Orig3n violated rules for years before being approved for COVID-19 testing; fourth investigation showed lab put patients at risk

By Jeannette Hinkle / MetroWest Daily News / and Trevor Ballantyne / Needham Times

Posted Oct 15, 2020

Posted Oct 15, 2020 

After facing investigation three times for quality control problems, consumer genetics company Orig3n this spring was allowed to administer COVID-19 tests in several states. By summer the Boston company halted testing in Massachusetts after producing hundreds of false positive test results.

Bailey the dog likely would be a skilled basketball player or boxer. Ginger the dog probably would experience mild trouble learning to read. And a few drops of kitchen sink tap water might need longer to develop skills required for language learning.

Those were a few of the findings of consumer genetics tests conducted by Boston-based startup Orig3n, a company that promises to tell customers how their DNA makeup could influence everything from cognitive abilities to sleep needs.

In all three cases, the company failed to identify the nonhuman samples sent to its labs by customers skeptical of Orig3n’s products.

By the time the Massachusetts Department of Public Health received its second complaint in September 2018 about Orig3n’s inability to identify canine DNA as nonhuman, a complaint that was also sent to the U.S. Food & Drug Administration, the company had generated red flags since 2016 at state and federal agencies tasked with ensuring labs that test human samples are operating properly, according to hundreds of pages of documents obtained by The MetroWest Daily News and the Needham Times through a public records request.

Despite the history of investigations, in the spring, as COVID-19 spread across Massachusetts with fatal consequences — especially among residents of long-term care facilities — the FDA gave Orig3n an emergency authorization to perform coronavirus tests. And the DPH and the Centers for Medicare & Medicaid Services gave the company permission to add virology and immunology as specialties.

The DPH even recommended Orig3n as a testing option to nursing homes struggling to contain deadly coronavirus outbreaks across the state.

By August, however, the company had halted its COVID-19 testing operation when it was investigated once more, this time after DPH staff noticed Orig3n’s lab was putting out an unusually high number of positive coronavirus test results.

On Oct. 2, the Centers for Medicare & Medicaid Services sent a letter to Orig3n’s lab director informing him the agency had suspended the company’s certificate to operate a clinical lab, and that it recommended a full revocation of that certificate. Orig3n has a right to appeal the decision within 60 days.

DPH investigators later found the company sent out at least 383 false positive COVID-19 test results to patients across the state between July 30 and Aug. 2. The false results put patients in “immediate jeopardy,” according to the DPH.

DPH investigators found serious deficiencies in the Boston-based lab’s coronavirus testing operation, some of which mirrored quality control issues found during previous investigations in 2018 and 2019.

But the pandemic offered an opportunity for Orig3n to fill a glaring need for increased COVID-19 testing capacity across the nation.

“When COVID-19 became a public health crisis,” Orig3n CEO Robin Smith wrote in an email on Tuesday, “we decided to dedicate our resources to providing testing for high-risk and high-need populations across the country, including school students and faculty, nursing home residents and staff, and private and public employers.”

Smith did not answer a question about why the company was qualified to conduct coronavirus testing in light of its history of lab violations.

Investigations begin

Centers for Medicare & Medicaid Services, which enforces federal regulations for clinical labs testing human samples, first investigated Orig3n’s Massachusetts lab on Jan. 31, 2018.

While documents don’t say what prompted the investigation, they show a federal surveyor found a litany of deficiencies at Orig3n’s Waltham lab, which the company had recently acquired.

The surveyor found the lab didn’t have a system in place to ensure test results and other patient-specific information were accurately and reliably sent to their final destinations. The lab also failed to show that a legally authorized person made requests for the genetic tests processed by Orig3n.

Four months later, shortly after the company told federal regulators it had corrected deficiencies outlined in the January investigation, the Massachusetts DPH sent its own surveyor to inspect the company’s lab operation, according to DPH documents.

The DPH’s May 2018 investigation was sparked by a May 2, 2018, report by NBC 5 in Chicago. The news organization sent dog DNA to similar at-home genetic testing companies and found that Orig3n was the only company not to flag the dog sample as unreadable.

The DPH surveyor ultimately concluded that Orig3n had corrected issues with its testing process when it underwent the Clinical Laboratory Improvement Amendments (CLIA) certification established by the Centers for Disease Control and Prevention, which occurred after NBC 5 sent the dog DNA for processing. The surveyor concluded no further action was required.

Quality control lacking

In 2019, Centers for Medicare & Medicaid Services sent out another surveyor for the third investigation of Orig3n by lab regulators in two years.

The surveyor’s visit came shortly after Bloomberg published an article in which 17 former Orig3n employees alleged the company’s consumer genetic testing kits, which ranged in price from $29 to $298, sometimes failed to work as advertised and often were contaminated or inaccurate.

The surveyor found a long list of quality control issues at the lab, which had by then moved from Waltham to Boston’s Seaport after scoring millions of dollars in venture capital from backers. One of those backers, LabCorp, operates one of the largest clinical lab networks in the world.

Echoing findings by previous investigators, basic records were inaccessible or missing, including reports that showed equipment and instruments were properly maintained and tested according to manufacturer guidelines. The surveyor also found the lab had failed to ensure that the temperature of refrigerators and freezers that contained patient samples and reagents were monitored and logged, a key protocol for making sure testing functions correctly.

