Developmental validation of the Yfiler Platinum PCR Amplification Kit for forensic genetic caseworks and databases

Y chromosome kits are successfully applied in cases where human biological material exists. With the development of genotyping ability, more Y chromosomal markers are needed for finer identification of male individuals and lineages. In this study, a developmental validation of a newly emerged Y chromosome kit that combines two different kinds of markers: 38 Y-STRs and 3 Y-indels are conducted. The results show that this kit has high sensitivity when there is a small amount of DNA (125 pg), more than one male (minor:major = 1:7), or a mixture of males and females (male:female = 125pg:1875pg), inhibited substances (800 μM hematin and more than 1600 ng/μL humic acid). The kit exhibits high precision level with a standard deviation of allele size no more than 0.14 nt. Locus DYS481 shows the largest stutter rate, with three stutters per true allele. Population samples are well identified (MP of 0.001106), and mutations can be observed in father–son pairs (46 mutations in 70 pairs, 10 in locus DYS627). Out of all the population samples, 13.2% belong to haplogroup M117-O2a2b1a1, with their ethnic group being Han Chinese. The results show that this kit can improve the performance of identifying male individuals, obtaining more unique haplotypes (increasing from 894 to 918 of 1000 male samples) and higher discrimination capacity (increasing from 0.942 to 0.955) in this study compared to previous widely used Yfiler Plus kit. Besides, it gives information about their paternal lineages in forensic genetic casework and genealogical database construction.     

Information-theoretical feature selection using data obtained by scanning electron microscopy coupled with and energy dispersive X-ray spectrometer for the classification of glass traces

In this work, a selection of the best features for multivariate forensic glass classification using Scanning Electron Microscopy coupled with an Energy Dispersive X-ray spectrometer (SEM-EDX) has been performed. This has been motivated by the fact that the databases available for forensic glass classification are sparse nowadays, and the acquisition of SEM-EDX data is both costly and time-consuming for forensic laboratories. The database used for this work consists of 278 glass objects for which 7 variables, based on their elemental compositions obtained with SEM-EDX, are available. Two categories are considered for the classification task, namely containers and car/building windows, both of them typical in forensic casework. A multivariate model is proposed for the computation of the likelihood ratios. The feature selection process is carried out by means of an exhaustive search, with an Empirical Cross-Entropy (ECE) objective function. The ECE metric takes into account not only the discriminating power of the model in use, but also its calibration, which indicates whether or not the likelihood ratios are interpretable in a probabilistic way. Thus, the proposed model is applied to all the 63 possible univariate, bivariate and trivariate combinations taken from the 7 variables in the database, and its performance is ranked by its ECE. Results show remarkable accuracy of the best variables selected following the proposed procedure for the task of classifying glass fragments into windows (from cars or buildings) or containers, obtaining high (almost perfect) discriminating power and good calibration. This allows the proposed models to be used in casework. We also present an in-depth analysis which reveals the benefits of the proposed ECE metric as an assessment tool for classification models based on likelihood ratios.     

Detection of cell-free fetal DNA in maternal plasma using two types of compound markers

With the discovery of circulating cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low-level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP-STR and SNP-STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele-specific forward primers for DIP-STR and SNP-STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP-STRs and 11 SNP-STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP-STR and SNP-STR markers, and DIP-STR outperforms SNP-STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.     

A convenient guideline to determine if two Y‐STR profiles are from the same lineage

Y chromosome STR loci are used in forensics primarily for identification purposes by determining the male lineages. The Henan province in China has established a large Y‐STR (>200 000 profiles) database for criminal investigations. A large proportion of the Y‐STR profiles in the database were generated using either the Applied Biosystems Yfiler^? or Yfiler^? Plus PCR Amplification kits. The additional loci in the Yfiler Plus kit as compared to the Yfiler kit results in a concomitant cumulative mutation rate increase across the loci. Therefore, in those cases when two profiles have one to a few mismatched loci, it is difficult to determine if they are from the same lineage. In this study, 7405 unrelated male profiles were manually selected from the database. Analysis showed higher power of discrimination than the corresponding Yfiler haplotypes. Further, the distributions of the number of mismatched loci and the mismatched steps were generated for father‐son, grandfather‐grandson, uncle‐nephew, and cousins (i.e. one, two, three, and four meioses, respectively) by exhaustive pairwise comparison of the unrelated profiles using a dynamic programming approach. The same distributions were generated for unrelated pairs with mutation rates of the loci. With the distributions, the false negative and false positive rates were determined. Two Yfiler profiles with ≤2 mismatched loci or ≤2 steps are more likely from the same lineage than unrelated lineages, and two Yfiler Plus profiles with ≤4 mismatched loci or ≤5 mismatched steps are more likely from the same lineage.     

