Genomic diagnostics company Veracyte, South San Francisco, Calif, is making its next-generation Percepta genomic sequencing classifier (GSC) available to physicians. An upgrade over the company’s Percepta test, the genomic sequencing classifier is designed to give doctors access to more information about their patients’ risk of lung cancer.
The RNA whole-transcriptome sequencing-based test is Veracyte’s first commercial product to emerge since the company signed a long-term, strategic lung-cancer collaboration with Johnson & Johnson Innovation. The collaboration was announced in January 2019.

“Lung nodules are often challenging to diagnose using traditional tools, which can lead to unnecessary invasive procedures or to delayed treatment,” says Giulia Kennedy, PhD, Veracyte’s chief scientific and medical officer. “The ability to use genomic testing such as the Percepta GSC to determine which patients need intervention and those who may be safely monitored with routine imaging can help improve patient outcomes.”

Veracyte’s commercial introduction of the Percepta GSC follows a May 2019 presentation of clinical data showing that the genomic test downclassifies patients with suspicious lung nodules to low risk with a negative predictive value of 91%. The finding means that such patients have a low likelihood of cancer and may therefore avoid unnecessary invasive procedures. The findings also show that the test upclassifies patients to high risk with a positive predictive value of 65%, suggesting that there is a higher likelihood these patients have cancer, which can help guide next intervention steps.

The American College of Chest Physicians recommends that lung-nodule patients with a low risk of cancer undergo monitoring with computed tomography imaging, and that patients with a risk of 65% or greater undergo surgical treatment. The Percepta GSC study involved 412 lung-nodule patients whose results were inconclusive following bronchoscopy, a common nonsurgical procedure to assess lung nodules for cancer. The new study findings were shared during the 2019 annual meeting of the American Association for Bronchology and Interventional Pulmonology.1


Bonnie Anderson, Veracyte.

The Percepta GSC utilizes machine learning and is built on novel ‘field of injury’ science, which identifies genomic changes associated with lung cancer in current or former smokers using a simple brushing of the person’s airway. The test is performed on a sample from the patient’s main lung airway, which is collected during a bronchoscopy. Veracyte estimates that approximately 360,000 bronchoscopies are currently performed each year to evaluate suspicious lung nodules for cancer and that up to 60% of these produce inconclusive results.

“We are excited to make the Percepta GSC available to physicians as an important tool that will help them further guide next steps for patients undergoing evaluation for suspicious lung nodules,” says Bonnie Anderson, Veracyte’s chairman and chief executive officer.

Veracyte is collaborating with the lung cancer initiative at Johnson & Johnson to advance the development and commercialization of novel diagnostic tests to detect lung cancer at its earliest stages, when the disease is most treatable. The collaboration is accelerating key lung cancer programs for Veracyte, including the commercialization of its Percepta classifier on the company’s RNA whole-transcriptome sequencing platform, and the development of the first noninvasive nasal swab test for early lung cancer detection. Veracyte expects to unveil early data for the nasal swab test later this year.

Under the terms of their agreement, Veracyte and the lung cancer initiative at Johnson & Johnson will combine clinical study cohorts involving more than 5,000 patients with multiple years of clinical outcome data. Veracyte will contribute bronchial and nasal samples from its clinical trials, which are part of the company’s extensive lung cancer-focused biorepository.

Lung cancer is the leading cause of cancer deaths worldwide. In the United States, lung cancer causes more than 154,000 deaths each year—more than the next three most prevalent cancers combined. Because lung cancer is difficult to diagnose before it has metastasized, only 16% of cases are detected at an early stage, when the disease is more treatable. Lung cancer’s 5-year survival rate is only 18%—much lower than that of other common cancers. Approximately 80% of lung cancer deaths are caused by smoking.

For more information, visit Veracyte.


  1. Bhorade S, Bernstein M, Dotson TL, et al. Accuracy of the next-generation Percepta genomic sequencing classifier (GSC) for the diagnosis of suspicious intermediate pulmonary nodules [poster, online]. Presentation at the annual meeting of the American Association for Bronchology and Interventional Pulmonology, Denver, August 15–17, 2019. Available at: Accessed August 26, 2019.