Roughly four months after Orig3n’s lab director told regulators the company had corrected or would correct the issues identified in the 2019 investigation, the FDA sent a letter notifying the company it was approved for inclusion under an umbrella Emergency Use Authorization to conduct certain types of COVID-19 testing.

In a press release announcing the news, Orig3n said the company’s coronavirus testing would be available to authorized health care providers and institutions nationwide.

FDA spokesperson Jim McKinney said Tuesday the agency authorizes tests, not labs.

“Qualifying a lab as CLIA certified would be a function of the Centers for Medicare & Medicaid Services,” McKinney wrote in an email.

A Centers for Medicare & Medicaid Services spokesperson said Wednesday that the FDA has sole authority to issue emergency authorizations, but as a CLIA-certified lab, Orig3n was authorized to conduct high-complexity testing.

The spokesperson also said the agency affords labs due process and an opportunity to address allegations of noncompliance. When Orig3n began COVID-19 testing, the spokesperson said, the Massachusetts DPH had deemed the lab fully compliant.

In May, both the Massachusetts DPH and Centers for Medicare & Medicaid Services concluded after “offsite” surveys that the company could add virology and immunology as specialties. The agencies found the company was in “full compliance” with applicable state licensure and CLIA requirements.

Spokespeople for both Centers for Medicare & Medicaid Services and the DPH said in statements the offsite approvals for the addition of specialties to CLIA-certified labs are standard procedure. Usually, the surveys involve a desk review of documentation, including procedures, personnel qualifications and training.

With approvals in place, Orig3n began conducting coronavirus testing across Massachusetts, and offering its COVID-19 testing services in other states.

In a memo to nursing homes last updated on June 1, the DPH recommended the company’s testing services to long-term care facilities sprinting to meet a May 25 deadline to test 90% of residents and staff for the virus. The company eventually would conduct coronavirus testing for at least 60 nursing homes statewide, most of which were dealing with deadly outbreaks.

Test results prompt fourth investigation

Records show federal regulators visited Orig3n twice in August after the company reported an unusually high number of positive COVID-19 test results. Earlier in the month, the company voluntarily agreed to halt COVID-19 testing.

On Aug. 8, Sandra Smole, director of the Massachusetts State Public Health Laboratory, sent an email to public health leaders in other states alerting them about Orig3n’s high rate of positive COVID-19 tests. Smole classified the email’s importance as “high” and sent it to public health officials in California, Michigan, Ohio and North Carolina, as well as the Association of Public Health Laboratories.

“The Orig3n Inc. Laboratory Director indicated that they also test specimens from your jurisdiction, and so we wanted to make you aware of this situation,” Smole wrote. “At this time, we have no specific information indicating that samples from your state have been impacted.”

DPH documents did not indicate whether there were problems in other states with Orig3n COVID-19 test results.

On Aug. 26, the Massachusetts DPH Division of Health Care Facility Licensure and Certification finished its investigation into Orig3n’s coronavirus testing operation, and found dangerous deficiencies in how the lab conducted its work.

According to the report, the lab failed to document basic sanitation measures, including the daily sanitizing of lab benches and equipment used in COVID-19 testing. The lab’s system for detecting potential errors in test results was inadequate and lacked controls that would detect contamination.

Both Orig3n’s lab director and its CEO confirmed in interviews with investigators that, while the lab tracked daily positivity rates, it failed to assess or correct any problems flagged by higher than normal positivity rates.

The report also slammed Orig3n’s lab director for failing to provide “overall management and direction,” which meant the director was unable to ensure the accuracy and reliability of patient test results.

Orig3n began coronavirus testing on April 27. Before it suspended COVID-19 testing in early August at the state’s request, the company had reported 23,513 results.

The Massachusetts DPH ultimately found the company sent out at least 383 false positive results to patients, according to agency documents, but because not all test samples processed by Orig3n were retested, that number could be higher.

It’s also unknown how many false negative coronavirus test results the company released to people, because false negative test results are harder to detect than false positives.

The DPH told Orig3n’s lab director in a Sept. 4 letter that the company’s deficiencies posed “immediate jeopardy to patient health and safety,” meaning the lab caused, was causing, or was likely to cause “serious injury or harm, or death, to individuals served by the laboratory or to the health and safety of the general public.”

Orig3n has not yet restarted coronavirus testing, according to Orig3n’s CEO. The company is waiting for “resolution of our regulatory discussions with CMS (Centers for Medicare & Medicaid Services) and the state of (Massachusetts),” Smith said in a statement to Gannett New England.

In an interview for a previous story about the DPH’s investigation into Orig3n’s coronavirus testing, Dr. Michael Mina, an assistant professor of epidemiology at Harvard T. H. Chan School of Public Health who has experience running laboratories, said mistakes do happen at labs, but “they don’t usually require an investigation.”

“It’s just important to keep all these things in check,” Mina said in September. “The frenzy to do coronavirus testing has been so extreme. I don’t think labs should be immediately shut down for mistakes, but we have to remain vigilant to ensure that all the testing that is being done is up to the highest standards.”