Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics

Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10⁻²⁹, which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.     

Systematic assessment of the performance of Illumina's MiSeq FGx™ forensic genomics system

This study assesses the performance of Illumina's MiSeq FGx System for forensic genomics by systematically analyzing single source samples, evaluating concordance, sensitivity and repeatability, as well as describing the quality of the reported outcomes. DNA from 16 individuals (9 males/7 females) in nine separate runs showed consistent STR profiles at DNA input ≥400 pg, and two full profiles were obtained with 50 pg DNA input. However, this study revealed that the outcome of a single sample does not merely depend on its DNA input but is also influenced by the total amount of DNA loaded onto the flow cell from all samples. Stutter and sequence or amplification errors can make the identification of true alleles difficult, particularly for heterozygous loci that show allele imbalance. Sequencing of 16 individuals’ STRs revealed genetic variations at 14 loci at frequencies suggesting improvement of mixture deconvolution. The STR loci D1S1656 and DXS10103 were most susceptible to drop outs, and D22S1045 and DYS385a‐b showed heterozygote imbalance.  Most stutters were typed at TH01 and DYS385a‐b, while amplification or sequencing errors were observed mostly at D7S820 and D19S433. Overall, Illumina's MiSeq FGx System produced reliable and repeatable results.  aSTRs showed fewer drop outs than the Y‐ and X‐STRs.     

Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population‐divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12‐STR multiplex composed of ancestry informative marker STRs (AIM‐STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM‐SNPs: Snipper, to handle multiallele STR data using frequency‐based training sets. We assessed the ability of the 12‐plex AIM‐STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM‐SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available.     

Resolving human DNA mixtures with F‐108 polymer and capillary electrophoresis single‐strand conformational polymorphism analysis

Current technologies have increased the sensitivity for analyzing forensic DNA samples, especially those considered “touch samples.” Because of this, there has been an increase in the number of forensic mixtures–two or more contributors within a single sample–submitted to the crime laboratories. Therefore, the need to resolve these mixtures has increased as well. Several technologies are currently utilized, but many of them are time consuming and do not resolve the entire profile. Therefore, CE‐Single‐Strand Conformational Polymorphisms coupled with the Pluronic F‐108 polymer was assessed for its ability to resolve human forensic mixtures. This technique has been able to detect sequence variation, such as single nucleotide polymorphism in short tandem repeat loci, such as D7S820 and vWA. Samples were first analyzed with the Performance Optimized Polymer‐7, and mixtures created from samples that shared alleles. These samples were sequenced to detect single base‐pair mutations and evaluated with the F‐108 and CE‐Single Strand Conformational Polymorphism analysis. Results from this study indicated the method would serve as a valuable screening tool to detect base sequence variation between individuals when they share alleles in a mixture and before using Massive Parallel Sequencing technology to distinguish which bases differ.     

Suspension bead array branch migration displacement assay for rapid STR analysis

STR analysis is commonly used in forensic and genetic studies. STRs are currently discriminated based on size, primarily by gel- and column-based approaches. Hybridization-based approaches have the potential to allow high-throughput analysis of STRs; however, development of such approaches has been limited by the difficulty in discriminating between STRs of similar length. We have recently described several innovations to enable STR analysis using an array-based hybridization approach for high- throughput STR analysis. Here we extend that approach by incorporating the array into microspheres and adding a discriminatory branch migration displacement step. This microsphere-based platform uses Luminex xMAP technology and improves the sensitivity, selectivity, and speed of the assay. We demonstrate the feasibility, speed, and reliability of the assay for STR detection by correctly analyzing two STR loci in 20 forensic DNA samples of known STR type. The multiplex, bead-based approach provides a high-throughput and more portable STR analysis.     

Reveal Salmonella enteritidis test for detection of Salmonella enteritidis in shell eggs and environmental samples

