Comparative validation of c-kit exon 11 mutation analysis on cytology samples and corresponding surgical resections of gastrointestinal stromal tumours

Objective:

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.

Detection of epidermal growth factor receptor variations by partially denaturing HPLC

Background: Epidermal growth factor receptor gene (EGFR) variants may be useful markers for identifying responders to gefitinib and erlotinib, small-molecule tyrosine kinase inhibitors of EGFR; therefore, sensitive and cost-effective assays are needed to detect EGFR variants in routine clinical samples. We have developed a partially denaturing HPLC (pDHPLC) assay that is superior to direct sequencing with respect to detection limits, costs, and time requirements.

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 study for prediction of iced aerofoil aerodynamics

Ice accretions can significantly change the aerodynamic performance of wings and rotor blades. Significant performance degradation can occur when ice accreations cause regions of separated flow, to predict this change implies, at a minimum, the solution of the Reynolds-Averaged Navier-Stokes equations. This paper presents validation for two generic cases involving the flow over aerofoil sections with added synthetic ice shapes. Results were obtained for two aerofoils, namely the NACA 23012 and a generic multi-element configuration. These results are compared with force and pressure coefficient measurements obtained in the NASA LTPT wind-tunnel for the NACA 23012, and force, PIV and boundary-layer measurements obtained at DNW for the multi-clement case. The level of agreement is assessed in the context of industrial requirements.

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.

Development and clinical validation of multiplex TaqMan® assays for rapid diagnosis of viral gastroenteritis.

There is a need to provide rapid, sensitive, and often high throughput detection of pathogens in diagnostic virology. Viral gastroenteritis is a serious health issue often leading to hospitalization in the young, the immunocompromised and the elderly. The common causes of viral gastroenteritis include rotavirus, norovirus (genogroups I and II), astrovirus, and group F adenoviruses (serotypes 40 and 41). This article describes the work-up of two internally controlled multiplex, probe-based PCR assays and reports on the clinical validation over a 3-year period, March 2007 to February 2010. Multiplex assays were developed using a combination of TaqMan™ and minor groove binder (MGB™) hydrolysis probes. The assays were validated using a panel of 137 specimens, previously positive via a nested gel-based assay. The assays had improved sensitivity for adenovirus, rotavirus, and norovirus (97.3% vs. 86.1%, 100% vs. 87.8%, and 95.1% vs. 79.5%, respectively) and also more specific for targets adenovirus, rotavirus, and norovirus (99% vs. 95.2%, 100% vs. 93.6%, and 97.9% vs. 92.3%, respectively). For the specimens tested, both assays had equal sensitivity and specificity for astrovirus (100%). Overall the probe-based assays detected 16 more positive specimens than the nested gel-based assay. Post-introduction to the routine diagnostic service, a total of 9,846 specimens were processed with multiplex 1 and 2 (7,053 pediatric, 2,793 adult) over the 3-year study period. This clinically validated, probe-based multiplex testing algorithm allows highly sensitive and timely diagnosis of the four most prominent causes of viral gastroenteritis.

Development and independent validation of a prognostic assay for stage ii colon cancer using formalin-fixed paraffin-embedded tissue

Purpose: Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples. Patients and Methods: A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery. Results: The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P <.001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P <.001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P <.001). Conclusion: This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples. © 2011 by American Society of Clinical Oncology.

Validation of Speciation Techniques: A Study of Chlorozincate(II) Ionic Liquids

The speciation of chlorozincate(II) ionic liquids, prepared by mixing 1-octyl-3-methylirnidazolium chloride, [C(8)mim]Cl, and zinc(II) chloride in various molar ratios, chi zncl(2), was investigated using Raman spectroscopy and differential scanning calorimetry; the Gutmann acceptor number, which is a quantitative measure of Lewis acidity, was also determined as a function of the composition. These results were combined with literature data to define the anionic speciation; in the neat liquid phase, the existence of cl(-), [ZnCl4](2-), [Zn2Cl6](2-), [Zn3Cl8](2-), and [Zn4Cl10](2-) anions was confirmed. From two chlorozincate(H) ionic liquids with [C(2)mim](+) cations (chi zncl(2) = 0.33 and chi zncl(2) = 0.50), crystals have been obtained, revealing the structures of [C(2)mim)(2)[ZnCl4] and [C(2)mim](2)[Zn2Cl6] forming three-dimensional hydrogen-bond networks. The compound [C(2)mim](2){Zn4Cl10} was crystallized from the chi zncl(1) = 0.75 composition, showing an open-framework structure, with the first example of zinc in a trigonal-bipyramidal chloride coordination. Reinvestigation of the electrospray ionization mass spectrometry of these systems demonstrated that it is an unreliable technique to study liquid-phase speciation.