Next-generation sequencing: a change of paradigm in molecular diagnostic validation

Next-generation sequencing (NGS) is beginning to show its full potential for diagnostic and therapeutic applications. In particular, it is enunciating its capacity to contribute to a molecular taxonomy of cancer, to be used as a standard approach for diagnostic mutation detection, and to open new treatment options that are not exclusively organ-specific. If this is the case, how much validation is necessary and what should be the validation strategy, when bringing NGS into the diagnostic/clinical practice? This validation strategy should address key issues such as: what is the overall extent of the validation? Should essential indicators of test performance such as sensitivity of specificity be calculated for every target or sample type? Should bioinformatic interpretation approaches be validated with the same rigour? What is a competitive clinical turnaround time for a NGS-based test, and when does it become a cost-effective testing proposition? While we address these and other related topics in this commentary, we also suggest that a single set of international guidelines for the validation and use of NGS technology in routine diagnostics may allow us all to make a much more effective use of resources.

Digital slide viewing for primary reporting in gastrointestinal pathology: a validation study

Despite the increasing availability of digital slide viewing, and numerous advantages associated with its application, a lack of quality validation studies is amongst the reasons for poor uptake in routine practice. This study evaluated primary digital pathology reporting in the setting of routine subspecialist gastrointestinal pathology, commonplace in most tissue pathology laboratories and representing one of the highest volume specialties in most laboratories. Individual digital and glass slide diagnoses were compared amongst three pathologists reporting in a gastrointestinal subspecialty team, in a prospective series of 100 consecutive diagnostic cases from routine practice in a large teaching hospital laboratory. The study included a washout period of at least 6 months. Discordant diagnoses were classified, and the study evaluated against recent College of American Pathologists (CAP) recommendations for evaluating digital pathology systems for diagnostic use. The study design met all 12 of the CAP recommendations. The 100 study cases generated 300 pairs of diagnoses, comprising 100 glass slide diagnoses and 100 digital diagnoses from each of the three study pathologists. 286 of 300 pairs of diagnoses were concordant, representing intraobserver concordance of 95.3 %, broadly comparable to rates previously published in this field. In ten of the 14 discordant pairs, the glass slide diagnosis was favoured; in four cases, the digital diagnosis was favoured, but importantly, the 14 discordant intraobserver diagnoses were considered to be of minor clinical significance. Interobserver, or viewing modality independent, concordance was found in 94 of the total of 100 study cases, providing a comparable baseline discordance rate expected in any second viewing of pathology material. These overall results support the safe use of digital pathology in primary diagnostic reporting in this setting

Production of a monoclonal antibody and its application in an optical biosensor based assay for the quantitative measurement of Pantothenic Acid (Vitamin B5) in foodstuffs

Pantothenicacid (PA), vitamin B5, is an essential B vitamin that may be fortified in food and as such requires robust and accurate methods of detection to meet compliance legislation. This study reports the production and characterisation of the first monoclonalantibody (MAb) specific for PA and the subsequent development of a surface plasmon resonance (SPR) biosensorassay for the quantification of PA. The developed assay was compared with an SPR based commercial kit which utilised a polyclonal antibody (PAb). Foodstuffs, including cereals (n = 43), infant formulas and baby food (n = 10) and fruit juices (n = 48) were analysed by both the MAb and PAb biosensorassays and comparison plots showed good correlation (R2 0.77–0.99). The results indicate that the MAb basedbiosensorassay is suitable for the measurement of PA in foodstuffs and has the added advantage of facilitating a constant, long term supply of identical antibody. Preliminary matrix studies suggest the MAb basedassay is an excellent candidate for further validation studies and routine quality assurance based analysis.

Modelling and Instrumentation of Stretch Blow Moulding

The injection stretch blow moulding process is used to manufacture PET containers used in the soft drinks and carbonated soft drinks industry. The process consists of a test tube like specimen known as a preform which is heated, stretch and blown into a mould to form the container. This research is focused on developing a validated simulation of the process thus enabling manufacturers to design their products in a virtual environment without the need to waste time, material and energy. The simulation has been developed using the commercial FEA package Abaqus and has been validated using state of the art data acquisition system consisting of measurements for preform temperature (inner and outer wall) using a device known as THERMOscan (Figure 1), stretch rod force and velocity, internal pressure and air temperature inside the preform using an instrumented stretch rod and the?exact?timing of when the preform touches the mould wall using contact sensors.? In addition, validation studies have also been performed by blowing a perform without a mould and using high sped imaging technology in cooperation with an advanced digital image correlation system (VIC 3D) to provided new quantitative information on the behaviour of PET during blowing.? The approach has resulted in a realistic simulation in terms of accurate input parameters, preform shape evolution and prediction of final properties.

Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma.

We have used whole exome sequencing to compare a group of presentation t(4;14) with t(11;14) cases of myeloma to define the mutational landscape. Each case was characterized by a median of 24.5 exonic nonsynonymous single-nucleotide variations, and there was a consistently higher number of mutations in the t(4;14) group, but this number did not reach statistical significance. We show that the transition and transversion rates in the 2 subgroups are similar, suggesting that there was no specific mechanism leading to mutation differentiating the 2 groups. Only 3% of mutations were seen in both groups, and recurrently mutated genes include NRAS, KRAS, BRAF, and DIS3 as well as DNAH5, a member of the axonemal dynein family. The pattern of mutation in each group was distinct, with the t(4;14) group being characterized by deregulation of chromatin organization, actin filament, and microfilament movement. Recurrent RAS pathway mutations identified subclonal heterogeneity at a mutational level in both groups, with mutations being present as either dominant or minor subclones. The presence of subclonal diversity was confirmed at a single-cell level using other tumor-acquired mutations. These results are consistent with a distinct molecular pathogenesis underlying each subgroup and have important impacts on targeted treatment strategies. The Medical Research Council Myeloma IX trial is registered under ISRCTN68454111.

Stimulating Neoblast-Like Cell Proliferation in Juvenile Fasciola hepatica Supports Growth and Progression towards the Adult Phenotype In Vitro

Fascioliasis (or fasciolosis) is a socioeconomically important parasitic disease caused by liver flukes of the genus Fasciola. Flukicide resistance has exposed the need for new drugs and/or a vaccine for liver fluke control. A rapidly improving 'molecular toolbox' for liver fluke encompasses quality genomic/transcriptomic datasets and an RNA interference platform that facilitates functional genomics approaches to drug/vaccine target validation. The exploitation of these resources is undermined by the absence of effective culture/maintenance systems that would support in vitro studies on juvenile fluke development/biology. Here we report markedly improved in vitro maintenance methods for Fasciola hepatica that achieved 65% survival of juvenile fluke after 6 months in standard cell culture medium supplemented with 50% chicken serum. We discovered that this long-term maintenance was dependent upon fluke growth, which was supported by increased proliferation of cells resembling the "neoblast" stem cells described in other flatworms. Growth led to dramatic morphological changes in juveniles, including the development of the digestive tract, reproductive organs and the tegument, towards more adult-like forms. The inhibition of DNA synthesis prevented neoblast-like cell proliferation and inhibited growth/development. Supporting our assertion that we have triggered the development of juveniles towards adult-like fluke, mass spectrometric analyses showed that growing fluke have an excretory/secretory protein profile that is distinct from that of newly-excysted juveniles and more closely resembles that of ex vivo immature and adult fluke. Further, in vitro maintained fluke displayed a transition in their movement from the probing behaviour associated with migrating stage worms to a slower wave-like motility seen in adults. Our ability to stimulate neoblast-like cell proliferation and growth in F. hepatica underpins the first simple platform for their long-term in vitro study, complementing the recent expansion in liver fluke resources and facilitating in vitro target validation studies of the developmental biology of liver fluke.

3D-QSAR studies on 4-Hydroxyphenylpyruvate Dioxygenase inhibitors by comparative molecular field analysis (CoMFA)

A comparative molecular field analysis (CoMFA) of alkanoic acid 3-oxo-cyclohex-1-enyl ester and 2-acylcyclohexane-1,3-dione derivatives of 4-hydroxyphenylpyruvate dioxygenase inhibitors has been performed to determine the factors required for the activity of these compounds. The substrate's conformation abstracted from dynamic modeling of the enzyme-substrate complex was used to build the initial structures of the inhibitors. Satisfactory results were obtained after an all-space searching procedure, performing a leave-one out (LOO) cross-validation study with cross-validation q(2) and conventional r(2) values of 0.779 and 0.989, respectively. The results provide the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of new HPPD ligands with predetermined affinities.

