RNA whole-transcriptome sequencing test informs thyroid cancer treatment decisions at time of diagnosis

Veracyte, Inc. (Nasdaq: VCYT) today announced the publication of new data demonstrating the clinical and analytical validity of its Afirma® Xpression Atlas (XA) genomic test, which is used to help guide surgery and treatment decisions for patients with likely or confirmed thyroid cancer. The new findings appear online in the journal Frontiers in Endocrinology.

The Afirma XA uses RNA whole-transcriptome sequencing to detect expressed DNA variants and RNA fusion partners in over 500 genes that are associated with thyroid cancer. The test is performed on fine needle aspiration (FNA) samples of thyroid nodules deemed suspicious for cancer by Veracyte’s Afirma Genomic Sequencing Classifier (GSC), as well as those that are suspicious for or have been diagnosed as cancer based on cytopathology. Importantly, the Afirma XA is performed on the same FNA sample as the Afirma GSC, obviating the need for patients to undergo an additional FNA procedure to obtain this genomic information about their thyroid.

To evaluate the Afirma XA’s clinical validity, researchers compared the test’s ability to identify genomic variants in an FNA sample’s transcriptome to currently accepted methods of targeted DNA and RNA sequencing. Using 943 blinded FNA samples, they found the Afirma XA had high positive predictive agreement (PPA) with targeted DNA sequencing (88 percent) and targeted RNA sequencing (89 percent). Similarly, using 695 blinded FNA samples to look for RNA fusions, the Afirma XA had an 82 percent PPA with targeted RNA sequencing. Conversely, 95 percent or more of variants and fusions identified by Veracyte’s RNA whole-transcriptome sequencing test were also identified by the reference method.

“Our findings suggest that the Afirma XA is sensitive and accurate in identifying gene alterations that are associated with thyroid cancer and confirm that the test can do this using one patient sample for all molecular testing,” said Trevor E. Angell, assistant professor of clinical medicine at the Keck School of Medicine of USC and lead author of the new paper. “The extensive genomic-alteration information provided by the Afirma test can help physicians tailor initial treatment for patients with likely or confirmed cancer and also provides information about the potential benefits of targeted therapies for those cancers that don’t respond to standard treatment.”

The researchers also investigated the reproducibility of the Afirma XA across laboratories and reagent lots. Using 69 variant-positive FNA samples, they found that the Afirma XA showed high accuracy between two different labs with different personnel for detecting variants (90 percent) and fusions (94 percent).

“The use of pre-operative molecular testing with minimally invasive FNA samples is expanding beyond cytologically indeterminate thyroid nodules to include those nodules with clear malignancy. Our findings demonstrate that physicians can be confident in the Afirma XA’s results at the time of diagnosis, which help guide surgery and treatment decisions,” said Richard T. Kloos, M.D., medical director of endocrinology for Veracyte and an author of the new study.

Source – BusinessWire

Angell TE et al. (2019) Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples. Front Endocrinol [Epub ahead of print]. [article]

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