A Novel Nasal Swab for Lung Cancer Detection

In the United States, lung cancer is the second most common cancer in both men and women. It’s also the leading cause of death from cancer. Treatments are more likely to be successful if tumors are found at an early stage, when small and prior to metastasis. To enable early detection, diagnostic tests are vital. The Percepta Nasal Swab test is used to detect smoking-related damage associated with lung cancer in current or former smokers using a sample collected from the nasal passage. The Percepta Genomic Atlas is then used to inform treatment by providing information on which gene variants are present in tissue samples.

Technology Networks spoke to Dr. Giulia Kennedy, chief scientific officer and chief medical officer for Veracyte, to learn more about the Percepta Genomic Atlas and nasal swab tests for the diagnosis of lung cancer.

Kate Robinson (KR): How is lung cancer typically detected?

Giulia Kennedy (GK): Lung nodules are typically the first sign of lung cancer and cannot be ignored; however, most of them are benign. Currently, we estimate that nearly one million patients with suspicious lung nodules are sent to a pulmonologist for a workup each year, with most nodules found incidentally. Lung cancer screening programs are increasing and recent U.S. Preventive Services Task Force recommendations expand the number of people eligible for annual lung cancer computed tomography (CT) screening to an estimated 15 million. So, we expect the number of patients identified with suspicious nodules will continue to grow.

Unfortunately, when evaluating these nodules, physicians currently lack objective tools to determine the likelihood that they are cancerous. This uncertainty can lead to unnecessary invasive diagnostic procedures, including surgery, or potentially to delayed diagnosis and treatment.

This is why we are so excited about the Percepta Nasal Swab test, which will provide physicians with a noninvasive, objective tool to help physicians determine which patients are low risk for cancer and may avoid unnecessary invasive procedures and which are high risk and may be confidently directed to further work-up and, if needed, treatment.

KR: Can you elaborate on the science and technologies behind the nasal swab test?

GK: This first-of-its-kind test is performed on cells collected from the nasal passage using a simple nasal swab. The test uses an established “field of injury” principle to detect smoking-related damage in the airway, which is associated with lung cancer and can be detected in the nose.

We used machine learning on whole-transcriptome RNA sequencing data from nasal swabs, along with clinical factors, to develop the test algorithm, which is comprised of 502 genes. We “trained” the algorithm to recognize cancer cells vs. non-cancerous cells using a large training set of nasal samples from over 1,100 patients. These samples included all types and stages of lung cancer, as well as a range of clinical factors – in other words, the same wide range of samples the test would encounter once available clinically.

We then clinically validated the locked classifier, or algorithm, on an independent test set of 249 patients. The test set was comprised of multiple cohorts of prospectively collected nasal samples of current or former smokers undergoing evaluation for lung nodules found on CT. All patients were followed up for one year or until physicians made a final, adjudicated diagnosis. Our findings – which were presented at the ASCO annual meeting – showed that the test can identify, with a high level of accuracy, which patients with lung nodules found on CT scans do not have cancer so they may avoid unnecessary invasive procedures. The data also suggest that the test can determine which patients are at high risk of cancer so they may be efficiently diagnosed and, if needed, obtain appropriate treatment more quickly. Veracyte plans to commercially introduce the test in the second half of 2021.

KR: Can you tell us about the Percept Genomic Atlas test that is being developed to inform treatment decisions in lung cancer?

GK: The in-development Percepta Genomic Atlas is for patients who have already been diagnosed with lung cancer. The test will provide comprehensive genomic profiling information on cancerous lung nodules, masses or lymph nodes, utilizing small samples from the same biopsy procedure used for diagnosis (i.e., transbronchial needle aspirate biopsies or TBNA). The test uses targeted DNA and whole-transcriptome RNA sequencing to detect alterations in more than 50 genes known to be present in lung cancer. Preliminary data demonstrating the test’s performance have been shared at the American Thoracic Society international conference and at the ASCO meeting. Veracyte plans to launch the test in the second half of 2021.

KR: What impact could these tools have on patient outcomes and prognosis?

GK: These tests are part of Veracyte’s comprehensive lung cancer portfolio, which also includes our Percepta Genomic Sequencing Classifier, which helps improve lung cancer diagnosis when results of bronchoscopy, a common tool for diagnosing potentially cancerous lung nodules, are inconclusive. Collectively, our tests are leveraging cutting-edge genomic science and technology to provide answers and insights that enable physicians and patients to make better, faster and more confident care decisions. Ultimately, we believe this will help save more lives and will take enormous waste out of the healthcare system.

Dr. Giulia Kennedy was speaking to Kate Robinson, Editorial Assistant for Technology Networks