SAN FRANCISCO (GenomeWeb) – Veracyte CEO Bonnie Anderson said this week that the company is working on two new products in the realm of thyroid and lung cancer diagnostics that would expand on the existing Afirma and Percepta tests it currently markets in those areas.
During a conference call to discuss the company's fourth quarter 2017 and full year performance, Anderson said that Veracyte plans to leverage its RNA sequencing and machine learning platform to "dig deeper into understanding the genomic underpinnings of disease."
Its first test, which it plans to launch in the second quarter of this year to improve thyroid cancer diagnosis, will be called Afirma Xpression Atlas. That test will be based on RNA sequencing and will analyze more than 760 variants and 130 fusions in 500 genes, as well as mitochondrial genes, and loss-of-heterozygosity. The product will "fill an important need and augment our current offering, allowing us to test more patients and inform a broader set of treatment decisions," Anderson said.
In a follow-up interview, Anderson said that the goal of the test is to help provide more information to physicians about how to manage patients who Afirma deems to be at risk of having cancer.
The new test follows an evolution of the Afirma pipeline. The first Afirma test, the Genomic Expression Classifier, was based on a microarray platform and helped physicians identify patients who were at low risk of thyroid cancer, reducing unnecessary surgeries. That test was able to identify about 50 percent of patients who were at low risk. Last year, Veracyte launched an updated version of that test, Afirma Genomic Sequence Classifier, which was based on RNA sequencing. That was the company's "entrée toward shifting our products over to the deep RNA sequencing platform," Anderson said. Afirma GSC identified 30 percent more patients who were at low risk of cancer.
The Afirma GSC test is based on deep whole transcriptome sequencing, but reports only whether a patient is likely to be benign or is suspicious for cancer. But, "we now have this rich platform," Anderson said, so the goal was to figure out what other information would be useful for physicians to manage patients.
The new test, Afirma Xpression Atlas, will report on markers that can help physicians make informed decisions about how to treat patients. For instance, it includes markers that are indicative of targeted therapies, as well as markers that can help to subtype the disease, which in turn could determine whether a particular cancer will be more or less aggressive. This information can help physicians decide whether a patient needs to have a surgery to remove the entire thyroid or whether a partial resection is sufficient. It will also provide advice on whether the standard treatment, radioactive iodine, can be used more sparingly, Anderson said.
"Thyroid biology is quite complicated," she said. For instance, some thyroid cancers contain Hürthle cells. These cells are found in two different subtypes of thyroid cancer, one of which is very aggressive and the other benign. Analyzing mitochondrial content is important for distinguishing between these two subtypes, Anderson said.
The second new test in Veracyte's pipeline aims to build off the Percepta test for lung cancer detection, using a nasal swab. Percepta looks at genomic changes in epithelial cells from the bronchial airway that are taken when physicians perform a bronchoscopy to evaluate lung nodules. Bronchoscopy is less invasive, less risky, and less costly than a lung biopsy. According to Veracyte's validation study of Percepta, which was published in the New England Journal of Medicine in 2015, using Percepta as a complement to bronchoscopy improved the sensitivity of identifying patients in two clinical trials to 96 percent and 98 percent, compared to 74 percent and 76 percent with bronchoscopy alone. The test also helped to identify cancer in patients for whom a bronchoscopy was non-diagnostic.
Percepta is based on the finding that there is a "field of injury" impacted by lung cancer, meaning that epithelial cells are impacted by cancer even though they are not themselves cancerous. In Percepta, epithelial cells from the bronchial airway are analyzed to help determine whether a patient may have lung cancer.
Now, though, Veracyte is looking to develop a test that will be even less invasive than Percepta, by analyzing cells from a nasal swab.
Last year, researchers from Boston University published a proof-of-concept study that showed that the field of injury may extend beyond the bronchial airway and into the nasal cavities. In a Veracyte-sponsored study published in the Journal of the National Cancer Institute last year, the researchers found that gene expression differences between patients with and without lung cancer could be seen in nasal swab samples.
That study identified just over 500 differentially expressed genes, but Anderson said the firm and its collaborators would continue to do discovery studies to determine what should be included in an eventual clinical test. She said that RNA sequencing would likely be used for those discovery studies, but that a clinical test may or may not be based on sequencing technology.
The nasal swab test would help set the stage for not only noninvasive detection but also, eventually, early detection, Anderson said. It will "use the field of injury technology to better stratify patients who are at risk for lung cancer and to improve early detection," she said.