Veracyte has acquired the rights to a gene signature that may serve as a tool, based on a simple blood sample, for determining likely disease outcomes for people with idiopathic pulmonary fibrosis (IPF).
The noninvasive blood-based 52-gene signature, developed by researchers at Yale University, will be offered as a complement to the company’s Envisia Genomic Classifier — the first commercially available genomic test for the diagnosis of IPF.
“The clinical implications of predicting outcomes in IPF are substantial,” Naftali Kaminski, MD, who developed the test at Yale, said in a press release. “For example, knowing which patients are likely to rapidly progress could allow more accurate and timely referral to appropriate treatments.”
“The implications for clinical trials and new drugs coming to the patients are also important because information about individual patients’ potential outcomes will allow better stratification of patients for trials and eventually tailoring of IPF therapies,” added Kaminski.
While IPF is the most common form of interstitial lung diseases (ILD), it is notoriously difficult to diagnose and to distinguish from other forms of ILD. High-resolution imaging scans are routinely used to identify a hallmark pattern of IPF known as usual interstitial pneumonia (UIP), but results are often inconclusive.
Veracyte developed Envisia to complement those imaging scans, enabling physicians to more confidently differentiate IPF from other ILDs. The test involves collecting lung samples during a bronchoscopy — a procedure in which a small tube is inserted through the nose or mouth to look inside the airways and collect samples.
A machine learning algorithm trained to identify UIP then examines the gene expression pattern (which genes are switched ‘on’ or ‘off,’ and to what extent) in samples taken from patient’s lungs, and to assign a score that tells doctors if the person has UIP.
In a previous study, this approach identified more UIP cases (70%) than high resolution scans (43%), while also identifying with high accuracy (88%) those who did not have UIP — meaning that false positives were low.
Now, in addition to Envisia, Veracyte has another genetic tool that helps to predict outcomes once a patient is diagnosed. The additional tool can help guide treatment decisions throughout the disease course.
This 52-gene signature assesses blood samples using the company’s nCounter FLEX Analysis System — a diagnostic platform licensed to Veracyte in December — and has been developed and validated by Kaminski and collaborators at NCH Healthcare System, in Italy, and the University of Virginia and University of Arizona College of Medicine in the U.S.
In an international multicenter validation study, the team found that patients with high scores in the gene signature (deemed at high risk) had an increased risk of death and were significantly more likely to need a transplant. Signature scores also changed when patients were under treatment, suggesting it could be used to monitor treatment responses.
“We are excited to advance groundbreaking research from Dr. Kaminski and his team into a commercially available, first-of-its-kind genomic test that may further help guide care for patients with IPF,” said Bonnie Anderson, Veracyte’s chairman and CEO.
“The addition of prognostic information to our Envisia classifier, which is already available as a genomic tool to help improve IPF diagnosis, enhances the value of this test for physicians and patients as we prepare it for global market expansion on the nCounter platform in 2021,” Anderson added.
Researchers at Veracyte, together with Kaminski and his team, are continuing to investigate genetic changes associated with ILDs, with the goal of further informing diagnosis and treatment decisions for these patients, including those with IPF.
“IPF is an overwhelming diagnosis for many patients and their caregivers,” said Gregory Cosgrove, chief medical officer of the Pulmonary Fibrosis Foundation. “Any additional, reliable information we can provide regarding their personal disease status will not only help guide important decisions, including individual treatment plans, but could help reduce anxiety and fear.”
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