Reveal Salmonella Enteritidis (SE) is a lateral flow-based immunodiagnostic assay used for rapid detection of Salmonella enterica serovar Enteritidis from pooled shell eggs and environmental samples. This assay uses highly specific antibodies to accurately detect S. Enteritidis. Studies were conducted to compare the performance of this test against reference procedures for detection of S. Enteritidis from both pooled shell eggs and environmental samples. Pooled shell eggs were inoculated with low levels ofS. Enteritidis and were enriched according to the procedure prescribed by the U.S. Food and Drug Administration. Uninoculated samples were included in each trial. Reveal SE exhibited 100% sensitivity and 100% specificity in comparison to the reference method in all trials. An abbreviated 48 h/(no hold) enrichment procedure was also developed and validated for detection ofS. Enteritidis from pooled shell egg samples. This shortened enrichment procedure can be used in conjunction with the Reveal SE test and offers a significant enrichment time savings of 96 h. Chi-square analysis revealed that there was no significant difference between the abbreviated Reveal method and the reference procedure for detection ofS. Enteritidis from pooled shell egg samples. Out of 245 natural drag swabs screened internally, only three samples tested Reveal SE positive and were confirmed by the reference procedure, resulting in 100% sensitivity and 100% specificity. An external laboratory screened 147 poultry house environmental samples and obtained 35 Reveal SE confirmed positives for Reveal SE sensitivity of 100% and specificity of 90%. Inoculation trials with drag swabs resulted in 96% sensitivity and 100% specificity. Thus, these data demonstrate that Reveal SE is a highly sensitive and specific assay for the detection of S. Enteritidis from both pooled shell eggs and environmental samples.     

Short tandem repeat analysis in Japanese population

Short tandem repeats (STRs), known as microsatellites, are one of the most informative genetic markers for characterizing biological materials. Because of the relatively small size of STR alleles (generally 100-350 nucleotides), amplification by polymerase chain reaction (PCR) is relatively easy, affording a high sensitivity of detection. In addition, STR loci can be amplified simultaneously in a multiplex PCR. Thus, substantial information can be obtained in a single analysis with the benefits of using less template DNA, reducing labor, and reducing the contamination. We investigated 14 STR loci in a Japanese population living in Sendai by three multiplex PCR kits, GenePrint PowerPlex 1.1 and 2.2. Fluorescent STR System (Promega, Madison, WI, USA) and AmpF/STR Profiler (Perkin-Elmer, Norwalk, CT, USA). Genomic DNA was extracted using sodium dodecyl sulfate (SDS) proteinase K or Chelex 100 treatment followed by the phenol/chloroform extraction. PCR was performed according to the manufacturer's protocols. Electrophoresis was carried out on an ABI 377 sequencer and the alleles were determined by GeneScan 2.0.2 software (Perkin-Elmer). In 14 STRs loci, statistical parameters indicated a relatively high rate, and no significant deviation from Hardy-Weinberg equilibrium was detected. We apply this STR system to paternity testing and forensic casework, e.g., personal identification in rape cases. This system is an effective tool in the forensic sciences to obtain information on individual identification.     

Genetic individualization of <Emphasis Type="Italic">Cannabis sativa</Emphasis> by a short tandem repeat multiplex system

Cannabis sativa is the most frequently used of all illicit drugs in the USA. Cannabis has been used throughout history for its stems in the production of hemp fiber, seed for oil and food, and buds and leaves as a psychoactive drug. Short tandem repeats (STRs) were chosen as molecular markers owing to their distinct advantages over other genetic methods. STRs are codominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power, and can be multiplexed. In this study, six STR markers previously described for C. sativa were multiplexed into one reaction. The multiplex reaction was able to individualize 98 cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 states of the USA) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single-reaction sixplex and apply it to the analysis of almost 100 cannabis samples of known geographic origin. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A SNaPshot assay for genotyping 44 individual identification single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs), which have relatively low mutation rates and can be genotyped after PCR with shorter amplicons compared with short tandem repeats (STRs), are being considered as potentially useful markers in forensic DNA analysis. Those SNPs with high heterozygosity and low Fst (F-statistics) in human populations are described as individual identification SNPs, which perform the same function as STRs used in forensic routine work. In the present study, we developed a multiplex typing method for analyzing 44 selected individual identification SNPs simultaneously by using multiplex PCR reaction in association with fluorescent labeled single base extension (SBE) technique. PCR primers were designed and the lengths of the amplicons ranged from 69 to 125?bp. The population genetics data of 79 unrelated Chinese individuals for the 44 SNP loci were investigated and a series of experiments were performed to validate the characteristic of the SNP multiplex typing assay, such as sensitivity, species specificity and the performance in paternity testing and analysis of highly degraded samples. The results showed that the 44-SNPs multiplex typing assay could be applied in forensic routine work and provide supplementary data when STRs analysis was partial or failed.     

