On April 1, 2020 Veracyte, Inc. (Nasdaq: VCYT) reported results of a study that identified over 100 novel or rare NTRK, ALK, RET and BRAF fusions in fine needle aspiration (FNA) samples of patients undergoing evaluation for thyroid cancer (Press release, Veracyte, APR 1, 2020, View Source [SID1234556070]). These gene fusions – 70 of which are previously unreported – may potentially be targeted with specific kinase inhibitor drugs that are currently available or in development for use in thyroid cancer patients. Veracyte also announced that it has launched an expanded version of its Afirma Xpression Atlas (XA) test, which uses RNA sequencing to detect gene alterations – including these novel or rare fusions – at the time of diagnosis.

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The new data are featured in an abstract that was accepted for an oral presentation this week at ENDO 2020*, the annual meeting of The Endocrine Society. The study was one of two Afirma XA-related abstracts accepted for the meeting.

For the new study, researchers performed RNA whole-transcriptome sequencing on over 37,000 thyroid nodule FNA samples whose cytopathology results were either indeterminate (Bethesda III/IV) or suspicious for cancer (Bethesda V/VI). They found 104 novel or rare gene fusions – 7 NTRK1/3, 8 ALK, 17 RET and 72 BRAF – none of which were previously reported for thyroid cancer in The Cancer Genome Atlas (TCGA) program, a United States government catalogue of gene alterations associated with cancer. The authors subsequently examined over 50,000 FNA samples that had undergone testing with Veracyte’s Afirma Genomic Sequencing Classifier (GSC) and found that none of the novel or rare gene fusions were detected among those deemed benign. NTRK, ALK, RET and BRAF fusions, including those in the new study, were identified in 3.2 percent of the 16,594 Bethesda III/IV samples that were deemed suspicious for cancer by the Afirma GSC and in 8.0 percent of the 1,692 Bethesda V/VI samples.

"Identification of receptor tyrosine kinase fusions is important because they are potential targets for small molecule inhibitors that are now FDA-approved or in clinical trials to treat advanced thyroid cancers," said Lori J. Wirth, M.D., medical director of the Center for Head and Neck Cancers at Massachusetts General Hospital and lead author of the study. "By examining a large cohort of patients with RNA whole-transcriptome sequencing, we identified potentially actionable RTK fusions in thyroid nodules beyond those described in TCGA, which may have an impact on treatment decisions for many patients."

Veracyte also announced the introduction of its expanded Afirma XA, which provides physicians with additional gene alteration content – including the novel or rare NTRK, ALK, RET and BRAF fusions from the new study – to further inform surgery and treatment decisions for patients with suspected or confirmed thyroid cancer. The Afirma XA utilizes RNA sequencing on the same FNA sample used for Afirma GSC testing. Compared to the original gene alteration panel, the expanded Afirma XA now reports 905 DNA variants (versus 761) and 235 RNA fusion partners (versus 130) in 593 genes (versus 511).

"By including additional gene fusion data that can potentially be targeted with new therapies, the expanded Afirma XA provides physicians with even more powerful information with which to guide surgery and treatment decisions in their patients with thyroid cancer," said Richard T. Kloos, M.D., senior medical director of endocrinology at Veracyte. "Importantly, the Afirma XA provides this information pre-operatively through a minimally invasive FNA sample."

In the second Afirma XA-focused abstract accepted for ENDO 2020 – as a poster presentation – researchers reported on the positive predictive value of TP53 gene variants among thyroid nodules deemed suspicious for cancer by the Afirma GSC following indeterminate cytopathology results.

About Afirma

The Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas provide physicians with a comprehensive solution for thyroid nodule diagnosis. The Afirma GSC was developed with RNA whole-transcriptome sequencing and machine learning and helps identify patients with benign thyroid nodules among those with indeterminate cytopathology results in order to help patients avoid unnecessary diagnostic thyroid surgery. For those with suspected thyroid cancer, the Afirma Xpression Atlas provides physicians with genomic alteration content from the same fine needle aspiration samples that are used in Afirma GSC testing and may help physicians decide with greater confidence on the surgical or therapeutic pathway for their patients.