Variation in likelihood ratios for forensic evidence evaluation of XTC tablets comparison

In forensic comparison casework, where it is investigated whether items are from the same source, the likelihood ratio (LR) is a measure for evaluating the strength of evidence of the observed (dis)similarity between these items. The paper concentrates on evaluation of various LR models for comparison of XTC tablets from different production batches. Starting from a two‐level random effect model, where means are considered random, the distribution of these means may be assumed normal or approximated by kernel density estimations (KDEs), and variation in the data may or may not be allowed to differ per batch. It is investigated what effect the corresponding model and estimation choices have on the distribution of LRs for same‐ and different‐batch comparisons. Copyright © 2010 John Wiley & Sons, Ltd.     

DuPont qualicon BAX system real-time PCR assay for Escherichia coli O157:H7

Evaluations were conducted to test the performance of the BAX System Real-Time PCR assay, which was certified as Performance Tested Method 031002 for screening E. coli O157:H7 in ground beef, beef trim, spinach, and lettuce. Method comparison studies performed on samples with low-level inoculates showed that the BAX System demonstrates a sensitivity equivalent or superior to the FDA-BAM and the USDA-FSIS culture methods, but with a significantly shorter time to result. Tests to evaluate inclusivity and exclusivity returned no false-negative and no false-positive results on a diverse panel of isolates, and tests for lot-to-lot variability and tablet stability demonstrated consistent performance. Ruggedness studies determined that none of the factors examined affect the performance of the assay. An accelerated shelf life study determined an initial 36 month shelf life for the test kit.     

Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs

This paper reports a method for the identification of those molecules in a database of rigid 3D structures with molecular electrostatic potential (MEP) grids that are most similar to that of a user-defined target molecule. The most important features of an MEP grid are encoded in field-graphs, and a target molecule is matched against a database molecule by a comparison of the corresponding field-graphs. The matching is effected using a maximal common subgraph isomorphism algorithm, which provides an alignment of the target molecule's field- graph with those of each of the database molecules in turn. These alignments are used in the second stage of the search algorithm to calculate the intermolecular MEP similarities. Several different ways of generating field-graphs are evaluated, in terms of the effectiveness of the resulting similarity measures and of the associated computational costs. The most appropriate procedure has been implemented in an operational system that searches a corporate database, containing ca. 173,000 3D structures.     

Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNPforID markers

The SNPfor ID consortium identified a panel of 52 SNPs for forensic analysis that has been used by several laboratories worldwide. The original analysis of the 52 SNPs was based on a single multiplex reaction followed by two single‐base‐extension (SBE) reactions each of which was analyzed using capillary electrophoresis. The SBE assays were designed for high throughput genetic analyzers and were difficult to use on the single capillary ABI PRISM 310 Genetic Analyzer and the latest generation 3500 Genetic Analyzer, as sensitivity on the 310 was low and separation of products on the 3500 with POP‐7™ was poor. We have modified the original assay and split it into four multiplex reactions, each followed by an SBE assay. These multiplex assays were analyzed using polymer POP‐4™ on ABI 310 PRISM® and polymers POP‐4™, POP‐6™ and POP‐7™ on the 3500 Genetic Analyzer. The assays were sensitive and reproducible with input DNA as low as 60 pg using both the ABI 310 and 3500. In addition, we found that POP‐6™ was most effective with the 3500, based on the parameters that we assessed, achieving better separation of the small SBE products; this conflicted with the recommended use of POP‐7™ by the instrument manufacturer. To support the use of the SNP panel in casework in Malaysia we have created an allele frequency database from 325 individuals, representing the major population groups within Malaysia. Population and forensic parameters were estimated for all populations and its efficacy evaluated using 51 forensic samples from challenging casework.     

