Molecular Testing Challenges in the Industry

CAP TODAY Publisher Bob McGonnagle sat down with ELITechGroup — A Bruker Company’s General Manager of Life Sciences, Scott Johnston, and Director of Customer Experience, Steven Swartzell, in this roundtable discussion covering ELITechGroup’s history, lab-developed tests for labs of all kinds, laboratory support, assay development, and the future of diagnostics.

The ELITechGroup team answered questions from Bob and live listeners, sharing their thoughts on topics ranging from selecting the correct assay for specific diseases and LDTs versus IDTs to CLIA assay requirements and implications of artificial intelligence.

It’s not too late to hear the discussion! Listen to the full roundtable or explore the topics covered and insightful quotes below.

Bob McGonnagle: Roundtable host, moderator, and Publisher at CAP TODAY – LinkedIn

Scott Johnston: General Manager of Life Sciences at ELITechGroup — A Bruker Company

Steven Swartzell: Director of Customer Experience at ELITechGroup — A Bruker Company – LinkedIn

ELITechGroup — A Bruker Company: Website | LinkedIn

CAP TODAY: Website | LinkedIn | Roundtable Discussions

[1:55] Scott and Steve introduce themselves, share their roles at ELITechGroup — A Bruker Company, and discuss the company’s history and current work.

[9:48] Were you pleased with the court’s decision on the LDT proposed regulation by the FDA?

[10:48] Do ELITechGroup customers span the entire spectrum of lab types, sizes, and areas?

[12:54] How do you select the correct assay for the specific disease?

[14:44] What are the validation challenges, both in labor and in process, for LDTs?

[15:57] Does ELITechGroup help labs that need sample exchange?

[16:47] What drives the decision for a laboratory to choose an LDT versus an IVD when there is an IVD-approved test?

[17:58] Does ELITechGroup have any support systems in place that they provide for labs that need help with decision-making?

[19:08] Do people ask about the potential for LDT regulation?

[20:40] Can your tests be run on open channels or platforms other than your own platforms?

[22:09] LDT assays have created a lot of confusion from regulatory perspectives. Can you explain what are the assay requirements from the CLIA side to adhere to? And also, can LDTs developed by a national reference lab be offered nationwide, or are the LDTs only restricted to the healthcare facility that has done all the validation?

[25:25] Were there any recurring themes or questions in conversations at the AMP meeting?

[26:14] Given the current ambiguity surrounding LDT regulation and the rapid pace of AI and automation in diagnostics, how is ELITech strategically prioritizing its investments to balance immediate operational efficiency and regulatory compliance with the long-term need for scalable, future-proof data integration and innovation?

[29:06] What are the factors to consider for sending out tests versus developing testing in-house?

[31:33] What are your suggestions for LDTs where reference standards for quality validations are limited or nonexistent?

[33:05] For cell gene therapy, where an in-house LDT is used to determine on-target or off-target analysis, do you have a suggestion for regulatory compliance?

[34:02] As AI helps enable a shift towards predictive maintenance and remote diagnostics, how are you looking at that future as an organization to help restructure some elements of the field service operations, to move beyond a reactive break-or-fix model?

[35:48] How can ELITechGroup help laboratories with LDT development?

[3:37] “…our goal here is to develop novel assays for use in the clinical testing environment, specifically for LDTs…as well as IVDs for use in the same space.”

[16:04] “What we can do is…put the labs that are wanting to validate the test in touch with our customers who are already using the test. And we’ve had pretty good luck doing that across a variety of different types of tests.”

[21:48] “That’s the beauty of a lab-developed test…that they’re hopefully designed to be able to allow the labs to develop on whatever platform they have.”

[35:04] “They [Bruker] have a very strong interest in AI. So as Steve said, currently, no, but in the near future, yes, because again, they’re looking at basically ways to optimize the company and how it reacts to these types of things, like an instrument being down, or how we’re monitoring the performance of these instruments, so be looking out for that in the near future.”

