Bayer Corp. and Veracyte Inc. are collaborating in the thyroid cancer space, with an eye toward identifying underlying genomic drivers, including NTRK gene fusions, within patients’ tumors.

South San Francisco-based Veracyte offers the Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas (XA), which aims to help physicians in terms of thyroid cancer diagnosis and individualized care. Clinicians can assess multiple clinical questions for their thyroid patients using a single, minimally invasive fine needle aspiration (FNA) sample.

Under this new partnership, Bayer will provide Afirma XA testing at no cost to all eligible patients when ordered by the physician, irrespective of the results and treatment decision. Physicians treating patients found to harbor NTRK gene fusions as an underlying driver in their thyroid cancer will learn of these results. The partners expect the program to launch in the first quarter of 2021.

“Our collaboration with Bayer will help ensure that all eligible thyroid cancer patients can be tested and identified for actionable genomic alterations … so they may potentially benefit from biomarker-driven therapies,” explained Bonnie Anderson, Veracyte’s chair and CEO. Anderson noted that it is Veracyte’s first collaboration with Bayer, which has a U.S. presence in Whippany, N.J.

Resolving uncertainty

Veracyte’s next-generation Afirma GSC is intended to resolve diagnostic uncertainty in the roughly 525,000 patients who undergo FNA biopsies each year to assess potentially cancerous thyroid nodules. The company has estimated that up to 30% of these patients receive unclear results in terms of being benign or malignant. Many patients ultimately undergo surgery, even as most nodules end up proving benign.

The Afirma XA uses RNA whole-transcriptome sequencing to identify 905 DNA variants and 235 RNA fusions in 593 genes, including novel NTRK fusions, on FNAs taken from thyroid nodules or lymph nodes. “The panel includes potential unknown variants that have not yet been published in the literature for their association with thyroid cancer,” Tracy Morris, vice president of corporate communications & investor relations for Veracyte, told BioWorld.

This new collaboration will focus on those with advanced or metastatic thyroid cancer that is radioactive iodine refractory (RAIR) and who may potentially benefit from biomarker-driven therapies.

This year alone, about 53,000 people in the U.S. are expected to be diagnosed with thyroid cancer. In about 30% of cases, the cancer has metastasized, with the nearby lymph nodes. NTRK gene fusions, which may drive tumor growth in some cancers, are more common in patients with RAIR thyroid cancer.

“Patients whose thyroid cancer contains actionable alterations and no longer responds to traditional radioactive iodine therapy now have targeted treatment options available to them. Our goal is to identify such patients so physicians can make more informed treatment decisions for their patients,” said Bhavesh Ashar, senior vice president and head of U.S. Oncology at Bayer. “With its comprehensive ability to identify broad genomic alterations through its Afirma XA test and its widespread reach among physicians who diagnose thyroid cancer, Veracyte is an ideal collaborator for this program.”

Chowdary Dondapati, executive director, head of CDx Marketing at Bayer, told BioWorld that the collaboration currently only includes eligible U.S. patients. He reaffirmed the expected launch date and that it is anticipated to last for a limited time.

Dondapati also stressed that providers alone will determine a patient’s treatment regimen.

Strong Q3, ongoing partnerships

Despite COVID-19, Veracyte saw strength in the third quarter, with revenue and volumes rising significantly over the prior quarter and bouncing back to pre-pandemic levels. During a call on results, Anderson said revenue from genomic testing and products came in at $30.3 million, representing an increase of 79% vs. the second quarter and 13% over the third quarter of 2019. “Our Afirma business led the recovery, with volumes surpassing the third quarter of last year by 6%,” she noted.

Anderson also highlighted partnerships, including ones with Johnson & Johnson (J&J) and Acerta, as well as its Loxo Eli Lilly program in thyroid cancer. The latter deal was disclosed in April 2018 and gives Loxo Oncology information regarding thyroid cancers with TRK fusions and RET alterations for use in developing its targeted cancer therapies.

Last week, Veracyte said it had expanded its collaboration with the Lung Cancer Initiative at J&J. The collaboration will cover the NOBLE trial, a 9,000-patient, prospective, multicenter clinical study that aims to distinguish genomic and other differences in lung cancer development and progression among patients with lung nodules detected by CT imaging.