NGS in more labs? IFCC group aims to ease the way

“The target moved during the time we were working on the assay, unfortunately. But that happens.”

Reimbursement is another issue. “If we want to perform NGS on the tissue, we can’t be reimbursed for the same genes being tested on ctDNA,” Dr. Sussman says. To build an affordable assay, the team determined, it would have to run on shared, dual-use equipment. “Because the hospital will not purchase something specifically for a use that will not be reimbursed.”

This is where they see a role for the Genexus. “It can have a dual-use purpose,” Dr. Morrissette says. First, Thermo Fisher is seeking FDA approval for a tissue and cfTNA assay for the instrument. “They advertise that it requires 20 ng of circulating cell-free total nucleic acid,” Dr. Sussman says, “and that’s so it can detect fusions off of the RNA and DNA hotspots.” Second, with the Genexus they may be able to provide results critical to treatment decision-making faster than is possible with the center’s large-scale panel.

“For example, you’ve got a patient with AML, and the question is, do they have a handful of mutations that will alter how clinicians would perform induction chemotherapy,” Dr. Morrissette says. Newly diagnosed AML patients currently receive FLT3 testing, cytogenetics, and FISH, “but they don’t get the broad panel before that three-day ‘I have to start chemotherapy’ window. With the Genexus, you would be able to give a broader but not complete picture of what is in that cancer.”

Dr. Sussman says ctDNA sequencing “seems like the next frontier.”

“But we’re still right at the cusp of it becoming clinically useful. It’s clinically actionable now, but the reimbursement landscape is difficult.” And the cell-free DNA assays are “in many cases not a replacement for tissue testing,” which may make investing in the capital equipment a tough sell, she says.

Still, Dr. Morrissette is optimistic. “There are situations where we would like broad enough testing to be able to identify all of the immediately actionable targets. And at the same time if we have ctDNA for those patients with smaller or no biopsies, or the tissue is necrotic, we would be able to salvage those patient [samples], as well as be able to follow all of our solid tumor patients—or at least a subset of our solid tumor patients—through the course of their disease.”

“I’ve always said my goal is to micromanage the genomics of all of our cancer patients,” she says. “I would love to know everything that’s going on with their cancers. And this would bring us one step closer to that.”

The IFCC working group members hope to bring some of the benefits of in-house NGS testing to more labs, one of which is greater ease in managing the specimen, Dr. Morrissette says. “Pathology departments know more about the patient than an outside laboratory. The laboratory, pathologists, and clinicians can determine the appropriate scope of testing—which are the ideal tissues for testing and which testing will be most meaningful for patient care.”

For example, a Penn thoracic oncologist called Dr. Morrissette about MET amplification as a resistance mechanism for EGFR-targeted therapy. “There are papers out now that say about a third of EGFR resistance is secondary to MET amplification,” she says. “So he asked whether I thought NGS was the ideal way to identify MET amplification. I explained that although you can see copy number changes for MET by NGS,” FISH is the better modality for determining if there is low-level copy number amplification in a subset of cells. With FISH, she told him, “you can analyze on a cell-by-cell basis and potentially identify small clusters of resistance within the sample.”

While send-out testing is a good option in some cases, Dr. Sussman says, reference laboratories often have stringent sample requirements. “If that is your only option, you may end up with a large number of patients who are unable to get any type of molecular testing.”

The Penn Center for Personalized Diagnostics currently runs a 152-gene solid tumor panel, a 116-gene hematological malignancies panel, and a 55-gene RNA fusion transcript panel. But it also runs small focused panels, Dr. Morrissette says, that can accommodate low input and poor-quality samples. “And a lot of the samples we get are poor quality. It’s not because they are mishandled; it’s just that some cancers are really necrotic. And some sampling methods can access only very small tissue samples.”

On-site NGS can also increase testing rates for actionable biomarkers in patients with diseases like non-small cell lung cancer. “One of the reasons is because it’s easy to incorporate genomic testing into clinical algorithms,” Dr. Morrissette says.

“Having laboratory expertise in-house to consult with the oncologist can be important,” Dr. Sussman says, including to help clinicians interpret reference lab reports. “We’ve seen misinterpretation with outside lab reports and with reports in our labs, and we have taken the approach of trying to use that as a quality improvement opportunity to make our reports as easily interpretable as possible for the clinicians.”

Ideally, finding a targetable biomarker should yield a discrete result in the EMR that triggers an alert for clinicians. “But that’s difficult to design in the EMR,” Dr. Morrissette says, “because you are sequencing many, many genes, and even within a gene you can have different variants with different actionability.” For example, “If you find a BRAF V600E in a melanoma, that’s directly actionable. But if you find a BRAF V600E in AML, they’re not going to put the patient on a clinical trial because they’re going for curative intent. So you can have different interpretations of the same variant depending on the clinical context,” which makes it tricky to design a straightforward alert.

In some cases in which ctDNA was sent out in parallel with Penn’s own internal tissue-based assay, ctDNA results were negative and the results on the internal assay were positive. “We’ve found multiple cases in which EML4-ALK gene rearrangements and EGFR resistance mutations associated with non-small cell lung cancers were not detected by circulating tumor DNA,” Dr. Morrissette says. “I think there have been misunderstandings about the technology and the biology of these cancers—where the nucleic acids are coming from and how to detect them on the part of the oncologist.” The findings can also be the opposite, she notes, since with ctDNA the assay is theoretically sampling all the metastatic sites, while tissue testing detects variants present in that piece of tissue.

“The onus is on the laboratory and the pathologist to explain why one test may be more appropriate than another, or where the positive predictive value of a certain test may differ, even though they’re both under the umbrella of next-generation sequencing,” she says. “Genomic testing is complex, and there’s always room for more clinician education.”

Charna Albert is CAP TODAY associate contributing editor.