PCR fragment of approximately 100, 119, and 133 bp for pork (Sus scrofa), mutton (Ovis aries), and chicken (Gallus gallus), respectively. Thirty-nine market samples were tested and a small number of fraudulent labeling was detected. In conclusion, we developed a rapid and inexpensive test for three meat species. This cost- and time-saving assay could be easily adopted in the world food hubs, which are mostly third-world countries.     

Population genetic data of 38 autosomal InDels in San Basilio de Palenque,the first free town in America

In order to increase the information about Indels, we report allele frequencies and statistical parameters of forensic efficiency obtained typing a sample of 114 unrelated healthy individuals living in San Basilio de Palenque – Colombia using a panel of 38 autosomal InDels. No significant deviations from Hardy–Weinberg expectations were found except in the marker rs10629077 (p = 0.0002). The present database will be useful for forensic and paternity purposes for the region studied. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples.     

Genetic characterization of a population from Cauca Department with 15 STRs markers

This study established allele frequencies and some parameters of forensic interest with 15 autosomal STRs markers in a sample of 172 unrelated individuals from the Department of Cauca – Colombia using the PowerPlex^® 16 BIO System (Promega CO) and Qiagen Multiplex PCR (Qiagen) kits. All markers analyzed showed more than 61% of heterozygosity. Penta E and Penta D were the only systems that are not in Hardy Weinberg equilibrium (p < 0.0033) after Bonferroni correction. The probabilities of paternity (W), the power of exclusion (PE) and of discrimination (PD) accumulated for all loci analyzed were 0.9999, 0.9999 and >0.9999, respectively. The parameters of forensic interest have values suitable for routine use in forensic genetics.     

Detection of dermcidin for sweat identification by real-time RT-PCR and ELISA

We evaluated the performance of real-time RT-PCR and ELISA assays for detection of dermcidin (DCD) in sweat and body-fluid stains. DCD, a small antibiotic peptide secreted into human sweat, was detected by real-time RT-PCR in 7-day-old stains containing as small as 10 μL of sweat, and the assay showed high specificity when testing 7-day-old stains containing 30 μL of other body-fluid. ELISA using anti-human dermcidin mouse monoclonal antibody detected DCD sweat diluted up to approximately 10,000-fold and could specifically detect DCD in 10 μL of body-fluid stains. The performance of the two assays was tested during winter on samples that simulated forensic case samples: an undershirt and a sock worn for 20 h, a handkerchief used to wipe the brow several times within 12 h, a cap and a cotton glove worn for 4 h, and a white robe worn at intervals for 2 years. The result showed that the former assay detected DCD in all sites of the undershirt examined (armpit, back, and breast), and the latter gave a relatively high OD value in the armpit among the three sites. For the socks, although the latter assay gave very high OD values in both the center and toe of the foot sole, the former could not detect DCD in both of them. These results indicate that highly damp conditions, such as inside a shoe, might promote the degradation of mRNA in samples such as socks. In the other case samples, sweat was adequately detected by both assays.This study is the first demonstration of the use of real-time RT-PCR to sensitively identify sweat among body-fluid stains, and it confirmed that dermcidin was an excellent marker for sweat identification. In addition, the usefulness of ELISA was also verified. Positive sweat identification using these assays is expected to assist forensic practice.     

Soil forensics: How far can soil clay analysis distinguish between soil vestiges?

Soil traces are useful as forensic evidences because they frequently adhere to individuals and objects associated with crimes and can place or discard a suspect at/from a crime scene. Soil is a mixture of organic and inorganic components and among them soil clay contains signatures that make it reliable as forensic evidence. In this study, we hypothesized that soils can be forensically distinguished through the analysis of their clay fraction alone, and that samples of the same soil type can be consistently distinguished according to the distance they were collected from each other. To test these hypotheses 16 Oxisol samples were collected at distances of between 2 m and 1.000 m, and 16 Inceptisol samples were collected at distances of between 2 m and 300 m from each other. Clay fractions were extracted from soil samples and analyzed for hyperspectral color reflectance (HSI), X-ray diffraction crystallographic (XRD), and for contents of iron oxides, kaolinite and gibbsite. The dataset was submitted to multivariate analysis and results were from 65% to 100% effective to distinguish between samples from the two soil types. Both soil types could be consistently distinguished for forensic purposes according to the distance that samples were collected from each other: 1000 m for Oxisol and 10 m for Inceptisol. Clay color and XRD analysis were the most effective techniques to distinguish clay samples, and Inceptisol samples were more easily distinguished than Oxisol samples. Soil forensics seems a promising field for soil scientists as soil clay can be useful as forensic evidence by using routine analytical techniques from soil science.     

