Multisite validation study to determine performance characteristics of a 92-gene molecular cancer classifier

Sarah E. Kerr, Catherine A. Schnabel, Peggy S. Sullivan, Yi Zhang, Veena Singh, Brittany Carey, Mark G. Erlander, W. Edward Highsmith, Sarah M. Dry, Elena F. Brachtel

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


Purpose: Accurate tumor classification is essential for cancer management as patient outcomes improve with use of site- and subtype-specific therapies. Current clinicopathologic evaluation is varied in approach, yet standardized diagnoses are critical for determining therapy. While gene expression-based cancer classifiers may potentially meet this need, imperative to determining their application to patient care is validation in rigorously designed studies. Here, we examined the performance of a 92-gene molecular classifier in a large multi-institution cohort. Experimental Design: Case selection incorporated specimens from more than 50 subtypes, including a range of tumor grades, metastatic and primary tumors, and limited tissue samples. Formalin-fixed, paraffinembedded tumors passed pathologist-adjudicated review between three institutions. Tumor classification using a 92-gene quantitative reverse transcriptase polymerase chain reaction (RT-PCR) assay was conducted on blinded tumor sections from 790 cases and compared with adjudicated diagnoses. Results: The 92-gene assay showed overall sensitivities of 87% for tumor type [95% confidence interval (CI), 84-89] and 82% for subtype (95% CI, 79-85). Analyses of metastatic tumors, high-grade tumors, or cases with limited tissue showed no decrease in comparative performance (P = 0.16, 0.58, and 0.16). High specificity (96%-100%) was showed for ruling in a primary tumor in organs commonly harboring metastases. The assay incorrectly excluded the adjudicated diagnosis in 5% of cases. Conclusions: The 92-gene assay showed strong performance for accurate molecular classification of a diverse set of tumor histologies. Results support potential use of the assay as a standardized molecular adjunct to routine clinicopathologic evaluation for tumor classification and primary site diagnosis.

Original languageEnglish (US)
Pages (from-to)3952-3960
Number of pages9
JournalClinical Cancer Research
Issue number14
StatePublished - Jul 15 2012

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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