[39:13] “While the pandemic was tragic in many ways, in terms of the overall development in laboratories, how quickly the labs adapted to the situation, was phenomenal. Let’s all, I mean, pat ourselves on the back for how quickly we were able to do that. But it also instilled kind of a newfound focus, as it would be, on testing, right, molecular testing.”

[39:47] “I think the confidence in these tests and the knowledge of using these molecular tests is much more elevated due to the activities after the pandemic. So I think at this point, we’re in a situation where, as we talk about LDTs and being able to develop these new assays for specific disease states, it gives us a huge opportunity to work collaboratively as a market, together, and then individually with different labs. So I think you know, all in all, you’re going to see a lot of great things over the next few years…”

A few of the questions came from the roundtable audience and are identified as such. 

Steve, how long have you been with ELITech and what is your background in molecular diagnostics?

Steve Swartzell: I am director of customer experience and have been with ELITechGroup for 22 years. My background is in microbiology. I started as a research scientist in R&D and I was an application specialist working directly with customers. I have many years of lab experience as well. Now I oversee all the field activities for ELITechGroup MDx in the U.S. 

Scott, introduce yourself and tell us about Bruker, which has acquired ELITech’s molecular diagnostics business.

Scott Johnston: I’m the general manager of ELITechGroup in Bothell, Washington. Bruker acquired ELITechGroup in 2024. Our goal here is to develop novel assays for use in the clinical testing environment, specifically for laboratory-developed tests and in vitro diagnostics.  

Bruker is known for its microbiology detection systems and the MALDI in particular. Bruker’s goal is to provide a total solution for the laboratory, from identification to PCR applications. Our portion is molecular testing—qualitative and quantitative assays for the detection of specific disease states. 

Tell us about ELITech.

Scott Johnston: ELITechGroup MDx started in the early 1990s as Epic Biosciences. Our goal was to develop novel diagnostic products for use as analyte-specific reagents for research use only or for in vitro diagnostic use. We also have a line of consumables and instrumentation for clinical testing. We have semifinished goods—dyes, quenchers, and probes that labs can use to develop their own assays. 

We have two FDA-cleared IVD assays, for HSV 1 and 2, and the IVD-cleared InGenius instrument and its consumables. We also have ASRs focused on transplant monitoring and respiratory and other viral infections. On the RUO side, we offer transplant monitoring and respiratory, vector-borne, gastrointestinal, sexually transmitted, and other bacterial and viral infection assays. 

Our BeGenius instrument is a medium-throughput system. It samples 72 results from 12 patients in a workday. It can run up to 24 samples in one run, inclusive of nucleic acid extractions. Our lower-throughput InGenius has 12 independent reactions. It’s good for medium to small labs that want to take testing in-house. 

To assist with these assays, we provide training and support for pre- and post-installation of the instrument and for reagents, chemistry, validation, and troubleshooting. Our system can handle anything from plasma to nasal swabs, lavages, sputums, and so on. We have a lot of flexibility. 

Many people in our R&D group have a long history with the development of novel chemistries for use in real-time PCR. A couple of people on staff were involved with the invention of the minor groove binder, which is used in the stability of PCR reactions and specificity. Our patents cover many of these technologies, and we are looking for opportunities to develop new assays. We recently released high-throughput hepatitis D virus and John Cunningham virus and norovirus 1 and 2 assays, and we’ll soon release high-throughput hepatitis A virus and Legionella assays and lower-throughput HDV and human herpes virus 7. Coming soon are mycoplasma, ureaplasma, measles, and parvovirus B19. 

You must have been pleased by the court’s decision on the FDA’s proposed regulation of laboratory-developed tests.

Scott Johnston: Yes, we are relieved but also excited because now we can continue to work on the assays and technologies we’ve been developing for the laboratory. 

Steve, many people may think LDTs are for small or niche labs or for large reference and academic labs. Do your customers span the spectrum of lab types and areas?

Steve Swartzell: Yes. We provide tests for clinical reference labs. Many of our primary customers are children’s hospitals and regional medical centers that serve a particular area and are often associated with an educational institution. 

Has ELITech molecular diagnostics played a role in developing LDTs for children’s hospitals?

Scott Johnston: Yes, we’ve worked for many years with partner groups that are testing laboratories to develop different assays. 

