Abstract 5354: Evaluation of quantity, quality and performance with the TruSight® Tumor 170 solid tumor profiling assay of nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) tissue sections
Authors: Jennifer S. LoCoco, Li Teng, Danny Chou, Xiao Chen, Byron Luo, Jennifer Sayne, Ashley Adams, Naseem Ajili, Cody Chivers, Beena Murthy, Laurel Ball, Allan Castaneda, Katie Clark, Brian Crain, Anthony Daulo, Manh Do, Tingting Du, Sarah Dumm, Yonmee Han, Michael Havern, Chia-Ling Hsieh, Tingting Jiang, Suzanne Johansen, Scott Lang, Rachel Liang, Jaime McLean, Yousef Nassiri, Austin Purdy, Jason Rostron, Jennifer Silhavy, June Snedecor, Natasha Talago, Li Teng, Kevin Wu, Chen Zhao, Clare Zlatkov, Ali Kuraishy, Karen Gutekunst, Sohela De Rozieres, Matthew Friedenberg, Han-Yu Chuang, Anne C. Jager
Journal: Cancer Research (2017)

Abstract Solid tumor profiling assays need to deliver accurate and consistent results in the face of decreased quality and quantity of nucleic acids extracted from FFPE samples. Understanding the performance of a particular solid tumor profiling assay with FFPE tissue is critical, but with limited and non-renewable samples available to most assay-developers, the sample number used to understand this performance can be small. TruSight® Tumor 1701 is an Illumina-developed comprehensive solid tumor profiling panel targeting 170 genes using DNA and RNA from FFPE samples. In order to confirm the robustness of the assay with FFPE tissue, 2310 FFPE samples were brought in-house and evaluated. Quantity of both DNA and RNA extraction were determined by various methods, including AccuClear™, Qubit™ and Quantifluor® fluourometric assays. Overall, &amp;gt;95% of the samples achieved the minimum concentrations required for the TruSight® Tumor 170 assay. As a surrogate for DNA quality, we measured the amplification potential of the nucleic acid by assessing a ΔCq value using quantitative PCR after normalization to a fixed input mass. To assess RNA quality, we used the DV200 metric, which measures the percentage of RNA fragments &amp;gt;200 nucleotides in length. We examined ΔCq and DV200 values across different tissues and didn’t find a significant difference between tissues. Finally, we assessed the ability of samples to pass the sample quality control (QC) metrics in the TruSight® Tumor 170 assay. These QC metrics ensure accurate variant calling, with a sensitivity and specificity of ≥95%. We found that samples that had a ΔCq value of ≤5 and a DV200 value of ≥20 achieved a QC success rate above 95%. This data highlights the need for further investigation into the methods for extraction, quantification and quality assessment of nucleic acids for solid tumor profiling and underscores the robustness of TruSight® Tumor 170 with FFPE samples. 1 For Research Use Only. Not for use in diagnostic procedures. Citation Format: Jennifer S. LoCoco, Li Teng, Danny Chou, Xiao Chen, Byron Luo, Jennifer Sayne, Ashley Adams, Naseem Ajili, Cody Chivers, Beena Murthy, Laurel Ball, Allan Castaneda, Katie Clark, Brian Crain, Anthony Daulo, Manh Do, Tingting Du, Sarah Dumm, Yonmee Han, Michael Havern, Chia-Ling Hsieh, Tingting Jiang, Suzanne Johansen, Scott Lang, Rachel Liang, Jaime McLean, Yousef Nassiri, Austin Purdy, Jason Rostron, Jennifer Silhavy, June Snedecor, Natasha Talago, Li Teng, Kevin Wu, Chen Zhao, Clare Zlatkov, Ali Kuraishy, Karen Gutekunst, Sohela De Rozieres, Matthew Friedenberg, Han-Yu Chuang, Anne C. Jager. Evaluation of quantity, quality and performance with the TruSight® Tumor 170 solid tumor profiling assay of nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) tissue sections [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5354. doi:10.1158/1538-7445.AM2017-5354