Validation of Next Generation Sequencing Technologies in Comparison to Current Diagnostic Gold Standards for BRAF, EGFR and KRAS Mutational Analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.

Software Products for Modelling and Simulation in Materials Science

Models and software products have been developed for modelling, simulation and prediction of different correlations in materials science, including 1. the correlation between processing parameters and properties in titanium alloys and ?-titanium aluminides; 2. time–temperature–transformation (TTT) diagrams for titanium alloys; 3. corrosion resistance of titanium alloys; 4. surface hardness and microhardness profile of nitrocarburised layers; 5. fatigue stress life (S–N) diagrams for Ti–6Al–4V alloys. The programs are based on trained artificial neural networks. For each particular case appropriate combination of inputs and outputs is chosen. Very good performances of the models are achieved. Graphical user interfaces (GUI) are created for easy use of the models. In addition interactive text versions are developed. The models designed are combined and integrated in software package that is built up on a modular fashion. The software products are available in versions for different platforms including Windows 95/98/2000/NT, UNIX and Apple Macintosh. Description of the software products is given, to demonstrate that they are convenient and powerful tools for practical applications in solving various problems in materials science. Examples for optimisation of the alloy compositions, processing parameters and working conditions are illustrated. An option for use of the software in materials selection procedure is described.

Assistive software tools for secondary-level students with literacy difficulties.

Study conducted to evaluate the effectiveness of four assistive technology (AT) tools on literacy: (1) speech synthesis, (2) spellchecker, (3) homophone tool, and (4) dictionary. All four of these programs are featured in TextHelp’s Read&Write Gold software package. A total of 93 secondary-level students with reading disabilities participated in the study. The participants completed a number of computer-based literacy tests after being assigned to a Read&Write group or a control group that utilized Microsoft Word. The results indicated that improvements in the following areas for the Read&Write group: (1) reading comprehension, (2) homophone error detection, (3) spelling error detection, and (4) word meanings. The Microsoft Word group also improved in the areas of word meanings and error detection, though performed worse on homophone error detection. The authors contend that these results indicate that speech synthesis, spell checkers, homophone tools, and dictionary programs have a positive effect on literacy among students with reading disabilities. This study was conducted by researchers at the Queen’s University in Belfast, Ireland.