Steve, can you discuss selecting the correct assay for a specific disease when developing an LDT?

Steve Swartzell: Let’s use the example of transplant patients. One of the most critical tests for viral load testing is BK virus, so we provide that test as an ASR. We also have tests for cytomegalovirus and Epstein-Barr virus, which are also implicated in transplant patients.

Labs with FDA-approved tests have to validate those tests in their own setting. What are the validation challenges in labor and process for LDTs?

Steve Swartzell: Labor is a big part of it. Having lab personnel who are capable of doing the validation and understand what it takes to make sure the test is functioning properly is a challenge. Many people who do validations have other duties also—they’re doing live testing at the same time they’re doing validations, so that can be a challenge. Getting positive samples of what you’re trying to validate is another hurdle, because you have to test actual patient samples. 

Do you help labs with sample exchange?

Steve Swartzell: We can help to an extent. We can put the labs that want to validate a test in touch with customers who are already using the test, and we’ve had good luck doing that. Getting samples for esoteric tests can be difficult, but we can guide our customers to where they should go to get the samples they need.

Scott, what drives the decision for a laboratory to choose an LDT versus an IVD when there is an IVD-approved test?

Scott Johnston: If there is an IVD and the lab wants to do an LDT, it may be a matter of flexibility. Some IVDs are set up for a higher-throughput environment than is right for the lab. Some customers are using platforms with IVDs that run thousands of samples. If the lab doesn’t get that many in a given month, it may be more cost-effective to run an LDT than an IVD for the same disease state. It’s more work in terms of validation, but it gives the lab more flexibility in terms of volume. 

Steve, do you counsel labs that have that decision to make?

Steve Swartzell: Yes, depending on the test type, whether an IVD, ASR, or RUO. We provide full assistance with an IVD test. ASRs and RUOs are trickier because of the regulatory environment for those tests; for those we provide consulting and troubleshooting support. For ASRs it’s up to the lab to develop the test and validate it on its system.  

Despite the recent decision on LDTs, concerns remain—there is still a chance for regulation. Do people ask you about that? 

Scott Johnston: They do. There is still uncertainty and trepidation about what the government is going to do. You can go with what is published, which is what we’re doing now. 

Can your tests run on open channels or on platforms other than those from ELITech? 

Steve Swartzell: Yes. We have several customers who are running [tests] on different platforms. Most of our dyes are designed to go on the open platforms present in most labs. If a customer has a question about a specific instrument, we can talk to them about what that would entail. 

The beauty of lab-developed tests is that labs can develop them on whatever platform they have. 

LDT assays have created confusion from a regulatory perspective. Can you explain the CLIA requirements for LDT assays? Can the LDTs developed by a national reference lab be offered nationwide, or are they restricted to the health care facility that performs the validation? 

Scott Johnston: Individual reference labs do their own LDT development and validation, and those [tests] go through groups like the Wadsworth Center [New York State Department of Health] for verification and approval. Those [tests] are specific to that institution. 

As for the CLIA requirements, you must be able to demonstrate within your laboratory in a subpopulation of those patients the assay’s performance with the specific configuration being used and that it is updated to show it is working as expected. That’s submitted to an accrediting body for approval. You must adhere to the quality management regulation in your laboratory so you can demonstrate you met the necessary study parameters to prove the LDT works and you’re maintaining the data over time. If something has changed, you can show you’re taking care of this assay accordingly.

Given the current ambiguity around LDT regulation and the rapid pace of AI and automation and diagnostics development, how is ELITech prioritizing its investments to balance immediate operational efficiency and regulatory compliance with the long-term need for scalable, future-proof data integration and innovation?

Scott Johnston: “Investments” and “balance” are the key words. There is only so much money, time, and labor, so the question is how to balance those and meet the market need. We look strongly at existing disease states that are of interest to a variety of groups. In the past few years we’ve seen a lot of steel on the floor, meaning many labs have purchased a lot of high-throughput equipment, and when the need decreased after the pandemic, they’re left with testing capability or volume that’s not being taken up. 