Genetic variation in a Japanese population,using the multiplex 24 STRs analysis system

Allele frequency distributions for 24 short tandem repeat (STR) loci were determined using the PowerPlex^R Fusion System (Promega) in 407 Japanese samples. The most informative locus among the 22 STR loci, excluding Amelogenin and DYS391, was Penta E (power of discrimination (PD) = 0.98), while the least informative was TPOX(PD = 0.831). The 22 loci combined matching probability (MP) was calculated to be 4.13 × 10⁻²⁶. These parameters indicated the usefulness of this 24 STR analysis in forensic personal identification and parentage testing among Japanese population.     

Forensic DNA laboratory automation – Principles and guidelines

There is a lack of clear guidelines for project managers, laboratory managers and forensic scientists on strategies for the automation of forensic DNA laboratory processes and operational implementation of new technologies. This is reflected in the failure rate of projects in the forensic DNA testing environment. We present a set of guidelines and concepts important for forensic laboratory automation. Some case studies from past projects are presented. These consist of partial (or modular) automation (n = 2) and full automated robotically integrated systems (n = 2).Technology Management principles and concepts are crucial to prevent failure of projects, e.g. early adoption of untried technologies, and organizational factors. The future of laboratory automation is modular until such time as new discontinuous technologies will replace the need of the traditional manual laboratory configuration in totality.     

Characterisation of forward stutter in the AmpFlSTR® SGM Plus® PCR

PCR amplification of tetrameric short tandem repeats (STRs) can lead to Taq enzyme slippage and artefact products typically one repeat unit less in size than the parent STR. These back stutter or n ? 4 amplification products are low-level relative to the amplification of the parent STR but are widely seen in the forensic community where tetrameric STRs are employed in the generation of DNA profiles. To aid the interpretation of DNA mixtures where minor contributor(s) might be present in comparable amounts to the back stutter products, the typical amounts of back stutter generated have been well characterised and guidelines for interpretation are in place. However, further artefacts thought to be Taq enzyme slippage leading to products with one repeat unit greater than the parent sequence (n + 4 or forward stutter) or two repeats less (n ? 8 or double back stutter) also occur, but these have not been well characterised despite their potential influence in mixture interpretations. Here we present findings with respect to these additional artefacts from a study of 10,000 alleles and include guidelines for interpretation.     

The acid phosphatase test two minute cut-off: An insufficient time to detect some semen stains

The ability to detect semen in sexual offence cases is a crucial first step to locating stains which may be suitable for DNA profiling. Since the development of the acid phosphatase test in the late1950s by Stuart S. Kind, the process undertaken to perform the test has gone largely unchanged. The method currently accepted by operational forensic science laboratories allows 2 min for a reaction to be obtained, and until relatively recently, this has not been challenged. In this research, samples of semen were obtained from three donors and a range of dilutions for each sample were prepared. Each dilution was subjected to acid phosphatase testing using both direct testing and the ‘press test’ method. The results showed that semen could be detected in excess of 15 min in dilutions up to 1 in 400 using the press test method and in dilutions up to 1 in 1000 using the direct method. Of further significance was the observation that using the press test method, the two minute cut-off was insufficient to detect the majority of stains and in some cases, semen stains as strong as 1 in 20 dilutions. This research provides compelling evidence for protocols currently utilised in forensic practice to be reviewed in order that forensic scientists do not overlook potential evidential material that may prove suitable for body fluid identification such as DNA STR profiling.     

Age estimation by pulp/tooth area ratio in canines: Cameriere's method assessed in an Indian sample using radiovisiography

