Molecular Testing

The best way to determine if a thyroid nodule is cancerous is to do a fine needle aspiration biopsy (FNA) of the nodule. The FNA biopsy specimen is read by the cytopathologist.

The results of the biopsy are classified into one of six categories according to the risk of cancer (see our page on thyroid cytology for details). Two of these categories, in particular, can be problematic:

  • About 20% of nodules are classified as suspicious for a follicular neoplasm (SFN). These neoplasms can be either benign (75% of cases) or malignant (25% of cases).
  • About 10-15% of nodules are classified as atypical cells of undetermined significance (ACUS) or follicular lesion of undetermined significance (FLUS). This category is associated with a 5-30% risk of cancer.

Until 2011, patients with these indeterminate results from thyroid nodule biopsies either had to undergo diagnostic surgery to make a definitive diagnosis or were monitored closely. With an average risk of cancer at about 20%, many patients underwent unnecessary diagnostic operations. On the other hand, the rate of cancer in these indeterminate nodules was unacceptably high to simply monitor in most patients. Many doctors and patients felt stuck.

At the University of Colorado Hospital, doctors in our Thyroid Tumor Program have been working hard to develop and bring two types of molecular tests into clinical use to reduce unnecessary operations and decrease the chance that a patient with thyroid cancer in an indeterminate thyroid nodule will need a second operation.

Genomic Test

The first test is a ‘genomic’ test called the Afirma® Gene Expression classifier (Veracyte, Inc.).  This test uses a pattern of RNA expression from a needle biopsy to distinguish benign nodules which do not need surgery from suspicious nodules that need surgery.

We typically use this test on patients with indeterminate biopsies in the atypical (AUS/FLUS) or neoplasm (FN/SFN) categories.

  • A benign Afirma result has a 95% accuracy rate and allows us to safely avoid a diagnostic operation. These nodules are monitored for growth or other changes.
  • A suspicious result is associated with a 40-50% risk of thyroid malignancy, which means a thyroidectomy will be necessary.

Since implementing use of this test, we have reduced the number of unnecessary thyroid surgeries by 50%.

Genetic Test

The second test is a ‘genetic’ test that looks for mutations in several genes know to be altered in thyroid cancer.  This test is marketed by different laboratories, with the most commonly used test being miRInform® (Asuragen Corp).  If the test is positive, we can be fairly certain that a patent with an indeterminate biopsy has a thyroid cancer.

We generally use this test for patients who have indeterminate nodules and are likely to opt for diagnostic surgery for various reasons (e.g., suspicious features on ultrasound, large nodules, or patient preference). The test results help guide the type of surgery. If the mutation test is negative, it may be worth considering removing only half of the thyroid, preserving the other half. If the mutation test is positive, we recommend removing the entire thyroid


This heatmap represents the level of expression of many genes across a number of cells obtained from ribonucleic acid (RNA). Image courtesy of Bryan Haugen, MD, and Rebecca Schweppe, PhD, University of Colorado School of Medicine.


Both tests have been very helpful in guiding us on the best care for our patients with thyroid nodules and indeterminate biopsies.  Both tests are fairly expensive, but they have been shown to be cost-effective and are generally covered by insurance.  These tests are becoming more common across the United State, and they started right here at the University of Colorado.  We are now working on the next generation of molecular tests that will help predict how thyroid nodules and cancer will behave and ‘personalize’ therapies even more for each patient.

This information is provided by the Department of Surgery at the University of Colorado School of Medicine. It is not intended to replace the medical advice of your doctor or healthcare provider. Please consult your healthcare provider for advice about a specific medical condition.