Abstract 3571: mRNA spike-in control materials for cancer fusion gene detection assays

Abstract

Abstract Oncogenic fusion genes underlie the mechanism of several common cancers and also constitute or encode important diagnostic and therapeutic targets. Studies using next-generation sequencing technologies, particularly RNA sequencing (RNA-seq), have revealed a growing number of recurrent fusions in a variety of cancers. As such, establishing analytic parameters, including the limit of detection, sensitivity, and specificity of detecting fusions in tumor RNA specimens is important. We have developed reference materials useful in assessing the ability to detect fusion events in RNA or DNA samples. These consist of a set of nine synthetic poly-adenylated RNA transcripts that correspond to common cancer fusion gene sequences. These synthetic fusion RNAs can be spiked at known concentrations into total RNA in the first stage of the mRNA sample prep and used as in-line controls to evaluate the sensitivity and specificity of the detection of these mutations. As a demonstration of the utility of these controls, we performed a series of spike-in experiments to investigate performance characteristics of three commonly used fusion-detection software algorithms. Our results show all three algorithms to be capable of detecting fusions in a dose-dependent manner. The results also show differences in performance among the algorithms for detecting specific fusions. Citation Format: Winnie Liang, Stephanie JK Pond, Waibhav D. Tembe, Han-Yu Chuang, Christophe Legendre, Nancy Kim, Valerie Montel, Shukmei Wong, Timothy K. McDaniel, David Craig, John Carpten. mRNA spike-in control materials for cancer fusion gene detection assays. [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 3571. doi:10.1158/1538-7445.AM2014-3571