In-house or send-out? Lab approaches to gene panels

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May 2023—Achieving standardization and setting up processes around the use of next-generation sequencing panels for the care of patients with cancer is a long road requiring a lot of expertise. That’s what Compass Group members told CAP TODAY publisher Bob McGonnagle in their April 4 call. In short, it’s a struggle. “If you’ve seen one example of how someone is using NGS, you’ve seen one example because there are so many variations,” said Gregory Sossaman, MD, of Ochsner Health.

The Compass Group is an organization of not-for-profit IDN system laboratory leaders who collaborate to identify and share best practices and strategies. Here, this month, is what they shared on biomarker testing in oncology.

The ongoing demand for expensive gene panels for detecting mutations that lead to targeted therapies for patients with cancer is an issue that is getting attention. Lauren Anthony, can you give us your view of this?
Lauren Anthony, MD, system laboratory medical director, Allina Health, Minneapolis: Getting consensus and standardization and establishing high-reliability processes around these labor-intensive manual send-outs is a challenge, and there’s an increasing desire for and use of the largest possible gene panels. Our organization had a push with the laboratory and the Cancer Institute leadership to standardize to one primary partner, rather than leave it to choice and add multiple overlapping processes for the same type of testing. We did a request-for-information, request-for-proposal process in which we looked at the different partners, what they offer, how they facilitate the send-outs to their lab, and how they support those processes to minimize labor and maximize reliability. These are all manual—you have to curate the case, get slides, get blocks, and make sure there’s enough tissue and tumor. Getting those out and getting the results back has been a challenge.

Dr. Anthony

Many of these big labs, such as Foundation Medicine and Caris Life Sciences, have established an Epic interface for orders and results. I’m not sure whether that comes through as a PDF or you need Epic’s genomic module to receive discrete data. There’s a lot of data coming through that people would want to mine, send to registries, apply for research, and so forth, but how the data are going to be integrated into the medical record may require extra packages. There was an announcement about one of the companies having a partnership with Epic to integrate genetic data into the medical record, but what form would that be? Is it a PDF? That’s not discrete data. So I can see the functionality starting out, but how to integrate it into the record and manage it to mine the data at your site will be important.

You’re looking to standardize on one send-out lab for gene panels, is that correct?
Dr. Anthony (Allina): One primary NGS partner to facilitate standard work and high reliability. We will then leverage that partner to support us and reduce the work of curating these cases, preparing them for send-out, and processing results.

Julie Hess, would you like to comment on this, because I’m sure your volumes are growing.
Julie Hess, VP, laboratory services, AdventHealth, Orlando, Fla.: We also are getting a lot of requests for the special panels. We went live March 31 with the TruSight Oncology 500 panel in-house. That felt monumental. It took a lot of resources and exploring technology to understand how to do that ourselves. We hope it gives us something comprehensive for a period of time, but this is a moving target. As soon as you feel like you have the answer, they change the question.

Was that a difficult decision? Did it take months to arrive at your current solution?
Julie Hess (AdventHealth): More than months. We started the conversation before COVID but came back to it in recent months. Validation was challenging, but resolving server storage space was also a concern.

Dwayne Breining, what are you looking at currently for a solution to the demand in your laboratory?
Dwayne Breining, MD, executive director, Northwell Health Laboratories, New York: We’re in the process of setting up in-house NGS for a couple of the standardized panels and standardizing the approach for blood-based and solid tumors. It’s a long road, and in New York State it’s even longer because all of these have to be done and validated like a laboratory-developed test and go through the New York State process, which is ultra-rigorous. The only way to support the treatment, educational, and research needs in the institution, even to the level of recruiting top-notch oncology staff who often come with a book of research they want to continue in your institution, is to set it up on your own.

We haven’t standardized on a single vendor, and it is a moving target, as Julie said. To a certain extent people want to keep directing tests to the companies that have the most genes on their panels, and that’s tough to keep up with. As we set up multidisciplinary molecular tumor boards to go through this, we’re hoping to urge everyone toward a more standardized approach, at least for the most common tumor types.

Clark Day, can you give us your perspective as a laboratory executive? No matter what you do, this gets to be pretty expensive, doesn’t it?
Clark Day, VP of system laboratory services, Indiana University Health: It is exceedingly expensive. We also use Foundation and Caris. At the IU School of Medicine we have physicians, faculty, and researchers who have their own testing capability, and we have agreements to send certain types of testing to them.

Our new chair of the Department of Pathology and Laboratory Medicine is Dr. Michael Feldman. He has experience in this realm and will be progressive and push us forward. I think his position is to not build something that duplicates what others can do—because it’s so expensive and can be unprofitable to do, let’s continue to send out where others have it figured out, and we’ll develop our own testing where it makes sense, for certain types of genetic testing for certain patients or conditions. That’s our strategy in the early stages.

The CAP TODAY cover story in the April issue points out that this is a wonderful new world but all too often the lab is left out in some cases regarding how it will be paid for this service. Eric Carbonneau, tell us about your experience at TriCore.
Eric Carbonneau, MS, MLS(ASCP), chief operating officer, TriCore Reference Laboratories, Albuquerque: We’ve been sticking with targeted panels, and our pathologists have been guiding that. We have attempted to partner mostly with Tempus on offering full gene panels when it’s necessary. We’re doing pathology review and having our pathologists talk to our oncologists about when it’s necessary. We are in the midst of redoing our myeloid panels to make them a little larger so we don’t have to rely on the full panels so often. But it’s going to be a give-and-take over time.

Joe Baker, tell us about the business and administrative side of doing these tests.
Joseph Baker, VP of laboratory, Baylor Scott & White Health, Dallas: From an administrative standpoint we have similar challenges to what other organizations are experiencing and are managing utilization as appropriate. We use a few reference labs in this area and have some NGS panels in-house within our central Texas region. We are working toward alignment in the system, but it will take some time to get there. It is very expensive, as we all know. The referral NGS space is a competitive one, and we have seen some aggressiveness in the approach used to get our business.

Peter Dysert, what’s your perspective at Baylor Scott & White?
Peter Dysert, MD, chief, Department of Pathology, Baylor Scott & White Health, Dallas: This is the future of surgical pathology, so it’s a strategic question, not just a cost-management one. It is a big opportunity for pathologists to be up front and involved more directly in the care and management of the patient. We know from a discovery and therapeutic perspective that this is going to be a rapidly changing playing field, with new and exciting advancements. You have to be prepared and see this as a significant part of your future.

We’ve been partnering with our medical staff using our molecular-boarded pathologists. We have site committees to cover the various parts of the body, and we bring those needs to the site committees to get their expertise in terms of picking what we’ll consider to be the front-line panels that go with diagnosis, in an attempt to agree on the best approach for the treatment of disease. Beyond that we have examples of off-label use of therapeutics and testing that have proved to be beneficial for the patients. You still must have another layer where the molecular pathologist can communicate directly with the clinicians when they decide to go a different direction and help them find the best solution. We also have molecular tumor boards, which we consider to be an ongoing educational effort to keep everyone informed. There are a lot of nuances in these panels that busy clinicians don’t always appreciate, so they’ve found the partnership with our molecular pathologists to be helpful and important.