Development and Single-Laboratory Validation of a Pseudofunctional Biosensor Immunoassay for the Detection of the Okadaic Acid Group of Toxins

A rapid analytical optical biosensor-based immunoassay was developed and validated for the detection of okadaic acid (OA) and its structurally related toxins from shellfish matrix. The assay utilizes a monoclonal antibody which binds to the OA group of toxins in order of their toxicities, resulting in a pseudofunctional assay. Single-laboratory validation of the assay for quantitative detection of OA determined that it has an action limit of 120 mu g/kg, a limit of detection of 31 mu g/kg, and a working range of 31-174 mu g/kg. The midpoint on the standard matrix calibration curve is 80 mu g/kg, half the current regulatory limit. Inter- and intra-assay studies of negative mussel samples spiked with various OA concentrations produced average coefficient of variation (CV) and standard deviation (SD) values of 7.9 and 10.1, respectively. The assay was also validated to confirm the ability to accurately codetect and quantify dinophysistoxin-1 (DTX-1), DTX-2, and DTX-3 from shellfish matrix. Alkaline hydrolysis was not required for the detection of DTX-3 from matrix. Excellent correlations with the data generated by the biosensor method and liquid chromatography/tandem mass spectrometry (LC/MS/MS) were obtained using a certified reference material (R-2 = 0.99), laboratory reference material, and naturally contaminated mussel samples (R-2 = 0.97). This new procedure could be used as a rapid screening procedure replacing animal-based tests for DSP toxins.

TRARESA: a tissue microarray-based hospital system for biomarker validation and discovery

Formalin fixed and paraffin embedded tissue (FFPE) collections in pathology departments are the largest resource for retrospective biomedical research studies. Based on the literature analysis of FFPE related research, as well as our own technical validation, we present the Translational Research Arrays (TRARESA), a tissue microarray centred, hospital based, translational research conceptual framework for both validation and/or discovery of novel biomarkers. TRARESA incorporates the analysis of protein, DNA and RNA in the same samples, correlating with clinical and pathological parameters from each case, and allowing (a) the confirmation of new biomarkers, disease hypotheses and drug targets, and (b) the postulation of novel hypotheses on disease mechanisms and drug targets based on known biomarkers. While presenting TRARESA, we illustrate the use of such a comprehensive approach. The conceptualisation of the role of FFPE-based studies in translational research allows the utilisation of this commodity, and adds to the hypothesis-generating armamentarium of existing high-throughput technologies.

Multiplex RT-PCR for the detection of leukemia-associated translocations - Validation and application to routine molecular diagnostic practice

The aim of this study was to validate the application of a commercially available multiplex reverse transcription polymerase chain reaction (RT-PCR) assay [He-mavision-7 System] for the seven most common leukemia translocations for routine molecular diagnostic hematopathology practice. A total of 98 samples, comprising four groups, were evaluated: Group 1, 16 diagnostic samples molecularly positive by our existing laboratory-developed assays for PML-RARalpha/t (15; 17) or BCR-ABL/t (9;22); Group 2, 51 diagnostic samples negative by our laboratory-developed assays for PML-RARalpha/t (15;17) or BCR-ABL/t (9;22); Group 3, 21 prospectively analyzed diagnostic cases, without prior molecular studies; and Group 4, 10 minimal residual disease (MRD) samples. Analysis of the two previously studied cohorts (Groups 1 and 2) confirmed the diagnostic sensitivity and specificity of the multiplex assay with regard to these two translocations. Additionally, however, in the

Validation of fixed speed induction generator models for inertial response using wind farm measurements

This paper outlines the use of phasor measurement unit (PMU) records to validate models of fixed speed induction generator (FSIG)-based wind farms during frequency transients. Wind turbine manufacturers usually create their own proprietary models which they can supply to power system utilities for stability studies, subject to confidentiality agreements. However, it is desirable to confirm the accuracy of supplied models with measurements from the particular installation, in order to assess their validity under real field conditions. This is prudent due to possible changes in control algorithms and design retrofits, not accurately reflected or omitted in the supplied model. One important aspect of such models, especially for smaller power systems with limited inertia, is their accuracy during system frequency transients. This paper, therefore, assesses the accuracy of FSIG models with regard to frequency stability, and hence validates a subset of the model dynamics. Such models can then be used with confidence to assess wider system stability implications. The measured and simulated response of a wind farm using doubly fed induction generator (DFIG) technology is also assessed.