Performance of two monoclonal immunoassays in mixtures of cross-reacting dithiophosphorus pesticides

A statistical approach for the analysis of complex samples by immunoassay is proposed in this article. Two enzyme-linked immunosorbent assays (ELISAs), one of them in the conjugate-coated format and the other in the antibody-coated format, were evaluated for their suitability to the analysis of mixtures of three organodithiophosphorus pesticides: azinphos-methyl, azinphos-ethyl and phosmet. It was found that the apparent affinity of the antibody to each analyte changed in the presence of a cross-reacting compound in the antibody-coated ELISA format, but not when the conjugate-coated ELISA format was used. The assays were thereafter applied to the analysis of mixtures of the three recognized pesticides. With the conjugate-coated ELISA format, accurate and precise determinations of mixtures could be performed if an azinphos-methyl standard curve was employed, with recoveries between 71% and 130% and with coefficients of variation lower than 12.7%. Neither accurate nor precise measurements could be accomplished with the enzyme immunoassay using the antibody-coated ELISA format, independently of the standard curve used. It is thought that the study presented here will have applicability in a variety of cases where the analytical goal is semiquantitative screening based on the total quantity of an unknown mixture of related compounds.     

Ascorbic Acid Determination by Hydrophobic Liquid Chromatography of the Osazone Derivative. Application to the Analysis of Aqueous Humor

Abstract

The dinitrophenylhydrazine colorimetric method for the analysis of ascorbic acid has been converted to a high-performance liquid chromatography (HPLC) procedure. The bis-(dinitrophenyl) hydrazone resulting from the reaction of ascorbic acid and dinitrophenylhydrazine is separated on a reversed-phase system from other components in the reaction mixture and used for quantitation purposes. The specificity of the analysis is thus greatly improved and its sensitivity is brought down to the picomol level. The HPLC procedure described here is therefore specially suitable for the analysis of very small volume samples when high specificity and sensitivity are of prime importance. With this method, as in the original colorimetric procedure, it is also possible to specify the contribution of the reduced and oxidized forms of ascorbic acid to the total amount present in the sample. Basically, the same approach could be advantageously used to improve other colorimetric methods of analysis. Human aqueous humor samples taken from senile cataract patients at the time of surgery show variable but significant amounts of oxidized ascorbic acid. This oxidized traction, therefore, should not be neglected as is frequently done when the ascorbic acid system of the aqueous humor is studied.     

Spectrophotometric determination of mixtures of 2-, 3-, and 4-hydroxybenzaldehydes by flow injection analysis and uv/vis photodiode-array detection

A multivariate approach to the quantitative determination of 2-hydroxybenzaldehyde (salicylaldehyde), 3-hydroxybenzaldehyde, and 4-hydroxybenzaldehyde in their mixtures is described. The method is based on second order data generated in a flow injection analysis system with a pH gradient and photodiode-array detection. Each injection gave rise to an 89 (times) x 101 (wavelength) matrix, containing both the acidic and the basic characteristics of the sample injected. A least-squares algorithm based on Lambert-Beers law was used for the prediction of concentrations in unknown samples. No assumptions concerning the qualitative mixture composition of the hydroxybenzaldehydes were necessary to perform concentration predictions. The following four data types were used in the least-squares modelling: (1) unfolded raw data, (2) acidic spectra, (3) basic spectra, and (4) first spectral derivative of the raw data. The prediction errors obtained were comparable to literature results. A graphic method, based on the model residuals for detecting erroneous samples, was developed.     

Development and optimization of a method for analyzing biodiesel mixtures with non-aqueous reversed phase liquid chromatography

Biodiesel (a mixture of fatty acid esters) is normally analyzed using gas chromatography/flame ionization detection, as specified by the ASTM D6584 and EN14105 standards. This paper proposes a binary gradient method for analyzing biodiesel mixtures using non-aqueous reverse phase HPLC with a UV detector capable of overcoming the drawbacks of the gas chromatographic technique normally used. The new analytical method was developed by means of a statistical sensitivity analysis applied to the main parameters influencing the recording, using the full factorial design method combined with the Yates algorithm and the steepest ascent optimization procedure. The present study shows the influence of the main biodiesel mixture separation analysis parameters. The resulting tool proved valid for analyzing not only biodiesel but also any traces of unreacted oil.     

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.     

Evaluation of a spectral searching algorithm for the comparison of Raman band positions

Raman spectroscopic identification of unknown materials involves often the comparison of the spectrum of the unknown spectrum with previously recorded reference spectra or data from literature. However, when spectra with many Raman bands or spectra of mixtures are involved, searching can be quite complex. Different chemometrical approaches have been proposed, but these have some drawbacks. Therefore, in this paper a novel approach is proposed, which is based on a multivariate comparison of Raman band positions. Different similarity measures can be used and are evaluated with spectra of test samples that were recorded on different spectrometers, using different laser wavelengths. Moreover, this study evaluates the performances of this algorithm for identifying different compounds in mixtures, by using an iterative approach.     

