CAP TODAY Pathology/Laboratory Medicine/Laboratory Management
“The expert panel seemed to advocate panel testing, and I think some of that is part of the maturation of next-generation sequencing,” Dr. Shiller said. “So other markers to consider, particularly when EGFR, ALK, and ROS1 are negative, include RET, BRAF, MET, HER2, and KRAS testing. They are not indicated or recommended as routine single-gene tests outside the context of a clinical trial for patients with lung cancer, but they are appropriate to include as part of a larger panel.”
KRAS mutations are present in about 20 percent to 30 percent of NSCLC, and they are characterized by point mutations. The RET alteration occurs between 1.2 and two percent of the time. It is a gene rearrangement, and there is no gold standard. It can be tested by NGS, real-time PCR, IHC, and FISH. “But immunohistochemistry and FISH can be challenging,” Dr. Shiller said.
MET occurs in NSCLC about two percent of the time, and testing should include exon 14 skipping mutations and MET amplification. “It can be a mechanism of resistance or a de novo event, and there is no gold standard in terms of how to detect it.”
HER2 is present two percent of the time and is usually an exon 20 insertion, “so it’s not necessarily HER2 amplification.” There is no gold standard for testing. “You can use multiplex assays or next-generation sequencing.”
BRAF has a frequency in NSCLC of 0.5 to 4.9 percent. “Most of the time in other sites of origin, we think of the V600E mutation as being the relevant site or hot spot. However, in the lung, greater than 50 percent of the time the alterations in BRAF do not involve V600E,” she said. “There is no gold standard,” and many tests are available that detect BRAF V600E alterations.
Dr. Johnson
A combination of two drugs (dabrafenib and trametinib) was approved by the FDA last year for patients whose metastatic NSCLC has a BRAF V600E mutation. RET drugs may be next. In a CAP TODAY interview, Bruce Johnson, MD, chief clinical research officer at Dana-Farber Cancer Institute, said it’s likely that drugs will be approved for RET rearrangements based on a presentation at this year’s ASCO meeting showing “response rates in excess of 70 percent.” (These drugs are more specific in their mechanism of action, Dr. Shiller tells CAP TODAY, with greater efficacy and improved adverse event profile, especially for particular RET alterations.) It also looks like the progression-free survival is going to exceed 10 months, Dr. Johnson says. “So that will be the fifth indication.” Alex Drilon, MD, of Memorial Sloan Kettering Cancer Center, was lead author of the presentation.
Pathologists Bio-Medical Laboratories “hits its turnaround times” for molecular testing, says Dr. Michelle Shiller, by time stamping specimens and relying on an institutionwide standing order for reflex testing with many of the sites for which testing is provided.
“We time stamp every step of the way, from the moment the specimen was received until it leaves the originating facility,” and when the specimen arrives in the molecular laboratory. A daily dashboard displays the status of the cases. “All of these measures help to maintain awareness,” she tells CAP TODAY.
The laboratory also uses time-saving tactics. For cases that have a clinical indication of lung nodule, they cut 15 unstained slides at the outset and H&E stain the first slide and the 15th slide, without knowing whether the tissue specimens are benign or malignant. That leaves “13 slides in the middle to work with for IHC and FISH, or if we are really low on tumor, we can also use those for the sequencing assays,” Dr. Shiller explains. “This not only helps to preserve tissue,” but since the slides are already cut, “there is no additional delay waiting for unstained slides to be prepared, unless you are running out of tissue from having to run other tests.”
Dr. Shiller finds that a lot of pathology groups wait for the clinician to send an order, in part because of concerns for reimbursement, as well as concerns about Stark law or kickback law violations (a legitimate concern, she notes), since the downstream testing also occurs within pathology laboratories. Her institution has a standing order from the clinicians to the pathologists for all cases diagnosed as primary lung adenocarcinoma to automatically reflex to the pertinent testing. “Once the diagnosis is made, the testing just happens immediately,” she says. These orders are also in place for the relevant primary lung squamous cell carcinoma (PD-L1).
She has heard that some insurers are beginning to oppose this approach. “If that’s the case, I think there is a need to educate the insurance companies because some patients are so sick that their illness will not tolerate these types of delays.”
In the institutions that don’t have a tumor site committee to recommend the reflex testing, the clinician could provide a written order to the pathologists who read the clinician’s cases, she suggests. The order could then be correlated with the specimen once it is received and the diagnosis made, “as long as the clinician is amenable to that.”
Dr. Shiller says PBM performs NGS testing for AKT1, BRAF, EGFR, HER2, KRAS, MEK, NRAS, PIK3CA, and PTEN. PBM also offers ALK, ROS1, RET, and MET by FISH. “We are not having reimbursement issues in terms of getting the panel testing reimbursed,” she says. “If you continue to do one gene at a time, it exhausts time and tissue and resources.”—Karen Lusky
Dr. Shiller shared a case to illustrate the value of extended-panel testing. A 59-year-old man had a CT of the chest and abdomen that identified a 6-cm lung mass and diffuse liver nodules. The pathology revealed adenocarcinoma. The oncologist requested a next-generation-sequencing–based multigene panel, and it is negative for EGFR mutations and ALK or ROS1 rearrangements. “Considering the guidelines and the negative testing, the oncologist orders an extended panel, which is positive for MET exon 14 skipping mutation, qualifying the patient now for a clinical trial.”
