Molecular profiling and feasibility using a comprehensive hybrid capture panel on a consecutive series of non-small-cell lung cancer patients from a single centre

Background: Targeted next-generation sequencing (NGS) is recommended to screen actionable genomic alterations (GAs) in patients with non-small-cell lung cancer (NSCLC). We determined the feasibility to detect actionable GAs using TruSight™ Oncology 500 (TSO500) in 200 consecutive patients with NSCLC. Materials and methods: DNA and RNA were sequenced on an Illumina® NextSeq 550 instrument and processed using the TSO500 Docker pipeline. Clinical actionability was defined within the molecular tumour board following European Society for Medical Oncology (ESMO) guidelines for oncogene-addicted NSCLC. Overall survival (OS) was estimated as per the presence of druggable GAs and treatment with targeted therapy. Results: Most patients were males (69.5%) and former or current smokers (86.5%). Median age was 64 years. The most common histological type and tumour stage were lung adenocarcinoma (81%) and stage IV (64%), respectively. Sequencing was feasible in most patients (93.5%) and actionable GAs were found in 26.5% of patients. A high concordance was observed between single-gene testing and TSO500 NGS panel. Patients harbouring druggable GAs and receiving targeted therapy achieved longer OS compared to patients without druggable GAs. Conversely, patients with druggable GAs not receiving targeted therapy had a trend toward shorter OS compared with driver-negative patients. Conclusions: Hybrid capture sequencing using TSO500 panel is feasible to analyse clinical samples from patients with NSCLC and is an efficient tool for screening actionable GAs

Calibration of the MCAO Canopus Bench

The final phase of implementation of all optical components, as well as their integration and tests on the Canopus MCAO bench is currently underway. We present here a detailed description of the LGS and NGS WFS calibration sequences implemented through MYST (MCAO Yorick Smart Tool), a yorick+python+glade software package developed in-house which allows multiple users to control and monitor the bench remotely over the network using EPICS

The Gemini MCAO bench: system overview and lab integration

We present Canopus, the AO bench for Gemini's Multi Conjugate Adaptive Optics System (GEMS), a unique facility for the Gemini South telescope located at Cerro Pachon in Chile. The MCAO system uses five laser beacons in conjunction with different natural guide stars configurations. A deployable fold mirror located in the telescope Acquisition and Guiding Unit (A&G) sends the telescope beam to the entrance of the bench. The beam is split within Canopus into three main components: two sensing paths and the output corrected science beam. Light from the laser constellation (589nm) is directed to five Shack-Hartman wave front sensors (E2V-39 CCDs read at 800Hz). Visible light from natural guide stars is sent to three independent sensors arrays (SCPM AQ4C Avalanche Photodiodes modules in quad cell arrangement) via optical fibers mounted on independent stages and a slow focus sensor (E2V-57 back-illuminated CCD). The infrared corrected beam exits Canopus and goes to instrumentation for science. The Real Time Controller (RTC) analyses wavefront signals and correct distortions using a fast tip-tilt mirror and three deformable mirrors conjugated at different altitudes. The RTC also adjusts positioning of the laser beacon (Beam Transfer Optics fast steering array), and handles miscellaneous offloads (M1 figure, M2 tip/tilt, LGS zoom and magnification corrections, NGS probes adjustments etc.). Background optimizations run on a separate dedicated server to feed new parameters into the RTC

The Gemini Multi-Conjugate Adaptive system sees star light

The Gemini Multi-Conjugate Adaptive Optics system (GeMS) has been in commissioning in the first 5 months of 2011. In this paper we present the first results of this commissioning period and plans for the future

The gemini MCAO system GeMS: Nearing the end of a lab-story

GeMS (the Gemini Multi-conjugated adaptive optics System) is a facility instrument for the Gemini-South telescope. It will deliver a uniform, diffraction-limited image quality at near-infrared (NIR) wavelengths over an extended FoV or more than 1 arcmin across. GeMS is a unique and challenging project from the technological point of view and because of its control complexity. The system includes 5 laser guide stars, 3 natural guide stars, 3 deformable mirrors optically conjugated at 0, 4.5 and 9km and 1 tip-tilt mirror. After 10 years since the beginning of the project, GeMS is finally reaching a state in which all the subsystems have been received, integrated and, in the large part, tested. In this paper, we report on the progress and current status of the different sub-systems with a particular emphasis on the calibrations, control and optimization of the AO bench

Gemini multiconjugate adaptive optics system review - I. Design, trade-offs and integration

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