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BOSTON -- Fewer thyroid nodules were deemed suspicious with the Afirma gene classifier technology, according to researchers here.

Compared with their first generation technology available since early 2011, the gene expression classifier (GEC), the next generation Afirma (Veracyte) genetic sequence classifier (GSC) showed improved specificity in determining thyroid nodule cytology marked by a 21% reduction in Bethesda 3 and 4 nodules classified as suspicious, reported R. Mack Harrell, MD, of Memorial Healthcare System in Hollywood, Florida, and colleagues:

• Afirma GEC: 39.3% (200) benign versus 53.9% (274) suspicious
• Afirma GSC: 60% (48) benign versus 32.5% (26) suspicious

The study was one of several late-breaking posters involving Veracyte’s RNA sequencing-based test presented at the American Association of Clinical Endocrinologists (AACE) annual meeting.

Harrell's group also reported that the percentage of oncocytic Bethesda 3 and 4 nodules was generally similar between the GEC and GSC groups, at 21% and 22% of indeterminate cytology thyroid nodules, respectively.

However, there was a significant decrease of around 50% in the percentage of oncocytic patients classified as having a suspicious nodule with the GSC technology:

• Afirma GEC: 17.8% (19) benign versus 77.6% (83) suspicious
• Afirma GSC: 66.7% (12) benign versus 27.8% (5) suspicious

Both technologies serve as an aid in determining which Bethesda 3 and 4 fine-needle aspiration biopsied nodules were suspicious and in need of surgical removal, or which nodules were benign and could undergo observation.

Harrell told MedPage Today that this second-generation technology, which was released for clinical use in August 2017, was the "rule out cancer molecular technology," designed to "decrease the percentage of falsely positive Afirma GEC tested patients who were sent to surgery."

Harrell, who is also past president of AACE and current president of the American College of Endocrinology (ACE), said that at his endocrine surgical practice, use of the Afirma GSC increased benign calls, and reduced the amount of surgeries in patients with Bethesda 3 and 4 nodules by around 19% over roughly 7 months.

"Much of this improvement could be attributed to improved specificity in Hürthle Cell dominant biopsies," he said. "Afirma GSC appears to be a better choice than the GEC in practices that have substantial numbers of Hürthle Cell dominant Bethesda 3-4 nodules in their thyroid biopsy population. Hürthle Cell dominant Bethesda 3-4 nodules account for 21% our indeterminate cytologies."

Giulia Kennedy, PhD, chief scientific and medical officer for Veracyte in South San Francisco, explained the difference between Afirma GEC and GSC to MedPage Today.

"The original Afirma Gene Expression Classifier used RNA-based gene expression, which was measured on a microarray platform, with machine learning algorithms to recognize benign thyroid nodules among those diagnosed indeterminate by cytology. The rates of transcription from expressed genes are the 'features' that feed into the algorithm, which uses a form of pattern recognition to determine if a nodule is benign," she said.

"With the next-generation Afirma Genomic Sequencing Classifier, we are combining RNA sequencing and newer machine learning techniques to leverage more enriched, previously undetectable genomic information. This includes not only gene expression, but also the presence of DNA variants, RNA fusions, copy number variants, and other information that may be predictive of thyroid cancer."

As a result, the clinician receives a "richer genomic content that enhances the classifier's ability to distinguish benign from malignant nodules," she stated.

"Think of it as going from standard- to high-definition television -- we're producing a much higher-resolution genomic picture of thyroid nodules," said Kennedy.

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