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Comment & Response
January 9, 2020

Concerns About Methodology in Study of Thyroid Nodule Gene Expression Classifier—Reply

Author Affiliations
  • 1Department of Head and Neck–Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
  • 2Department of Endocrinology and Nutrition, Hospital Universitario Ramón y Cajal, IRYCIS, Ctra, Colmenar Viejo, km. 9, 100, 28034 Madrid, Spain
  • 3Department of Biostatistics and Bioinformatics. H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
JAMA Otolaryngol Head Neck Surg. 2020;146(3):313-314. doi:10.1001/jamaoto.2019.4201

In Reply We appreciate Dr Kloos’s interest in our work,1 but respectfully disagree with his conclusions. He states that our analysis supports Afirma’s validated 94% or greater negative predictive value (NPV) on the basis that only 23 of the 1071 (2.1%) Afirma gene expression classifier (GEC) benign nodules were reported as malignant on surgical pathologic analysis. However, only a total of 149 such nodules were actually resected in the postmarketing studies, yielding a false-negative rate of 15.4% in these resected nodules, for an NPV of 84.6%.1 We recognize and acknowledge that selection bias likely exists in the decision to operate on GEC-benign nodules in these studies, based on ultrasound appearance, growth patterns, or other clinical features, which will enrich the number of cancers being resected despite a benign classifier result. However, there remain an unknown number of cancers in the unresected majority and the claimed NPV of Afirma GEC is as yet unverified.

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