Abstract 3580: Hotspot mutation and fusion transcript detection from the same non-small lung adenocarcinoma sample

Abstract

Abstract The presence of certain chromosomal rearrangements and the subsequent fusion gene derived from translocations has been implicated in a number of cancers. Hundreds of translocations have been described in the literature recently but the need to efficiently detect and further characterize these chromosomal translocations is growing exponentially. The two main methods to identify and monitor translocations, fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH) are challenging, labor intensive, the information obtained is limited, and sensitivity is rather low. Common sample types for these analyses are biopsies or small tumors, which are very limited in material making the downstream measurement of more than one analyte rather difficult; obtaining another biopsy, using a different section or splitting the sample can raise issues of tumor heterogeneity. The ability to study mutation status as well as measuring fusion transcript expression from the same sample is powerful because you're maximizing the information obtained from a single precious sample and eliminating any sample to sample variation. Here we describe the efficient isolation of two valuable analytes, RNA and DNA, from the same starting sample without splitting, followed by versatile and informative downstream analysis. This methodology was applied to FFPE and degraded samples as well as fresh tissues and cells. DNA and RNA were recovered from the same non-small lung adenocarcinoma sample and both mutation analysis, as well as fusion transcript detection was performed using the Ion Torrent PGM™ platform on the same Ion 318™ chip. Using 10ng of DNA and 10ng of RNA input, we applied the Ion AmpliSeq™ Colon and Lung Cancer panel to analyze over 500 COSMIC mutations in 22 genes and the Ion AmpliSeq™ RNA Lung Fusion panel to detect 40 different fusion transcripts. Citation Format: Angie Cheng, Varun Bagai, Joey Cienfuegos, Natalie Hernandez, Mu Li, Jeff Schageman, Richard Fekete, Rosella Petraroli, Alexander Vlassov, Susan Magdaleno. Hotspot mutation and fusion transcript detection from the same non-small lung adenocarcinoma sample. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3580. doi:10.1158/1538-7445.AM2014-3580