Workflow, regulatory unknowns tax molecular IT

Create PDF

Anne Paxton

April 2015—Alexis Carter, MD, immediate past president of the Association for Pathology Informatics, isn’t under any illusion about how well information technology is meeting the needs of molecular diagnostics. “Laboratory information systems right now do a fairly decent job of getting samples to the right lab, tracking the sample, and reporting results,” Dr. Carter says. But when it comes to molecular diagnostics laboratories, “LISs are really not where they should be. They’re kind of moving at a turtle’s pace to keep up.”

For molecular diagnostics laboratories, “LISs are really not where they should be,” says Dr. Alexis Carter (left), at Emory with Jordan Magee Owens, MLS (center), and molecular diagnostics supervisor Heather Jones, MB, CHS.

Even Dr. Carter was somewhat surprised, however, by the results of a survey she recently conducted, which found that molecular diagnostic labs are heavy users of manual processes and paper. “The vast majority of them have no electronic communication of data between the LIS and the actual instrument that’s doing the testing. They’re literally manually typing data into these instruments and using paper logs to track work and paper printouts to evaluate test results. Which is completely the opposite of our general chemistry lab.”

While knowledge of the genome and demand for molecular diagnostics continue to expand, IT in molecular diagnostics is lagging behind, Dr. Carter and other informatics experts agree. They suggest that the complexities of molecular data, along with big regulatory uncertainties, are among the factors holding back innovation and progress.

In molecular diagnostics, the bioinformatics pipeline is the generation and interpretation of data, particularly for next-generation sequencing or microarrays. Clinical informatics “really wraps over all of that,” says Dr. Carter, who is director of pathology informatics at Emory University School of Medicine. “It’s how we validate in the laboratory, how we make sure we’re doing the right tests for the right patients with the specimen we’re looking at, how we automate the workflow process in the lab, how we retrieve data later. Clinical informaticists deal with all of that plus the human-computer interface.”

LIS manufacturers like Cerner, Sunquest, and Soft Computer have developed software modules geared to handling molecular diagnostics data, including Millennium Helix, Sunquest Molecular, and SoftMolecular. “Often, the way worksheets are created is not how the molecular lab does testing,” Dr. Carter says. “So people end up manually typing in data anyway, and it’s kind of a point and click thing. It’s not totally automated and electronic.”

Moreover, molecular laboratories are rarely flush with cash. “Molecular testing is increasing at a far higher rate than general laboratory testing, but molecular is still not the big moneymaker in the laboratory.” Even at a large institution like Emory, she says, molecular makes up a small part of the budget. “When you are trying to purchase a specialized information system that will help support your workflow, that becomes a real challenge.”

In a large molecular laboratory, it can cost $1 million to $2.5 million just to implement a specialized molecular diagnostics system, Dr. Carter says, plus hundreds of thousands more each year in maintenance. “So your molecular lab has to be quite sizable for you to be able to afford doing this.” This reality, in turn, places the vendors in a difficult position. “In order to put resources into developing their systems to better accommodate molecular testing, they have to have people wanting to buy them, and there are not a lot of laboratories with that kind of funding.”

Her laboratory is in the process of issuing a request for proposals from multiple companies to support its molecular workflow. However, among her colleagues, Dr. Carter says, “Nobody is really telling me they have massive automation in their molecular labs, and the few that are more highly automated have very homegrown systems that have not been purchased from a commercial vendor.”

But the biggest factor stalling sales in molecular IT, in her view, is the threat of serious regulation, as the Food and Drug Administration readies a final rule on laboratory-developed tests—expected to be issued at some point in the next year or so, but possibly later. The FDA issued a draft guidance document on LDTs last October, and public comments were accepted until Feb. 2.

“If the oversight framework for LDTs that the FDA has proposed goes through,” Dr. Carter says, “there are going to be even fewer molecular labs out there that can purchase such systems.” Vendors would naturally want to be cautious about putting a lot of resources into developing molecular lab systems, she says, “because there may not be very many, if any, clients to buy it at the end of the day.”

All the molecular tests and FISH tests done at Emory, for example, are LDTs, she points out. “Even though the FISH tests themselves were FDA approved, because we’re such a big lab and we do so much FISH testing, we have to use automated wash steps, which means we have to revalidate as an LDT because we’ve made modifications to the FDA-approved test.”

With FDA charges for premarketing approval of a test being in excess of $250,000 per test per indicated use, Dr. Carter says chances are not high that Emory or other similar labs would continue performing LDTs if they had to put them all through the FDA. While she can’t predict what Emory would do, she suspects that in such a case, many laboratories will start sending their molecular testing out.

When the FDA draft guidance will be finalized, and in what form, is unknown. “It could change very little or it could change a huge amount between now and when they decide to finalize it. But the very fact that the draft guidance is out there is probably going to stifle innovation and investors willing to invest in IT, because of the threat of regulation,” Dr. Carter says.

Nevertheless, demand for new molecular tests remains high. “The threat of regulation can scare investors off, but every day there are more discoveries about various genes and their potential significance for cancer therapeutics, for inherited diseases, for what drugs can be given to patients that won’t be toxic to them. There’s a huge amount of demand out there, and practically every day we’re getting messages from our oncologists asking ‘when are we going to develop this next test?’” Manual data entry is one of the things diverting resources, she adds, so the lack of safe automation is hobbling progress in making new tests available.

The FDA confronted serious issues when it took up regulation of LDTs, Dr. Carter says. “They were actually trying to protect patients from some very unscrupulous people who develop some very poor tests. Some patients had ovaries removed that didn’t need to be; some patients got chemotherapy who didn’t need chemotherapy.” But while she understands where the FDA standards are coming from, “I think making us all go through FDA approval probably is not going to be as helpful as they think it is. And until we figure out exactly what the FDA is going to do, there may be even less innovation in this area.”

There is a big gap between employing information technology in molecular and its use in the clinical lab, says Federico A. Monzon, MD, former medical director of molecular diagnostics at Houston Methodist Hospital. “We’re starting to see instruments that are more geared toward the clinical testing environment, but still there’s no specific requirement for molecular instruments to be able to communicate with LISs or produce information specific to laboratories,” he points out.