Will a boom in genetic testing of tumors be a boon for Soon-Shiong?

Cancer patients across the country are increasingly being tested for “microsatellite instability,” or MSI status — characterized by a set of genetic markers that can help doctors identify the most effective treatment.

In this boom, Dr. Patrick Soon-Shiong has spotted a business opportunity.

The biotech billionaire has been struggling to find a market for his pricey diagnostic test, GPS Cancer, which recommends treatments based on an analysis of tumor genetics. Now, he says the test will start reporting MSI status. On an earnings call last week for his company NantHealth (NH), Soon-Shiong boasted with characteristic bravado that his test is superior to others on the market because it compares the patient’s tumor tissue with his or her normal tissue.

The problem with this rationale? That kind of comparative analysis is nothing new. Plenty of other tests do the same. And Soon-Shiong has produced no documentation that his test improves patient survival — or that it’s any more accurate than its competitors.

Yes, it is important to know MSI status. And it is important to compare tumor and healthy tissue. “But that’s also what we’ve been doing for 10 years,” said Dr. Jan Nowak, a pathologist at Roswell Park Cancer Institute in Buffalo, N.Y.

It’s long been standard to use a patient’s normal tissue as a control when testing for MSI status using the traditional methods. What’s more, those tests have been shown to generate highly concordant results. Some, though not all, of the newer gene panels on the market use this tumor-normal comparison, too, Nowak said.

(Until about a year ago, Nowak was chief medical officer of OmniSeq, a company that offers a test for MSI status that runs the same type of comparative analysis.)

During the earnings call, Soon-Shiong slammed existing gene panel tests for MSI status as “grossly inadequate from an accuracy perspective.” He said that when a tumor-normal comparison isn’t used, “you end up with a huge number of false positives and even false negatives.”

To back up that claim, Soon-Shiong pointed to a test his team undertook with collaborators in Singapore that he said identified 150 cases in which patients had MSI-type tumors that had not previously been diagnosed as such. But it’s not clear whether the study has been vetted by independent scientists.

Soon-Shiong’s spokeswoman, Jen Hodson, did not return STAT’s request for documentation of that study. Nor would she provide more details about NantHealth’s plans, saying that the company would provide additional information when it launches the upgraded test.

Soon-Shiong also pointed to another study, conducted by his team and presented last month at a lung cancer conference, as evidence of the importance of doing a tumor-normal comparison. That study analyzed samples from 44 lung cancer patients and found that a certain genetic sequencing method runs the risk of turning up false positives. But it did not look at MSI status.

Nowak said he wasn’t aware of any widespread concern in the pathology community about the quality of existing gene panel tests for MSI status. To the contrary, he said, they’re generally considered reliable and solid, though he emphasized that he doesn’t know the methods behind all the latest tests on the market.

About 15 percent of colorectal cancer patients are thought to have MSI-type tumors, which means they have a great deal of genetic abnormality. Endometrial cancer patients are also thought to have the abnormality at relatively high rates. In other solid tumor types, the rates of MSI status drops up significantly, to percentages in the low single digits. But for this small slice of patients, MSI status can be very meaningful in dictating treatment.

Just this spring, the Food and Drug Administration made a groundbreaking decision to let Merck (MRK) market its blockbuster cancer drug Keytruda for patients with MSI-type tumors, regardless of where in the body their advanced cancer first originated. That decision sparked a boom for MSI testing in patients with many types of solid tumors.

Soon-Shiong is launching his test for MSI status at a turbulent time for NantHealth.

The company reduced its headcount by 300 employees over the summer and last week reported that it had lost another $42 million in the third quarter. Meanwhile, its stock price is mired at half of where it was trading at the start of this year. But there are also signs NantHealth might be turning a corner: Sales of GPS Cancer increased 44 percent in the third quarter compared to the second quarter, and October was the best sales month yet.

When NantHealth soon launches the upgraded test, it will enter a crowded market: MSI testing has long been offered by many well-known players, including companies like Quest Diagnostics and Foundation Medicine and hospitals like the Mayo Clinic and the University of North Carolina Medical Center.