Utilizing the Genexus System to Detect Complex Genetic Variants in Human Tissue Specimens

To identify genetic variants in archival human samples, researchers need a powerful NGS platform that can accommodate input DNA and RNA that is often low quality and/or low quantity. This challenge is compounded the diversity of frequently co-existing complex variants underlying somatic changes. Consequently, robust NGS assays capable of identifying single nucleotide variants (SNV), small indels, fusions, and copy number variation (CNV) in a single workflow are required. Molecular pathology research lab are now adopting the Thermo Genexus NGS platform for routine analysis of archival, formalin-fixed, paraffin embedded (FFPE) human tissue samples.  Compared to earlier NGS-based assays, the Thermo Genexus offers several important advantages. The amount of input DNA and RNA is lower than other assays permitting testing of a wider range of samples. Sequencing costs are reduced due to lower reagent costs and less hands-on time. Turnaround times are significantly faster. The Genexus assays are sensitive for detecting challenging variants such indels and copy number variation, as well as sequencing G-C rich DNA.  Examples several classes of genetic variants detected in archival, human FFPE samples using the Genexus are provided to demonstrate the performance of the Genexus NGS system.

Learning Objectives:

1. Demonstrate detection of copy number variation and single nucleotide variants in archival human tissue research samples

2. Discuss germline EGFR T790M in hereditary non-small cell lung cancer