September 27, 2016
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Development and Evaluation of an NGS Assay for Detecting RNA Fusions and Splicing Events in Lung Cancer


Chief Operating Officer, Molecular Pathology Center, Jewish General Hospital

Senior Scientist II and Group Leader, Asuragen, Inc.

This webinar described the design, development, and evaluation of a new gene panel for targeted RNA sequencing of formalin-fixed, paraffin-embedded lung cancer samples.

Dr. Richard Blidner, Senior Scientist II and Group Leader at Asuragen, first provided an overview of Asuragen's QuantideX NGS RNA Lung Cancer Kit. This product integrates reagents, controls, and bioinformatics software for sensitive, targeted NGS of RNA or total nucleic acid from challenging tumor biopsies.

Dr. Blidner briefly presented the kit design, workflow, and sample input requirements, and compared and contrasted the approach with other NGS methods. He also discussed supporting data and implications for low-copy number analytical sensitivity that can be achieved with the technology. Finally, he described the features and benefits of the companion QuantideX NGS Reporter software for fast and simple bioinformatic analysis that can be deployed on a conventional desktop computer.

Our second speaker, Dr. Léon van Kempen, Scientific Director of the Dubrovsky Molecular Pathology Center at the Jewish General Hospital, shared how his lab evaluated the QuantideX NGS RNA Lung Cancer Kit in a lung cancer study.

Dr. van Kempen and colleagues used the kit to analyze a cohort of 30 total nucleic acid isolates derived from FFPE residual tumor biopsies and cancer cell lines. Sequencing was performed on Illumina's MiSeq platform and data was analyzed using the QuantideX NGS Reporter software suite.

Dr. van Kempen discussed the results of the evaluation, which yielded 100% agreement for fusion and splice variant calling across 11 ALK fusions, 1 ROS1 fusion, 1 FGFR3 fusion, 1 MET exon 14 skipping and 16 negative samples.

The detection of 3’/5’ ALK expression imbalances in known fusion-positive samples indicated potential utility for the detection of fusions not explicitly targeted by the panel.

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