Comparison of Afirma Gene Expression Classifier with Gene Sequencing Classifier in indeterminate thyroid nodules: A single‐institutional experience

Introduction The Afirma test has been used in the diagnosis of cytologically indeterminate thyroid nodules to reduce diagnostic uncertainty and unnecessary surgeries. Gene Sequencing Classifier (GSC) was developed to improve the positive predictive value and overall test performance of Gene Expression Classifier (GEC). Here we present our experience comparing the performance of first‐generation assay of Afirma (GEC) with the new assay (GSC). Methods Retrospective analysis was performed on all Bethesda III and IV cytology thyroid nodules tested with GEC and GSC. Test performance was evaluated by surgical pathology outcomes. Results In total, 167 cases were tested with GEC, of which 49% were reported as benign. Fourteen cases had surgical follow‐up with 11 benign, one non‐invasive follicular thyroid neoplasm with papillary‐like nuclear features (NIFTP) and two malignant diagnoses. Of the 167 cases, 51% had suspicious GEC result. Fifty‐seven of these suspicious GEC cases had surgical follow‐up with 28 benign, nine NIFTP and 20 malignant histology. There 133 cases tested with GSC, of which 61% were reported as benign. Ten cases had surgical follow‐up, all of which showed benign results and 32% of the cases were tested as suspicious. Thirty‐six cases with suspicious GSC had surgical follow‐up. Fourteen of them had benign, five NIFTP, and 17 malignant surgical pathology. Based on molecular testing, surgical resection could have been be prevented 61% with GSC, compared to 49% with GEC test. Conclusion Our experience shows that GSC has a better test performance than GEC. Also, our data support that GSC identify more cases as benign and reduces the number of unnecessary surgeries compared to GEC. Afirma Gene Sequencing Classifier has a better test performance than the previous version of Afirma Gene Expression Classifier in indeterminate thyroid nodules.