Age estimation of an individual whether living or dead is an intimidating task in forensic investigations. Since teeth are more resistant to most peri- and post-mortem changes, they are frequently used for identification and age estimation when skeletal remains are in poor condition. However, most methods are destructive and warrant extraction of teeth which is not feasible in living individuals. Cameriere's et al. put forth a radiographic method of age estimation by pulp to tooth area ratio (AR) in canines and revealed a linear regression between age and the AR. In the present study, we estimated the AR in 456 canines (upper, lower and both) in an Indian sample (114 males and 114 females) using radiovisiography technique. Linear regression equations were derived for upper canine, lower canine and both using the AR to estimate chronological age. Additionally, the efficacy of these equations was also evaluated in younger age group (<45 years). The formulas derived, i.e., age = 96.795 ? 513.561x₁ (Eq. (1)) for upper canine, age = 88.308 ? 458.137x₂ (Eq. (2)) for lower canine and age = 99.190 ? 283.537x₁ ? 306.902x₂ + 400.873x₁x₂ (Eq. (3)) for both the canines were applied to predict the chronological age. The mean value of residuals using these regression equations ranged from 4.28 to 6.39 years with upper canine equation generally giving a precise result. When these equations were applied for younger ages (<45 years), the regression equation derived from both canines gave a better result (mean residual 2.70 years). Overall these equations were better able to predict the age in younger ages, i.e., up to 45 years.     

Forensic oral imaging quality of hand-held dental X-ray devices: Comparison of two image receptors and two devices

Recently, different portable hand-held and battery-powered dental X-ray units have become available. Especially for forensic odontological purposes, they offer diverse advantages such as for use in disaster areas and crime-scene locations as also in autopsy rooms and mortuaries. For any application, the most important feature of these hand-held devices is the delivered image quality. The aim of this study is to evaluate the radiographic image quality acquired by two portable X-ray devices in combination with two types of image receptors and to compare the findings with the image quality of a standard intra-oral X-ray device.Eleven samples consisting of eight teeth, two dry skeletal specimens and one formalin-fixed mandible part were mounted on blocks for standardised (re)positioning. Radiological images were acquired with two hand-held (AnyRay^® 60 kVp, 0.02–4.00 mAs and NOMAD^® 60 kVp, 0.023–2.277 mAs) and one wall-mounted (MinRay^® 60/70 kVp 0.14–22.4 mAs) X-ray device combined with two image receptor systems (VistaScan^® phosphor storage plate (PSP) and SIGMA^® M CMOS Active Pixel technology sensor). The effect of X-ray source-to-object distance (SOD) was checked at 20 cm in conjunction with object to image receptor distances (OIDs) of 0.8 and 2.5 cm. For each parameter setup, the exposure times were run from low till high. An expert consent statement was achieved by agreement of four expert observers selecting the optimal images based on a developed four point quality rating system. Next, a selection of the images was assembled in a set of 198 observation screens and scored by seven observers. The observation screens were designed to compare observer scores, relations between devices, receptors and OIDs and images obtained from the different devices at equal exposure levels (mAs). All results were statistically analysed.Radiological image quality was significantly higher for phosphor plate compared with the CMOS digital receptor system (p < 0.0001). Furthermore, a significantly superior image quality was obtained for OID = 0.8 than for OID = 2.5 (p = 0.039). A significant difference in image quality between the three devices was also established (p = 0.02). The present study demonstrated the feasibility of portable X-ray systems for forensic odontological applications based on rendering optimal image quality, provided an in vitro guideline of optimal parameter settings and offered a radiological image database usable in further research.     

Development and validation of highly selective screening and confirmatory methods for the qualitative forensic analysis of organic explosive compounds with high performance liquid chromatography coupled with (photodiode array and) LTQ ion trap/Orbitrap mass spectrometric detections (HPLC-(PDA)-LTQOrbitrap)

An LTQ-Orbitrap FTMS is a new (hybrid) mass spectrometric (MS) analyzer. It allows for the acquisition of full scan MSⁿ (n-stage fragmentations, n = 1 − n) spectra with the linear ion trap detector (LTQ) at high speed and/or with the Fourier Transform-detector (Orbitrap) with ultra high mass resolution (> 60,000 at m/z < 400 amu) and high mass accuracy (≤ 1 ppm with internal calibration). In addition it may be coupled with liquid chromatography (LC) with photo diode array (PDA) detection.Two methods for the forensic screening and confirmation of all common trace explosives in post-blast residues have been developed on this instrument using atmospheric pressure chemical ionization (APCI). In one run, the nitrogen-containing explosives are analyzed with the combination of “LC-(PDA)-APCI(−)-LTQ MS²/Orbitrap FTMS” (Method 1). In another run, peroxide explosives are analyzed with “LC-APCI(+)-LTQ MS²/Orbitrap FTMS” (Method 2).The performance of both methods has been validated according to procedures defined in the EU COMMISSION DECISION implementing Council Directive 96/23/EC concerning the performance of analytical methods and the interpretation of results (DC 2002/657/EC) and other standards (NEN 17025 and NEN 7777). The methods are highly selective due to the simultaneous utilization of the Orbitrap FTMS and LTQ MS², both of which are highly selective detectors Tested explosive compounds can be detected in the molecular ion form by the Orbitrap analyzer with minimal mass interference in different matrices when using an extremely narrow mass tolerance detection window (≤ 2 ppm). The identification of a detected compound follows an identification point system. Experimental results show that almost all explosive compounds meet the confirmation criteria (minimum 4 points) required for the positive identification by the DC 2002/657/EC.     

