Invitae genetics lab to retest 50,000 patients after finding errors

For 11 months, Invitae genetics testing lab failed to test for the MSH2 Boland Inversion

This is an excerpt from a 1,400-word article in the August 28, 2017 issue of THE DARK REPORT. The complete article is available for a limited time to all readers, and available at all times to paid members of the Dark Intelligence Group.

CEO SUMMARY: In recent weeks, a client notified Invitae genetics lab of discordant results on a patient. The notification caused the genetic testing company to discover it had a systemic error that failed to test for a specific rare mutation associated with inherited cancer. Company officials believe only 2 to 15 patients received a false negative test result due to this error, yet because the error went undetected for 11 months, the company will retest 50,000 patients.

ONE OF THE NATION’S LARGER GENETIC TESTING COMPANIES is dealing with a significant problem that may have long-term consequences for how genetic testing labs are regulated at the federal and state level.

Last week, THE DARK REPORT was first to break the news that Invitae Corporation reported inaccurate genetic test results for what it said could be is as many as 50,000 patients over 11 months, starting in September 2016 and ending in July 2017.

The company admitted it failed to test for a specific rare mutation associated with hereditary cancer. In recent weeks, Invitae became aware of the problem and began contacting clinicians to notify them of the error in Invitae’s genetic test results it reported for certain patients and to arrange to retest those patients. Invitae would not say exactly when it discovered the problem beyond saying, “in recent weeks.”

In a statement to THE DARK REPORT, Invitae said, “For the past several weeks, Invitae has been working with clinicians to address an issue related to our analysis of a rare genetic variant in the MSH2 gene associated with Lynch syndrome (0.007% of inherited cancer tests), also known as the Boland inversion, which we believe could have led to a false negative report for a small number of patients (estimated 2-15 patients impacted).

But several medical directors at genetic testing laboratories expressed their personal opinion to THE DARK REPORT that the problem represents an important failure of the genetic testing company and should be taken seriously.

One lab industry executive says that the primary service every genetic testing laboratory provides to physicians and patients is its ability to accurately and consistently identify rare mutations that would be clinically-relevant for the individual patient.

“Think of it in this way,” stated Richard Faherty, formerly Executive VP, Administration, for BioReference Laboratories, Inc. and its GeneDx subsidiary. “The essential product of a genetic testing laboratory that says it detects rare mutations for inherited genetic disease is the ability to always find that one mutation in a million for the patient. After all, isn’t that why the referring physician and the patient ask a genetic testing lab to identify whether any such mutations are present?

“Thus, for any lab like Invitae to tell its physicians that the genetic test performed for ‘only a few patients’ may have reported a false negative result betrays the quality and accuracy that all physicians, patients, and their families expect of our labs,” explained Faherty.

Invitae’s statement explained the problem this way:

“Because of the unique characteristics of how we were testing for the MSH2 Boland inversion, our quality control checks did not catch omission of the components of the assay,” the statement continued. “As soon as the omission was recognized and relevant components returned to the assay, it once again performed properly. We have added two separate quality controls to ensure this issue will not reoccur.”

For two reasons, this failure may have significant repercussions—not just for genetic testing companies, but also for the entire clinical laboratory industry. First, Invitae genetics lab determined that the tests for 50,000 patients were subject to this systemic testing error, a number that is likely a record high for such an error. Second, these assays are laboratory-developed tests (LDTs), which the FDA said in 2014 should be subject to regulation.

There are also additional factors that make this a significant event for the clinical laboratory profession, and this story will unfold in two dimensions: among investors and among clinicians. Clinicians include physicians and genetic counselors who use genetic tests, and pathologists and laboratory scientists who perform genetic tests.

News reports and financial analyst commentary will die down quickly after investors decide this episode won’t affect Invitae’s ability to pursue its growth plans. In this dimension, the problem at Invitae genetics lab will be deemed as not material to the company’s future profitability. Wall Street and the news media may dismiss Invitae’s characterization that the errors should affect only 2 to 15 patients (out of 50,000 genetic tests) as not material and continue to cover the company as usual.

Aside from investors, how do you think clinicians and lab regulators will react to this situation? Please share your thoughts with us in the comments below.


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