We want to look into disease states that have enough volume to justify a lab’s investment in an LDT, because it’s not inexpensive and it requires a lot of labor. We’re looking at investing in new assays such as for measles, which is top of mind these days. Is that a lot of samples? No. But it is growing. HHV-7 and other herpes viruses have enough volume and interest from the laboratory that it’s worth the development. We listen closely to what labs are telling us.

We also look at sample types—is whole blood, sputum, or plasma of interest? What samples are people working with? From there, we can say what the matrix is—the number of samples they’re going to process, the cost of running the samples, the reimbursement rate. At the end of the day, is it cost-efficient for a laboratory to take on this assay? This is the balance we’re trying to achieve with our R&D investment along with our overall investment in technology. 

What do you suggest when reference standards for quality validations for LDTs are limited or nonexistent?

Steve Swartzell: Getting samples and controls for esoteric tests can be a challenge. Tickborne illnesses come to mind—there aren’t many choices for controls right now. There are companies that will start offering controls and calibrators for emerging diseases and conditions as they become more prevalent. In the meantime, many labs will culture their own for the test they’re trying to develop. There are places like ATCC [American Type Culture Collection] where you can get samples and spike it into the sample type you’re validating. It can be a difficult landscape to navigate. 

Scott, the question of whether to send out tests or develop testing in-house is a golden oldie. The send-out can be expensive and time-consuming, but sometimes it’s appropriate for a given test.

Scott Johnston: Yes. It comes down to what resources the lab has. If the lab says, “We can take this in-house and we have enough samples that we want to process them,” then it makes sense. If the volumes are small and turnaround times are not a big issue, sending it out is probably the way to go. My hat’s off to my colleagues in reference labs and how quickly they can turn things around. But there’s an associated cost. If you look at the cost per data point, it’s probably more economical to internalize some tests if possible. 

I’m struck by how many academic institutions now have testing networks that dominate large geographic areas. The University of Alabama at Birmingham, IU Health in Indiana, and Geisinger come to mind. Are LDTs attractive to large integrated delivery networks?

Scott Johnston: Yes. Small, medium, and large laboratories tend to look at similar types of diseases. Large networks like the ones you mentioned have figured out a way to optimize their testing capabilities. UAB in particular across that geography is much more efficient for that health network. But that doesn’t preclude the small lab. Small and regional labs don’t want to spend $150 for one data point when they could bring it in for $25 or $30. That makes sense to them. 

How can ELITech and the ELITech molecular diagnostics group help a laboratory with LDT development? Tell us more about your large portfolio of ASR and RUO assays and the two validated IVD assays.

Scott Johnston: ASRs come in a specific configuration, and the government defines how to do the validations. The research-use-only assay is a CGMP [current good manufacturing practice] product, but it’s not configured in the same way as an ASR. It allows more flexibility. You have to do more upstream validation work to get the design of the study done and then push it forward. We see many folks who are interested in RUOs, but for the sake of overall validation purposes, an ASR is a little easier for them. 

Steve, we all are exposed to the staffing shortages in laboratories and the retirements of senior laboratory scientists and others, but there’s still enough value in LDTs for many labs to pursue them. You needn’t be a 30-year MD/PhD—you can do this more readily than people in labs might imagine. Can you speak to that? 

Steve Swartzell: Once the tests are validated, many labs will get it to a place where it is relatively simple to use, especially if you have a system that can do a full sample-to-result. Automated systems are becoming more prevalent and the use of LDTs has come along with those systems. 

Scott, we would not have fared as well in the pandemic were it not for the vast number of LDTs that laboratories developed to deal with the testing load. Do you agree?

Scott Johnston: Yes. The speed with which labs adapted was phenomenal. It also instilled a newfound focus on molecular testing. The confidence in these tests and the knowledge around their use are much greater post-pandemic.

As we talk about LDTs and developing new assays for specific disease states, it gives us an opportunity to work collaboratively as a market and individually with different labs. You will see great things over the next few years, especially with AI and the different sequences that will be looked at. You’ll see a lot more creativity. We’re seeing it now at Bruker ELITech. It’s an exciting time.