BackgroundThe epidermal growth factor receptor (EGFR) mutation status assessment has become increasingly important given the significant impact of tyrosine kinase inhibitors in lung cancer management.Our aim was to compare real life operational characteristics for three EGFR mutation assays - two targeted approaches and a next generation sequencing (NGS) technique.MethodsEGFR mutation status was assessed for lung adenocarcinoma samples (formalin fixed- paraffin embedded samples) using qPCR, SNaPshot and NGS (Ion Torrent™) techniques.ResultsA total of 15 high clinical significance mutations were identified by at least one technique from the total of 64 samples. All mutations were identified by the TaqMan qPCR technique while SNaPshot in conjunction with fragment analysis identified 11 EGFR mutations. The NGS approach followed by an automatic analysis using the default calling parameters identified 10 mutations from the SNaPshot/qPCR panel and other three insertions, five point mutations and 58 silent variants; manual data review identified all 15 high significance mutations.ConclusionsPerformance was similar for high tumor content samples but careful data analysis and post hoc variant calling filter alterations were necessary in order to obtain robust results from low tumor content samples by NGS. NGS is able to generate a comprehensive mutational profile albeit at a higher cost and workload. Result interpretation should take into account not only general run parameters such as mean read depth but also relative coverage and read distribution; currently there is an acute need to define firm recommendations/standards concerning NGS data interpretation and quality control.
Mycobacteria culture remains the cornerstone of tuberculosis diagnosis. Naturally contaminated samples need pre-inoculation processing but some economically challenged medical facilities may benefit from a simpler and cheaper sputum decontamination procedure. The aim of this study was to test a simple decontamination method lacking a centrifugation step to be used in conjunction with the culture on Löwenstein-Jensen medium. A total of 7446 sputum samples collected from 3229 patients were microscopically examined and then cultured on Löwestein-Jensen medium using a simplified Petroff method. All positive cultures were confirmed by direct microscopic examination and biochemical identification. Culture and microscopic status and time to positivity were recorded. Mean and median times to culture and contamination rate were similar as compared to classical Löwenstein-Jensen culture method. Overall results suggest that the described modified of Petroff method may be used with adequate results in resource poor settings as the method does not require an aerosol safe centrifuge and relies on cheap, stable and readily available reagents.
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