Profiling of illicit heroin samples by high-resolution capillary gas chromatography for forensic application

Summary Glass capillary gas chromatographic methods for profile analysis of trace impurities of illicit heroin samples have been developed. The procedure consists of extracting the impurities by toluene from acidic solution and examination by capillary GC. Derivatized and nonderivatized extracts of illicit heroin from different sources are reported. The reproducibility of the procedure and the detection with FID and N-FID are studied. Results obtained by application of the profiling procedure, as an additional pattern for comparison of samples in forensic casework, have shown the distinct advantage of this method.Presented at the 14th International Symposium on Chromatography London, September, 1982     

A potential pitfall in 18O-based N-linked glycosylation site mapping

A common procedure for identifying N-linked glycosylation sites involves tryptic digestion of the glycoprotein, followed by the conversion of glycosylated asparagine residues into (18)O-labeled aspartic acids by PNGase F digestion in (18)O water. The 3 Da mass tag created by this process is readily observable by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis, and is often used to identify the sites of N-linked glycosylation. While using this procedure, we noticed that 60% of the asparagines identified as being glycosylated were not part of the consensus sequence required for N-linked glycosylation, and thus were not biologically possible. Investigation into the source of this unacceptably high false positive rate demonstrated that even after reversed-phase cleanup and heat denaturation, the trypsin used for proteolysis was still active and led to the incorporation of (18)O into the C-termini of the peptides during the deglycosylation step. The resulting mass shift accounted for most of the false positive sites, as the database search algorithm confused it with an (18)O-labeled Asp residue near the C-terminus of a peptide. This problem can be overcome by eliminating trypsin from the solution prior to performing the deglycosylation process, by resuspending the peptides in natural abundance water following deglycosylation, or by allowing (18)O incorporation into the C-terminus as a variable modification during the database search. These methods have been demonstrated on a model protein, and are applicable to the analyses of glycoproteins that are digested with trypsin or another serine protease prior to enzymatic release of the carbohydrate side chains. This study should alert investigators in the field to this potential and unexpected pitfall and provide strategies to overcome this phenomenon.     

Databases, quality control and interpretation of DNA profiling in the Home office Forensic Science Service

The history of DNA profiling in the Home Office Forensic Science Service began with the introduction of multilocus probes into casework in 1986. The use of single-locus probes was introduced in 1990, supported by databases of three ethnic groups; interpretation is backed up using a Bayesian approach. Databases were compiled using an image analysis computing system. Quality control systems are described, detailing requirements before a sample can be included in the database.     

Fluorescence energy transfer-labeled primers for high-performance forensic DNA profiling

A fluorescence energy transfer (ET) dye-labeled STR typing system (ET 16-plex) is developed for the markers used in the commercial STR typing kit PowerPlex 16, and its performance assessed using a 96-lane microfabricated capillary array electrophoresis (muCAE) system. The ET 16-plex amplicons displayed 1.6-9-fold higher fluorescence intensities compared to those produced using the single-dye (SD)-labeled multiplex kits. The ET multiplex delivered full STR profiles from 62.5 pg of DNA; half the input required for the SD kits while maintaining a similar heterozygote allele balance. This increased sensitivity should improve typing of poor-quality DNA samples by making minor or imbalanced alleles more readily detectable at the low copy number (LCN) threshold. The ET 16-plex also generated complete profiles with only 28 PCR cycles; this capability should improve LCN typing by reducing the amplification time and drop-in allele incidence. To confirm the practical advantages of ET-labeled primers, six previously problematic casework samples were tested and only the ET 16-plex kit was able to capture additional allele data. The successful development and demonstration of ET primers for higher sensitivity STR typing offers a simple solution to improving current commercial multiplex typing capability. The superior spectral properties and universal compatibility with any primer sequence provided by ET cassettes will make future multiplex construction more facile and straightforward. The pairing of ET cassette technology with the muCAE system illustrates not only an enhanced STR typing platform, but a significant step toward a higher-efficiency forensic laboratory enabled by better chemistry and microfluidics.     

Determination of rendering plant sterilization conditions using a commercially available ELISA test kit developed for detection of cooked beef.

A commercially available enzyme-linked immunosorbent assay (ELISA) test kit developed for detection of cooked beef in meat samples was used to determine appropriate heat treatment of rendered materials. An improved extraction procedure increased the absolute difference in R-values between 2 rendered materials treated under different conditions (average temperature 129 and 134 degrees C, respectively). To evaluate the influence of the main sterilization parameters on ELISA results, a factorial design approach was used. The parameters investigated were temperature, time, particle size, and meat composition. Lean meat samples containing beef and pork were sterilized under strictly controlled conditions in a laboratory autoclave. The experiments demonstrated that the R-values obtained with the ELISA test kit for beef are strongly influenced by temperature and time, whereas particle size has a minor influence. The proportion of bovine material did not have any impact on R-values. Autoclave-processed lean meat samples were analyzed by using an ELISA test kit for pork, which was validated in a collaborative trial. The ELISA test kit for pork proved to be more sensitive for the investigated parameters, thus verifying and extending previous investigations.     

