OA01.04 A Comparability Study Verifying the Analytic Performance of a Blood-based Gene Expression Classifier to Identify Benign Pulmonary Nodules: Topic: Pulmonology

Abstract

We developed a blood gene expression classifier for lung cancer in current and former smokers with pulmonary nodules. The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group and the Centers for Disease Control’s ACCE Project (analytic validity, clinical validity, clinical utility, and associated ethical, legal, and social implications) recommend studies to evaluate analytical validity of novel genomic tests. Here we report results of the test’s analytic performance. A total of 299 previous or current smokers with nodules ranging from 5-30mm were enrolled in a multicenter prospective observational study. A blood sample was obtained at baseline. RNA was isolated from PAXgene tubes and analyzed utlilizing three separate NanoString nCounter® gene expression platforms. Using NanoString’s recommended protocol, we evaluated: accuracy across repeat samples (n=134); reproducibility across multiple instruments (n=24) and across multiple operators (6 unique runs); analytical precision (one benign and one malignant pool run 33 times, total n=66); analytic sensitivity/limits of detection (two benign and two malignant samples at eight different concentrations, total n=32); and analytic specificity/interfering substances (n=10). The accuracy study resulted in sensitivity 94.4% and specificity 67.5%. Reproducibility was measured at 93.1% and analytic precision at 100%. The analytic sensitivity study confirmed NanoString’s published RNA input recommendations, and the presence of interfering substances did not impact final test results. We developed a gene expression classifier that demonstrated reproducibility and robustness across multiple studies. These studies are consistent with EGAPP recommendations. Additional studies to show consistent performance when the test is transferred from the research lab to a CLIA setting as well as to demonstrate clinical validity and clinical utility are planned.