On May 26, 2021 Veracyte, Inc., (Nasdaq: VCYT) reported new data that show the company’s Afirma Xpression Atlas (XA) can identify clinically relevant gene fusions in thyroid nodule samples collected via fine needle aspiration (FNA) (Press release, Veracyte, MAY 26, 2021, View Source [SID1234580622]). The findings, which will be presented June 4 at the 2021 American Society of Clinical Oncology (ASCO) (Free ASCO Whitepaper) Annual Meeting, support use of the whole transcriptome RNA-sequencing test to detect gene fusions that may guide the use of targeted treatments for thyroid cancer.

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"The increasing availability of targeted therapies for thyroid cancer, including tyrosine kinase inhibitors, means physicians must have tools that reliably identify the patients who may benefit from these therapies," said Lori J. Wirth, M.D., medical director of the Center for Head and Neck Cancers, Mass General Cancer Center, who will present the data. "Using the Afirma XA test, we were able to identify and report the prevalence of clinically relevant gene variants and fusions in real-world thyroid nodule samples."

The American Cancer Society predicts that more than 44,000 individuals will be diagnosed with thyroid cancer in the United States this year. Pathologists use the Bethesda system to classify thyroid nodules into several categories – from benign to malignant – using FNA samples. The Afirma XA uses whole transcriptome RNA sequencing to identify 905 DNA variants and 235 RNA fusions in 593 genes on FNAs taken from thyroid nodules. Increasing numbers of these gene fusions can be targeted by small-molecule therapies.

In the study to be presented at ASCO (Free ASCO Whitepaper) (Abstract 6803), researchers analyzed data from 50,644 thyroid FNA samples submitted to Veracyte’s CLIA laboratory to determine the prevalence of selected receptor tyrosine kinase (RTK) fusions of ALK, BRAF, NTRK1/3 or RET fusions. The Afirma Genomic Sequencing Classifier (GSC) had been used to classify samples as benign or suspicious following an indeterminate result by cytopathology (Bethesda III-IV). Researchers performed the Afirma XA on samples that were deemed suspicious by the GSC or that were likely or confirmed cancerous by cytopathology (Bethesda V/VI).

More than 32,000 samples were classified as benign with the Afirma GSC and no RTK fusions were identified. Of the 16,594 samples classified as suspicious by the Afirma GSC, 3% harbored RTK fusions. In the nearly 1,700 samples classified as either suspicious for malignancy or malignant, 8% were found to have RTK fusions. The most common fusion was ETV6/NTRK3, while BRAF fusions had the most diversity with 80 different gene partners.

"These findings suggest that by using the Afirma GSC and XA tests, physicians can confidently classify individual patients’ thyroid nodules and, for nodules that are malignant, determine whether treatment with a targeted therapy is appropriate," said Richard T. Kloos, M.D., Veracyte’s executive medical director. "We look forward to future analyses of how Afirma XA test results impact initial treatment and patient outcomes."