Duplex-specific nuclease (DSN): A method for the rehabilitation of low-copy number DNA profiles

A continual challenge in the field of forensic DNA analysis is the amplification and interpretation of degraded and low-copy number (LCN) DNA obtained from amounts of limited biological evidence. It has been well established that DNA profiles obtained from the amplification of low quality, degraded, and/or LCN DNA samples are often of limited value due to the frequent occurrence of preferential amplification during polymerase chain reaction (PCR). The by-products of preferential PCR amplification are often observed as inter- and intra-locus peak imbalance, allelic dropout, and/or locus dropout. These are all artifacts that are identified during the interpretation phase of analysis rather than by improving the quality of the DNA present. While it is theoretically possible to obtain a complete DNA profile from a single cell, in reality, profiles obtained from suboptimal amounts of DNA are difficult to interpret and frequently inconsistent when replicated. Inspired by advances in next-generation sequencing techniques, we propose a methodology for simultaneously normalizing the abundance of PCR products across all short tandem repeat (STR) loci using the DNA exonuclease, duplex-specific nuclease (DSN). DSN is an enzyme isolated from the hepatopancreas of Red King (Kamchatka) crab that possesses a strong affinity for digesting double stranded DNA (dsDNA) and has limited activity toward single stranded DNA (ssDNA). Degraded DNA known to display peak imbalance and allele dropout was amplified using AmpFlSTR^® Identifiler^® Plus for 28 cycles. Following amplification, samples were denatured at 99.9 °C for 5 min and incubated with one unit of DSN at 62 °C in a 28 μl volume for 1 min. Nuclease activity was terminated through the addition of equal volume of 10 mM EDTA and 95 °C incubation for 2 min. Following DSN treatment, 21 of 30 alleles within the known profile exhibited some improvement in peak height balance. The findings obtained support the potential use of DSN treatment as a method for normalizing STR profiles and improving the quality of data from degraded and low quantity DNA samples.     

Recovery of human DNA profiles from poached deer remains part 2: Improved recovery protocol without the need for LCN analysis

Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and amplified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and amplification protocol which removes the need for low template analysis.Samples from 10 deer (40 samples total — one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer samples. Four samples analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5 pg ± 43.2 pg, 31 × greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpF?STR® SGM Plus® kit at 30 cycles (Applied Biosystems). Re-analysis of the samples from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 samples, 71% of the samples analysed using the optimised protocol showed sufficient amplification for comparison to a reference profile and gave match probabilities ranging from 7.7690 × 10^? 05 to 2.2706 × 10^? 14.The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime samples. The technique is suitable for immediate use in poaching incidents.     

Estimation of legal age using calcification stages of third molars in living individuals

The increased number of adolescents and young adults with unknown or inaccurately given date of birth is a current issue in justice and legal medicine. The objective of this study was to determine the extent to which third molar calcification stages assessed on panoramic X-rays could be useful as additional criteria for forensic age estimation in living individuals, focusing on the legally important ages 17 and 18.In a retrospective multi-center study, the developmental stage of each individual's third molar was analyzed using Demirjian's scale in 2360 cases. Additionally, sex, age and ancestry were assessed.Individuals with the lowest calcification stage of all present molars in stage H were ≥ 18 years with a likelihood of ≥ 99.05% in the female (n = 388), and ≥ 99.24% in the male (n = 482) population.The lowest calcification stage of all present third molars proved to be useful as an additional reliable criterion for the determination of an age ≥ 18 years.     