New approach for rapid detection of known hemoglobin variants using LC-MS/MS combined with a peptide database

The identification of hemoglobin (Hb) variants is usually performed by means of different analytical steps and methodologies. Phenotypic methods, such as gel electrophoresis and high performance liquid chromatography, are used to detect the different electrophoretic or chromatographic behaviors of hemoglobin variants in comparison to HbA0 used as a control. These data often need to be combined with mass spectrometry analyses of intact globins and their tryptic peptide mixtures. As an alternative to a 'step-by-step' procedure, we have developed a 'single step' approach for the identification of Hb variants present in biological samples. This is based on the microHPLC-ESI-MS/MS analysis of the peptide mixture generated by a tryptic digestion of diluted Hb samples and an in-house new database containing solely the variant tryptic peptide of known human Hb variants. The experimental results (full MS and MS/MS spectra) are correlated with theoretical mass spectra generated from our in-house-built variant peptide database (Hbp) using the SEQUEST algorithm. Simple preparation of samples and an automated identification of the variant peptide are the main characteristics of this approach, making it an attractive method for the detection of Hb variants at the routine clinical level. We have analyzed 16 different samples, each containing a different known variant of hemoglobin.     

A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis

Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3 h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples.     

Time‐of‐flight SIMS characterization of hydrolysed organofunctional and non‐organofunctional silanes deposited on Al,Zn and Al–43.4Zn–1.6Si alloy‐coated steel

In this paper Al, Zn and Al–43.4Zn–1.6Si (AlZn) alloy‐coated steel have been treated with the organofunctional silane γ‐mercaptopropyltrimethoxysilane (γ‐MPS) and the non‐organofunctional silane 1,2‐bis(triethoxysilyl)ethane (BTSE). Also, a two‐step treatment of metal substrates was performed: the metal substrates were treated with the BTSE silane followed by a γ‐MPS treatment. The influence of metal substrate and the pH value of the silane film properties were investigated using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). The results show that the BTSE silane is fully hydrolysed but the γ‐MPS silane is not. The presence of negative ions of the type HSi_xO_y^? indicates that both types of silane films are highly cross‐linked via Si–O–Si bonds. The two‐step treatment gave a γ‐MPS silane layer on top of the BTSE silane layer but the thickness of the total silane film become thinner than for a single BTSE film, indicating that some of the BTSE is dissolved during the γ‐MPS deposition step. Furthermore, the ToF‐SIMS results show that the thiol group of the γ‐MPS silane is oxidized. Finally, no major influence, either in the positive or the negative mass spectra, from the different metal substrates could be detected for the silane films investigated. Copyright © 2003 John Wiley & Sons, Ltd.     

Phosphorylation site localization in peptides by MALDI MS/MS and the Mascot Delta Score

Owing to its broad biological significance, the large-scale analysis of protein phosphorylation is more and more getting into the focus of proteomic research. Thousands of phosphopeptides can nowadays be identified using state-of-the-art tandem mass spectrometers in conjunction with sequence database searching, but localizing the phosphate group to a particular amino acid in the peptide sequence is often still difficult. Using 180 individually synthesized phosphopeptides with precisely known phosphorylation sites (p-sites), we have assessed the merits of the Mascot Delta Score (MD score) for the assignment of phosphorylation sites from tandem mass spectra (MS/MS) generated on four different matrix-assisted laser desorption ionization (MALDI) mass spectrometers including tandem time-of-flight (TOF/TOF), quadrupole time-of-flight, and ion trap mass analyzers. The results show that phosphorylation site identification is generally possible with false localization rates of about 10%. However, a comparison to previous work also revealed that phosphorylation site determination by MALDI MS/MS is less accurate than by ESI-MS/MS particularly if several and/or adjacent possible phosphorylation acceptor sites exist in a peptide sequence. We are making the tandem MS spectra and phosphopeptide collection available to the community so that scientists may adapt the MD scores reported here to their analytical environment and so that informatics developers may integrate the MD score into proteomic data analysis pipelines.     

