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Journal Articles Show Veracyte Percepta Lung Cancer Test Development, Utility


NEW YORK (GenomeWeb) – Veracyte launched its new Percepta bronchial genomic classifier test for lung cancer last month and now has two peer-reviewed publications to help support the validity of the biomarker panel and its efficacy in averting potentially risky lung biopsies.  

One paper in BMC Medical Genomics described the development of the test while another in the New England Journal of Medicine reported on findings from two large multicenter clinical trials that suggest the Percepta test could provide a way to rule out cases of lung cancer following an indeterminate bronchoscopy.

"What [doctors] need are biomarkers with high negative predictive value" when attempting to diagnose lung cancer, Douglas Arenberg, a professor at the University of Michigan Medical School who was not involved in either publication, told GenomeWeb.

Often, a CT scan of the lung will show a suspicious nodule, prompting a minimally invasive bronchoscopy to look for signs of cancer, but 40 percent of those return an indeterminate result. Seemingly normal cells may actually have altered gene expression profiles in patients with lung cancer, especially in smokers.  The microarray-based Percepta test is performed in conjunction with a bronchoscopy, with airway epithelial cells harvested to evaluate the expression of 23 genes. RNA collected from the cells is converted to cDNA and run on Affymetrix Human Gene 1.0 ST arrays.

Arenberg said several similar tests have been proposed, but the Percepta test is "probably one of the better ones so far. It has the best combination of features when used the way it was used in this study," he said, referring to the NEJM paper. "We may be changing our practice with something like this."

Scientists led by Duncan Whitney of Veracyte and Avrum Spira of Boston University School of Medicine published a paper earlier this month in BMC Medical Genomics describing the development of the test. Taking bronchial epithelial cells from 299 current or former smokers, the scientists found 232 genes for which altered expression levels were associated with lung cancer. They selected 17 to create a gene expression panel, which was able to correctly give a negative diagnosis in 94 percent of patients.

"It can give you confidence that if the test is negative, it's highly unlikely to be cancer," said Spira, who is also a paid consultant to Veracyte and who co-founded Percepta developer Allegro Diagnostics, which Veracyte acquired in September 2014. "Those are patients physicians can follow noninvasively." If doctors can rule out cancer with the test, they will not need to bring patients in for a surgical biopsy to do so. Biopsies can provide a definitive diagnosis, but result in significant complications in 4 to 5 percent of patients.

The second paper, published in NEJM this week and also led by Spira and the members of the Airway Epithelial Gene Expression in the Diagnosis of Lung Cancer (AEGIS) study team, presented results from the AEGIS-1 and AEGIS-2 multi-center studies that indeed showed Percepta could help rule out lung cancer and prevent biopsy.

Between the two AEGIS studies, there were 639 patients at 28 sites who were current or former smokers and were undergoing a bronchoscopy to find lung cancer. The combination of the classifier plus bronchoscopy had a sensitivity of 96 percent in AEGIS-1 and 98 percent in AEGIS-2, independent of lesion size and location, the authors wrote in the NEJM publication.

"The bottom line is [the] biomarker panel has high sensitivity and high predictive value," Spira said. "We picked up more than 90 percent of lung cancers in the study with our test."

The test has some limitations, Arenberg, the University of Michigan professor, said. It doesn't work for never-smokers, which account for about 10 to 15 percent of lung cancer cases, and it requires a bronchoscopy, which can cost several thousand dollars and is a somewhat invasive procedure, though not as invasive as a lung biopsy. There's also the risk that the test might encourage more bronchoscopies, he said, but the number of those procedures might be on the rise regardless of the success of the Percepta test.

Spira estimated that there are about 250,000 bronchoscopies performed for suspicion of lung cancer each year in US, but said that number is about to get much bigger. In February, the Centers for Medicare & Medicaid Services issued a final national coverage definition providing coverage for CT scans for lung cancer screening. And when a CT scan reveals a suspicious nodule, bronchoscopy is often the next step used to try and rule out lung cancer.

So if the doctor is going to do a bronchoscopy, adding on the Percepta test could help limit the number of unnecessary biopsies, Arenberg said. The NEJM paper could spur institutions to band together and validate the test in an even larger cohort in a clinical setting. "Does this work when done in practice? That's the question that remains unanswered," he said.

Percepta is commercially available through Veracyte's CLIA lab. "We're already testing patient samples," Veracyte CEO Bonnie Anderson told GenomeWeb. "We've had some sites come on early to get access to the test and being using it in patient care decision making."

Anderson wouldn't say how much the test costs, only mentioning that Veracyte's Afirma thyroid nodule gene expresssion classifier test had a sticker price of $4,875 and that "the retail price of Percepta could be in the same range," but she doesn't think patients will pay that sticker price. Anderson said the papers are two key parts of evidence the firm will submit to insurers and to CMS to garner coverage and reimbursement for the test.

"We save a surgery for every two [Afirma GEC] tests we perform," Anderson said. "We believe Percepta offers the same level of value. We hope to garner value in the $3,000 to $4,000 range."

Anderson said that the firm plans to commercialize the test separately from Afirma, with a small sales team that she said could grow to three or four people by the end of the year and form the basis for a separate commercial channel to market to pulmonologists. Anderson added that Veracyte plans to introduce a second product for pulmonology in 2016, which would be sold through the same channel as Percepta.

For now, Veracyte is taking a measured approach. The firm is gathering data to demonstrate how Percepta is changing care at the early adopter sites, which could soon lead to another peer-reviewed publication.