A new 15 autosomal STRs multiplex for domestic horse genotyping

Horse genotyping has a wide range of applications such as identification, pedigree verification, parentage test, forensic investigation, population genetics, analysis of diversity, legitimate registration, among others. Following the recommendations of the International Society for Forensic Genetics (ISFG) regarding the use of non-human (animal) DNA in forensic genetic investigations we have developed a multiplex PCR system of 15 autosomal tetra-nucleotide STRs loci to Equus caballus. The system includes the newly described ECAC2, ECAC4, ECAC5, ECAC9, ECAC10, ECAC12, ECAC14, ECAC15, ECAC18, ECAC21, ECAC23, ECAC26, ECAC28, ECAC29 and ECAC30 loci (on chromosomes 2, 4, 5, 9, 10, 12, 14, 15, 18, 21, 23, 26, 28, 29 and 30, respectively). The polymorphism is in average 8 alleles per marker with a maximum of eleven and a minimum of five for the population studied. All markers were in Hardy–Weinberg equilibrium, except ECAC5 (p = 0.0007). The probabilities of paternity (W), exclusion (PE) and cumulative discrimination (PD) for all loci were greater than 0.9999. This work will contribute to the implementation of standardized horse genotyping systems in the forensic community and the horse industry.     

Determination of amphetamine-type stimulants,ketamine and metabolites in fingernails by gas chromatography–mass spectrometry

A gas chromatography–mass spectrometry (GC–MS) method was developed and validated for the simultaneous qualification and quantification of methamphetamine (MA), amphetamine (AP), 3,4-methylenedioxy-N-methylamphetamine (MDMA), 3,4-methylenedioxy-N-amphetamine (MDA), ketamine (KET) and norketamine (NKT) in fingernails. Fingernail samples (20 mg) were washed with distilled water and methanol, digested with 1.0 M sodium hydroxide at 95 °C for 30 min, and then extracted with ethyl acetate. Extract solutions were evaporated to dryness, derivatized using heptafluorobutyric anhydride (HFBA) at 60 °C for 30 min, and analyzed by GC–MS. The linear ranges were 0.1–20.0 ng/mg for AP, MDMA and NKT, 0.2–20.0 ng/mg for MA and MDA, and 0.4–20.0 ng/mg for KET, with the coefficients of determination (r² ≥ 0.9989). The intra- and inter-day precisions were within 7.1% and 10.6%, respectively. The intra- and inter-day accuracies were ?10.9% to 0.8% and ?4.3% to 4.5%, respectively. The limits of detections (LODs) and the limits of quantifications (LOQs) for each analyte were lower than 0.094 ng/mg and 0.314 ng/mg, respectively. The recoveries were in the range of 72.3–94.9%. The average fingernail growth rates of two subjects for three years and six subjects for two months were 3.12 mm/month and 3.16 mm/month, respectively. The method proved to be suitable also for the simultaneous detection and quantification of MA, MDMA, KET and their metabolites in fingernails.     

Rapid GC–MS confirmation of amphetamines in urine by extractive acylation

Amphetamine and related derivatives are widely abused central- and psychostimulants. Detection of certain derivatives, such as methcathinone, by commonly available immunoassay screening techniques is insufficient. Multi-analyte confirmations for amphetamine type stimulants are therefore required, but traditional gas chromatography–mass spectrometry methods necessitate lengthy analytical procedures with prolonged sample turn-around times. A validated rapid GC–MS assay for urinary confirmation of amphetamine, methamphetamine, methcathinone, ephedrine, norephedrine, methylenedioxyamphetamine, methylenedioxymethamphetamine, methylenedioxyethylamphetamine and N-methyl-1-(3,4 methylenedioxyphenyl)-2-butanamine is reported. The method entailed in situ derivatization of urine specimens by extractive acylation with pentafluoropropionic anhydride, followed by rapid chromatography on a microbore capillary column. Analytes were separated in less than 3 min and quantified simultaneously by selected-ion monitoring using stable isotope substituted internal standards. The total instrument cycle-time was 6 min per sample. The limits of detection were between 1.5 ng/mL and 6.25 ng/mL for the various analytes. Intermediate precision and accuracy were in the range of 6.3–13.8% and 90.5–107.3% for the respective analytes at the lower limit of quantitation, and between 5.8–12.6% and 95.4–103.1% for the high control. Long-term storage of methcathinone positive specimens at ?20 °C proved insufficient stability of this analyte. The proposed assay is precise and accurate for confirmation of amphetamine and derivatives in urine. The complementary approach of extractive-derivatization and fast GC–MS analysis is especially applicable in routine clinical settings where reduced sample turn-around times are required. Further investigation of cathinone as a possible metabolite of methcathinone is warranted, based on results from analyzed authentic urine samples.