Do smokers with chronic obstructive pulmonary disease report their smoking status reliably?:A comparison of self-report and bio-chemical validation

Chronic obstructive pulmonary disease (COPD) is predominantly caused by cigarette smoking and is considered a worldwide preventable chronic illness. Smoking cessation is considered the primary intervention for disease management and nurses should play a major role in assisting patients to stop smoking. Currently there is a lack of professional consensus on how cessation interventions should be evaluated. The vast array of biochemical markers reported in the literature can be confusing and can make the comparisons of results difficult.

The impedance cardiogram recorded through two electrocardiogram/defibrillator pads as a determinant of cardiac arrest during experimental studies

OBJECTIVE: Laypersons are poor at emergency pulse checks (sensitivity 84%, specificity 36%). Guidelines indicate that pulse checks should not be performed. The impedance cardiogram (dZ/dt) is used to assess stroke volume. Can a novel defibrillator-based impedance cardiogram system be used to distinguish between circulatory arrest and other collapse states?

DESIGN: Animal study.

SETTING: University research laboratory.

SUBJECTS: Twenty anesthetized, mechanically ventilated pigs, weight 50-55 kg.

INTERVENTIONS: Stroke volume was altered by right ventricular pacing (160, 210, 260, and 305 beats/min). Cardiac arrest states were then induced: ventricular fibrillation (by rapid ventricular pacing) and, after successful defibrillation, pulseless electrical activity and asystole (by high-dose intravenous pentobarbitone).

MEASUREMENTS AND MAIN RESULTS: The impedance cardiogram was recorded through electrocardiogram/defibrillator pads in standard cardiac arrest positions. Simultaneously recorded electro- and impedance cardiogram (dZ/dt) along with arterial blood pressure tracings were digitized during each pacing and cardiac arrest protocol. Five-second epochs were analyzed for sinus rhythm (20 before ventricular fibrillation, 20 after successful defibrillation), ventricular fibrillation (40), pulseless electrical activity (20), and asystole (20), in two sets of ten pigs (ten training, ten validation). Standard impedance cardiogram variables were noncontributory in cardiac arrest, so the fast Fourier transform of dZ/dt was assessed. During ventricular pacing, the peak amplitude of fast Fourier transform of dZ/dt (between 1.5 and 4.5 Hz) correlated with stroke volume (r2 = .3, p < .001). In cardiac arrest, a peak amplitude of fast Fourier transform of dZ/dt of < or = 4 dB x ohm x rms indicated no output with high sensitivity (94% training set, 86% validation set) and specificity (98% training set, 90% validation set).

CONCLUSIONS: As a powerful clinical marker of circulatory collapse, the fast Fourier transformation of dZ/dt (impedance cardiogram) has the potential to improve emergency care by laypersons using automated defibrillators.

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.

Genome-wide association studies (GWAS) have identified ten loci harboring common variants that influence risk of developing colorectal cancer (CRC). To enhance the power to identify additional CRC risk loci, we conducted a meta-analysis of three GWAS from the UK which included a total of 3,334 affected individuals (cases) and 4,628 controls followed by multiple validation analyses including a total of 18,095 cases and 20,197 controls. We identified associations at four new CRC risk loci: 1q41 (rs6691170, odds ratio (OR) = 1.06, P = 9.55 × 10?¹° and rs6687758, OR = 1.09, P = 2.27 × 10??, 3q26.2 (rs10936599, OR = 0.93, P = 3.39 × 10?8), 12q13.13 (rs11169552, OR = 0.92, P = 1.89 × 10?¹° and rs7136702, OR = 1.06, P = 4.02 × 10?8) and 20q13.33 (rs4925386, OR = 0.93, P = 1.89 × 10?¹°). In addition to identifying new CRC risk loci, this analysis provides evidence that additional CRC-associated variants of similar effect size remain to be discovered.