The measurement of molecular diversity by receptor site interaction simulation

The assembly of large compound libraries for the purpose of screening against various receptor targets to identify chemical leads for drug discovery programs has created a need for methods to measure the molecular diversity of such libraries. The method described here, for which we propose the acronym RESIS (for Receptor Site Interaction Simulation), relates directly to this use. A database is built of three-dimensional representations of the compounds in the library and a set of three-point three-dimensional theoretical receptor sites is generated based on putative hydrophobic and polar interactions. A series of flexible, three-dimensional searches is then performed over the database, using each of the theoretical sites as the basis for one such search. The resulting pattern of hits across the grid of theoretical receptor sites provides a measure of the molecular diversity of the compound library. This can be conveniently displayed as a density map which provides a readily comprehensible visual impression of the library diversity characteristics. A library of 7500 drug compounds derived from the CIPSLINEPC databases was characterized with respect to molecular diversity using the RESIS method. Some specific uses for the information obtained from application of the method are discussed. A comparison was made of the results from the RESIS method with those from a recently published two-dimensional approach for assessing molecular diversity using sets of compounds from the Maybridge database (MAY).     

Polyoxometalate-based metal organic frameworks (POMOFs): structural trends, energetics, and high electrocatalytic efficiency for hydrogen evolution reaction

The grafting of the triangular 1,3,5-benzene tricarboxylate linkers (denoted trim) on tetrahedral ε-Keggin polyoxometalates (POMs) capped by Zn(II) ions, formed in situ under hydrothermal conditions, has generated three novel POM-based metal organic frameworks (POMOFs). (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(36)(OH)(4)Zn(4)][C(6)H(3)(COO)(3)](4/3)·6H(2)O (ε(trim)(4/3)) is a 3D open-framework built of molecular Keggin units connected by trim linkers, with channels occupied by tetrabutylammonium (TBA) counterions. ε(trim)(4/3) is a novel (3,4)-connected net, named ofp for open-framework polyoxometalate, and computer simulations have been used to evaluate its relative stability in comparison with ctn- and bor-like polymorphs, showing the stability of this novel phase directly related to its greatest density. A computational study was also undertaken with the aim of locating TBA molecules, the positions of which could not be deduced from single crystal X-ray diffraction, and further rationalizes their structure directing role. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)] (ε(2)(trim)(2)), the building unit is not the molecular Keggin but a dimerized form of this POM. Their connection via trim linkers generates a 3D framework with channels filled by TBA cations. In (TBA)(3)[PMo(V)(8)Mo(VI)(4)O(37)(OH)(3)Zn(4)][C(6)H(3)(COO)(3)]·8H(2)O ([ε(trim)](∞)), zigzag chains are connected via the organic linkers, forming 2D grids. Modified electrodes were fabricated by direct adsorption of the POMOFs on glassy carbon or entrapment in carbon paste (CPE). A remarkable electrocatalytic hydrogen evolution reaction (HER) was detected with a yield greater than 95%, and a turnover number as high as 1.2 × 10(5) was obtained after 5 h. The reported POMOF-based electrodes are more active than platinum, with a roughly 260 mV anodic shift. Finally, the electrocatalytic activities of ε(trim)(4/3)/CPE electrodes in various XCl (X = Li, Na, K, Cs) media have been studied. This allowed us to detect a cation effect and propose an electrocatalytic mechanistic pathway for the HER.     

Rapid Analysis of PCBs in Soil by Enzyme Immunoassay

Abstract

A commercially available kit has been applied successfully to screening for polychlorinated biphenyls (PCB's) in soil samples. The kit uses a competitive inhibition Enzyme ImmunoAssay (EIA) for recognition of the PCB structure. Test specificity is restricted to PCB's, primarily Aroclors 1016, 1242, 1248, 1254, and 1260. Soil sample preparation and analysis can be performed in the field or lab using disposable kit components. Screening of unidentified Aroclors at 4 levels from 1 to 50 μg/g in soil is possible using the calibrators in the kit. This screening use has been reviewed by the USEPA Office of Solid Waste and will be proposed for inclusion in the 4000 series of screening methods in the next SW846 update. Conventional analysis (Soxhlet/GC-ECD) and the EIA kit were compared by Manitoba Hydro using 112 field samples over one year. EIA technology was found to be an effective screening tool for determining PCB concentration at contaminated sites. Routine use of these kits in conjunction with conventional Soxhlet extraction procedures has increased the lab's testing capability and reduced the amount of samples requiring conventional testing, providing substantial savings to the corporation.