Afirma® Thyroid Analysis

Genetic analysis of indeterminate lesions on FNA can evaluate malignant potential

Generally, the risk of thyroid cancer in any one thyroid nodule is low. When a patient has a thyroid FNA biopsy in our clinic result of "indeterminate", essentially the diagnosis is not more clear than prior to the biopsy. This can be very frustrating to the physician and the patient. Indeterminate results on thyroid FNA samples are a common (5-15% of biopsies depending on where biopsy done). Current guidelines recommend that most of these patients have a partial or total thyroid surgery, depending on risk factors, if a final diagnosis is desired.

As of 2011, genetic evaluation of these indeterminate thyroid nodules has been shown to be cost-effective by reducing unnecessary thyroid surgeries. We can offer these tests as part of our thyroid nodule evaluation and management.

The gene expression classifier is proprietary and owned by the company Veracyte.

Here are the details for those that are interested:

When our cytopathology assessment yields an indeterminate diagnosis, Veracyte's proprietary Gene Expression Classifier is performed and classifies the nodule as benign (>95% NPV) or suspicious. The test includes 142 genes, which were identified through whole-genome analyses of hundreds of thyroid samples to best differentiate benignity from malignancy in indeterminate thyroid FNA samples. Data from an independent, prospective multicenter validation trial involving more than 40 academic and community practices across the United States showed the test to have a negative predictive value of greater than 95 percent.

Key medical statistics for this test based on available data: Negative predictive value 96% Positive predictive value 57% Sensitivity 95% Specificity 63% (1,2,3,4)

Oct. 29, 2014 A poster entitled, "Long Term Clinical and Imaging Follow-Up of an Office-Based Gene Expression Classifier Used to Manage Thyroid Nodules" (Poster #269), summarized data from a study of patients with thyroid nodules who avoided surgery due to benign Afirma GEC results and were followed for up to three years. All 13 patients in the single-center study remained cancer-free, based on physical exam and ultrasound findings. Additionally, three patients with benign Afirma genomic test results who underwent surgery due to clinical symptoms were confirmed to have benign nodules – further validating the genomic test's accuracy.

Oct. 29, 2014 A poster entitled, "Performance of the Afirma Gene Expression Classifier on Indeterminate Thyroid Fine Needle Aspirates (FNAs) From Large Nodules" (Poster #39), summarized the Afirma GEC's performance on cytologically indeterminate nodules of >3 cm for which surgical pathology results were subsequently available. All five nodules identified as benign by the Afirma GEC were confirmed by surgery as benign, for a test sensitivity of 100% – underscoring the test's accuracy regardless of nodule size.


1. Lewis CM et al. 2009 Thyroid 19(7) 717-722.

2. Cooper DS et al. 2009 Thyroid 19(11) 1167-214.

3. Gharib H, AACE/AME/ETA Thyroid Nodule Guidelines, Endoc Pract. 2010:16(Suppl 1).BR,

4. Haugan et al. Abstract#LB137,International Thyroid Congress. Paris, FR 2010 (oral abstract).

5. Cost-effectiveness of a novel molecular test for cytologically indeterminate thyroid nodules.