“Every scenario is different, from tissue availability to what is going on with the patient and so on, but the first test took five days to get a result. The second test 18 days, so the total cycle to get the results of the exon 14 skipping mutation qualifying the patient for a clinical trial was 23 days.”
In her view, pathologists can be of great value to clinicians by assisting them in understanding the strengths and other considerations of using extended-panel testing versus multiple single-gene tests. How probable is it that the patient’s tumor has an initial oncogenic driver—EGFR, ROS1, or ALK, for example? Is there enough tissue? “We are the ones who have that answer and can help to guide them along with that,” she said. “And what are the implications of the total turnaround time for the patient? In other words, how sick are they, and do we have enough time to wait 23 days for a final result?”
“We can educate our colleagues regarding the strengths and considerations of particular individual tests, including weighing the individual variables for each patient, to facilitate ordering the right test on the right patient at the right time, with the most relevant results,” Dr. Shiller says.
The 2018 expert panel prefers multiplexed genetic sequencing over multiple single-gene testing when testing beyond EGFR, ALK, and ROS1. “And part of this is a tissue stewardship and turnaround time consideration,” Dr. Shiller said, noting that studies have demonstrated 100 percent concordance between single-gene assays and NGS.
Dr. Johnson says a study presented at the 2018 ASCO meeting by Nathan A. Pennell, MD, PhD, of Cleveland Clinic, showed that doing an NGS panel was faster and less costly than performing sequential or single-gene tests. “Rather than saying how much each individual test is indicated, we would advocate for doing a large panel for testing, so that you don’t have to have discussions about whether you should or shouldn’t do a RET rearrangement, if a drug for this indication is likely to be approved in the next six months to a year,” says Dr. Johnson, who is also a professor of medicine at Harvard Medical School.
For the past five years, Dana-Farber Cancer Institute has been performing a large panel of several hundred genes. “All of the genes you think could be actionable during the lifetime of the patient are available for patient management,” Dr. Johnson says, “not only for the FDA-approved agents but also the genomic changes for which there are promising therapies.”
Dr. Shiller presented a final case to highlight that all molecular test results must be incorporated in treatment strategies. A 79-year-old man is diagnosed with lung adenocarcinoma. A tissue specimen is sent for in-house testing, which is immunohistochemistry for PD-L1 using the SP263 clone and EGFR IHC mutation screening using SP111 and SP125 antibodies. Results available after five working days show PD-L1 expression of 25 percent and no EGFR mutation. “What would you do next?” Dr. Shiller asked.The information is insufficient to make a decision about therapy, she said. “EGFR testing by IHC is not considered adequate. It needs to be done by next-generation sequencing, so we still have some testing to do.” Molecular testing performed at an external laboratory for EGFR, ALK, ROS1, and BRAF uncovered an EGFR mutation with an exon 19 deletion.
Can a lung cancer have more than one oncogenic driver?
“The technical answer is yes,” Dr. Michelle Shiller tells CAP TODAY. “We have historically thought of all of the oncogenic drivers as being mutually exclusive, which is what we see as a majority, hands down, but we are finding out that’s not always true.”
You can have concomitant ROS1 and EGFR, according to the findings of a study published in the Journal of Thoracic Oncology, she says. “The n was 1,345, and 25 were ROS1 positive.” In the article, titled “High prevalence of concomitant oncogene mutations in prospectively identified patients with ROS1-positive metastatic lung cancer,” the authors write, “Of 25 cases with ROS1 positivity at IHC analysis, six involved tumors harboring EGFR mutations, including one with an EGFR mutation plus a PIK3CA mutation, two with a KRAS mutation, and one with a BRAF V600E mutation” (Wiesweg M, et al. J Thorac Oncol. 2017;12[1]:54–64). Five of the six treated for EGFR positivity responded, Dr. Shiller says.
As for treatment, Harvard oncologist Dr. Bruce Johnson says there’s data from a phase one study on combining erlotinib, an EGFR inhibitor, with crizotinib, which is the drug that’s approved for ROS1 (Ou SI, et al. J Thorac Oncol. 2017;12[1]:145–151). “If you have those oncogenic drivers, you can try to give both drugs at the same time. If there hasn’t been a phase one, so you don’t know the doses, it becomes a challenge,” he says. In that case, “we commonly treat with one and then add the second drug in later with a small dose escalation.” —Karen Lusky
The physician should wait for all molecular results before selecting therapy. PD-L1 results are often available well before all of the other results. “All of the indications for PD-L1 therapy assume EGFR– and ALK-negative status. So not releasing PD-L1 results until everything is available, with the exception of the case of a very sick patient, is one way to make sure they are acted on in the right order.”
Dr. Shiller says her laboratory releases all test results at the same time. “The only time we fall outside of that is when the clinicians communicate, ‘For this patient, any result we can get sooner than later is great,’ and so I literally will call the clinician and report the results individually.” This is the exception rather than the rule in the lab, she adds. “I think it’s important to have that nimbleness since people’s lives are on the line.”
Karen Lusky is a writer in Brentwood, Tenn.