Supervised pattern recognition applied to the discrimination of the floral origin of six types of Italian honey samples

In this work a supervised chemometric approach to the discrimination of Italian honey samples from different floral origin is presented. The analytical data of 73 Italian honey samples from six varieties (chestnut, eucalyptus, heather, sulla, honeydew, and wildflower) have been processed by Linear Discriminant Analysis (LDA), using two different variable selection procedures (Fisher F-based and stepwise LDA). Three and two variables, respectively have been necessary to obtain a 100% predictive ability as evaluated by cross-validation. Successively, a class modeling approach has been followed, using UNEQ. The resulting models showed 100% sensitivity and specificity.     

Template tailoring: Accurate determination of heterozygous alleles using peptide nucleic acid and dideoxyNTP

Measurement of the length of DNA fragments plays a pivotal role in genetic mapping, disease diagnostics, human identification and forensic applications. PCR followed by electrophoresis is used for DNA length measurement of STRs, a process that requires labeled primers and allelic ladders as standards to avoid machine error. Sequencing‐based approaches can be used for STR analysis to eliminate the requirement of labeled primers and allelic ladder. However, the limiting factor with this approach is unsynchronized polymerization in heterozygous sample analysis, in which alleles with different lengths can lead to imbalanced heterozygote peak height ratios. We have developed a rapid DNA length measurement method using peptide nucleic acid and dideoxy dNTPs to “tailor” DNA templates for accurate sequencing to overcome this hurdle. We also devised an accelerated “dyad” pyrosequencing strategy, such that the combined approach can be used as a faster, more accurate alternative to de novo sequencing. Dyad sequencing interrogates two bases at a time by allowing the polymerase to incorporate two nucleotides to DNA template, cutting the analysis time in half. In addition, for the first time, we show the effect of peptide nucleic acid as a blocking probe to stop polymerization, which is essential to analyze the heterozygous samples by sequencing. This approach provides a new platform for rapid and cost‐effective DNA length measurement for STRs and resequencing of small DNA fragments.     

Mass spectrometric characterization of tamoxifene metabolites in human urine utilizing different scan parameters on liquid chromatography/tandem mass spectrometry

Different liquid chromatographic/tandem mass spectrometric (LC/MS/MS) scanning techniques were considered for the characterization of tamoxifene metabolites in human urine for anti‐doping purpose. Five different LC/MS/MS scanning methods based on precursor ion scan (precursor ion scan of m/z 166, 152 and 129) and neutral loss scan (neutral loss of 72 Da and 58 Da) in positive ion mode were assessed to recognize common ions or common losses of tamoxifene metabolites. The applicability of these methods was checked first by infusion and then by the injection of solution of a mixture of reference standards of four tamoxifene metabolites available in our laboratory. The data obtained by the analyses of the mixture of the reference standards showed that the five methods used exhibited satisfactory results for all tamoxifene metabolites considered at a concentration level of 100 ng/mL, whereas the analysis of blank urine samples spiked with the same tamoxifene metabolites at the same concentration showed that the neutral loss scan of 58 Da lacked sufficient specificity and sensitivity. The limit of detection in urine of the compounds studied was in the concentration range 10–100 ng/mL, depending on the compound structure and on the selected product ion. The suitability of these approaches was checked by the analysis of urine samples collected after the administration of a single dose of 20 mg of tamoxifene. Six metabolites were detected: 4‐hydroxytamoxifene, 3,4‐dihydroxytamoxifene, 3‐hydroxy‐4‐methoxytamoxifene, N‐demethyl‐4‐hydroxytamoxifene, tamoxifene‐N‐oxide and N‐demethyl‐3‐hydroxy‐4‐methoxytamoxifene, which is in conformity to our previous work using a time‐of‐flight (TOF) mass spectrometer in full scan acquisition mode. Copyright © 2010 John Wiley & Sons, Ltd.     

A new approach to near-infrared spectral data analysis using independent component analysis

This paper presents a new approach to near-infrared spectral (NIR) data analysis that is based on independent component analysis (ICA). The main advantage of the new method is that it is able to separate the spectra of the constituent components from the spectra of their mixtures. The separation is a blind operation, since the constituent components of mixtures can be unknown. The ICA based method is therefore particularly useful in identifying the unknown components in a mixture as well as in estimating their concentrations. The approach is introduced by reference to case studies and compared to other techniques for NIR analysis including principal component regression (PCR), multiple linear regression (MLR), and partial least squares (PLS) as well as Fourier and wavelet transforms.