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Analytical performance of a bronchial genomic classifier

  • Hu, Zhanzhi1
  • Whitney, Duncan1
  • Anderson, Jessica R.1
  • Cao, Manqiu1
  • Ho, Christine1
  • Choi, Yoonha1
  • Huang, Jing1
  • Frink, Robert1
  • Smith, Kate Porta1
  • Monroe, Robert1
  • Kennedy, Giulia C.1
  • Walsh, P. Sean1
  • 1 Veracyte, Inc., 6000 Shoreline Ct., Suite 300, South San Francisco, CA, 94080, USA , South San Francisco (United States)
Published Article
BMC Cancer
Springer (Biomed Central Ltd.)
Publication Date
Feb 26, 2016
DOI: 10.1186/s12885-016-2153-0
Springer Nature


BackgroundThe current standard practice of lung lesion diagnosis often leads to inconclusive results, requiring additional diagnostic follow up procedures that are invasive and often unnecessary due to the high benign rate in such lesions (Chest 143:e78S-e92, 2013). The Percepta bronchial genomic classifier was developed and clinically validated to provide more accurate classification of lung nodules and lesions that are inconclusive by bronchoscopy, using bronchial brushing specimens (N Engl J Med 373:243–51, 2015, BMC Med Genomics 8:18, 2015). The analytical performance of the Percepta test is reported here.MethodsAnalytical performance studies were designed to characterize the stability of RNA in bronchial brushing specimens during collection and shipment; analytical sensitivity defined as input RNA mass; analytical specificity (i.e. potentially interfering substances) as tested on blood and genomic DNA; and assay performance studies including intra-run, inter-run, and inter-laboratory reproducibility.ResultsRNA content within bronchial brushing specimens preserved in RNAprotect is stable for up to 20 days at 4 °C with no changes in RNA yield or integrity. Analytical sensitivity studies demonstrated tolerance to variation in RNA input (157 ng to 243 ng). Analytical specificity studies utilizing cancer positive and cancer negative samples mixed with either blood (up to 10 % input mass) or genomic DNA (up to 10 % input mass) demonstrated no assay interference. The test is reproducible from RNA extraction through to Percepta test result, including variation across operators, runs, reagent lots, and laboratories (standard deviation of 0.26 for scores on > 6 unit scale).ConclusionsAnalytical sensitivity, analytical specificity and robustness of the Percepta test were successfully verified, supporting its suitability for clinical use.

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