Validation of the Oncomine focus panel for next-generation sequencing of clinical tumour samples.

The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM) and validate the Oncomine Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue.

Could molecular pathology testing in lung cancer be more cost-effective?

Aims: EGFR and ALK analysis is routinely undertaken prior to targeted treatment of non-squamous non-small cell lung carcinoma (NSCLC). Increasingly, limited resources require molecular pathology services to be cost-effective without detriment to patient care.

Methods: Data from an audit of molecular pathology testing in the South East Scotland Cancer Network (SCAN) network have been used to explore different testing strategies with the aim of reducing costs; including investigation of thyroid transcription factor 1 (TTF1) expression as a negative predictor for EGFR mutations.

Molecular pathology in lung cancer: a guide to the techniques used in clinical practice.

Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology.

Making the most of pathological specimens: molecular diagnosis in formalin-fixed, paraffin embedded tissue.

The development of commercial reagents designed specifically for use with formalin-fixed paraffin-embedded (FFPE) tissue has unlocked the diagnostic potential of this prolific resource. The availability of archival FFPE tissue and tissue from current patients make it an ideal resource for molecular testing. Despite its stability and ability to preserve morphological information, FFPE provides a number of technical challenges to the study of biomolecules.

The reliable detection of Barley yellow and mild mosaic viruses using real-time PCR (TaqMan).

Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV) are economically-important, soil-borne pathogens of winter barley. Until recently, laboratory diagnosis of these pathogens has relied upon ELISA using polyclonal antiserum. However, due to the unstable nature of these viruses, combined with the inability to sap transmit BaYMV, high quality antiserum has been difficult to obtain and as a result the performance of ELISA is often unsatisfactory.

The detection of tuber necrotic isolates of Potato virus Y, and the accurate discrimination of PVY(O), PVY(N) and PVY(C) strains using RT-PCR.

Potato tuber necrotic ringspot disease (PTNRD) is a damaging disease of potatoes, causing unsightly necrotic rings on the surface of tubers. The causal agent is thought to be tuber necrotic isolates of Potato virus Y, known as PVY(NTN). The disease spoils tubers for processing and table use, and the lack of a diagnostic method makes control especially difficult.