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GenomeWeb Feature: The Rise of Lung Cancer Genetic Testing

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Originally published May 7.

Over the past several years there has been a major shift in cancer diagnostics from systems based on physical and histological findings to methods that assess and treat tumors based on the presence of distinct, targetable genomic mutations. A primary example of this shift is lung cancer, a disease that was long viewed as monolithic and with few treatment options, but now is known to have many molecular subtypes and genetic tests that can match patients with those subtypes to treatments.

Though the first molecularly targeted drugs for non-small cell lung cancer — EGFR inhibitors like Tarceva (erlotinib) and Iressa (gefitinib) — were approved almost a decade ago, the last few years have marked some of the greatest changes in how the disease is viewed by clinicians. With the approval of Xalkori (crizotinib) for patients with ALK gene fusions in 2011 and the identification of more and more subpopulations of lung cancer patients with other actionable mutations during the last few years, large cancer centers now have incorporated a number of genetic tests into their routine assessment of the disease and are beginning to shift toward even broader mutational profiling as standard of care.

"The biggest change to me, in the last year or two, has been going from the situation where this was some new-fangled idea, something that people were proposing should be routine, to something that has really become accepted," said Dennis Wigle, a thoracic surgeon at the Mayo Clinic.

"We are coming to a point where if you are not doing up-front EGFR and ALK testing in making decisions for NSCLC [patients], then you are not providing the best care. That may even have been a controversial issue up until recently, but there is really wide consensus now that you have to do that," he added.

In many ways, changes in clinical assessment practices have outpaced efforts to codify what oncologists consider an optimal paradigm for routine testing. This year, the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology issued a joint guideline establishing recommendations for molecular diagnostic testing. The new guide suggests that all patients with advanced lung adenocarcinoma — a subset of NSCLC patients — should be tested for EGFR and ALK abnormalities that would make them more likely to respond to tyrosine kinase inhibitor therapy, regardless of their clinical variables such as smoking history, gender, or ethnicity.

But leaders at several large cancer centers say that these recommendations represent only the baseline in terms of what many major practices now view as required for the diagnosis and treatment of lung cancer.

According to Gregory Riely, a medical oncologist at Memorial Sloan-Kettering Cancer Center, the new guidelines "really define what I would describe as the bare minimum standard in what people should be either able to do or able to send out for their patients. … If you are doing less than what those guidelines suggest, then you are not doing enough," he said.

Standard practice

Many clinicians — at least at large cancer centers — are doing more. In addition to testing for EGFR mutations and ALK rearrangements, healthcare providers at these centers also routinely test for rearrangements in ROS1 as well as for mutations in KRAS and BRAF, and in some cases in other genes like HER2 and MET. Several groups are also in the process of shifting from testing using panels of 10 or so genes to gauging a broader range of markers based on targeted next-generation sequencing.

EGFR mutations are believed to be present in about 10 percent to 15 percent of NSCLC patients, while ALK fusions appear to strike around 3 to 5 percent of sufferers. The prevalence of other mutations is even lower. For example, BRAF mutations appear to be present in between one percent to three percent of NSCLC patients.

Patients with certain EGFR mutations make up an NSCLC subset who may respond well to Tarceva and those with ALK fusions can be considered for treatment with the ALK inhibitor Xalkori. Other mutations, like ROS1 rearrangements, have also been associated with response to Xalkori (PGx Reporter 6/6/2012).

But if a patient belongs to the one percent to three percent of NSCLC patients with a BRAF mutation, or has an even rarer alteration, only the growing use of broader profiling approaches will identify them, said Lauren Byers, a thoracic oncologist at MD Anderson Cancer Center. And while many mutations are still relatively poorly understood, several — like BRAF and HER2 — are known targets of existing or emerging drugs developed for cancers in other parts of the body, like Zelboraf for melanoma patients with BRAF mutations or Herceptin for breast cancer patients with HER2 mutations.

Byers said that MD Anderson currently tests all patients with advanced or metastatic lung cancer, routinely focusing on EGFR, ALK, and ROS1, and frequently also looking at KRAS and BRAF. But clinicians are not limited to these mutations because the center's testing is already targeted-sequencing based, using a 46-gene panel on the Ion Torrent platform. Whenever a test for EGFR mutations is ordered, that test is also extended to the other 45 genes on the panel, allowing doctors to refer back to those results if they want to consider an additional mutation like KRAS or BRAF or others. "This can guide us especially when thinking about second- or third-line therapy, or what clinical trials might be promising if a patient fails one therapy, or if they don't have one of the more common mutations," Byers said.

Still, the concept of molecular profiling in lung cancer is still a relatively new one and some cancer centers are making a more measured transition to personalizing treatments. The Mayo Clinic's Wigle said that patients there with advanced disease are currently tested using single-gene tests for EGFR and ALK as a first-line approach.

"But we've quickly moved from where we didn't do any testing at all [to where] — I'd hesitate to [say] 100 percent of all biopsy specimens for patients with advanced disease or resected early stage disease get tested — but God, it's awfully close," he said.

"And certainly any scenario where someone is going to get chemo, it would be part of our standard of care to test for EGFR and ALK before contemplating what treatment they should be on," he added.

Moving on to sequencing

"EGFR and ALK [testing have] become clearly standard. The question is: Where is the future moving?" posited MSKCC's Riely.

Currently, his center routinely looks for mutations in EGFR, BRAF, KRAS, AKT, PI3K, MEK1, HER2, and NRAF on a multiplex mass spectrometry-based platform from Sequenom, as well as ALK, ROS1, and RET fusions using FISH.

But by the end of the year, he said, the center is planning on moving from the Sequenom platform to a next-gen sequencing approach. "It is a key question, how we get to a place where we can use next-gen sequencing — both if it makes sense to do it, and how we interpret the results from that if we can do it," he said. Riely added that while those questions haven't been answered yet, next-gen sequencing is making its way out of the center's research lab, and he expects it to be "rolled out over the coming year."

To prepare for this, MSKCC is experimenting with several sequencing platforms: the Illumina HiSeq and MiSeq, and also the Ion Torrent PGM. "We have pilot initiatives on all of them and it seems like the one that is going to roll out soonest is on the MiSeq, with an expansion of what we do with the Sequenom array currently," Riely said.

Massachusetts General Hospital, meanwhile, has been testing another multiplex test system called SNAPshot, which is a PCR-based array approach (PGx Reporter 12/7/2011). Rebecca Heist, a lung cancer specialist at MGH, said that the test has gone through several iterations over the last few years, and now the hospital is planning on moving beyond it to targeted sequencing.

In addition to profiling patients using the SNAPshot panel, MGH currently tests patients separately for ALK, ROS1, and RET fusions using FISH, according to Heist. MGH also tests patients with squamous-cell carcinoma — another subset of NSCLC — for additional alterations.

But with next-gen sequencing, potentially all of these mutations could be uncovered using a single, multiplex approach, said Lecia Sequist, a thoracic specialist and leader of MGH's molecular profiling program. The move to NGS would enable MGH oncologists to make the leap from looking at 15 genes in a lung cancer patient to testing for more than 500 genes.

According to Heist, MGH only routinely tests advanced-stage patients, not early stage patients for potentially actionable genetic lesions.

The ideal situation, in Riely's view, would be to conduct a complete molecular analysis of a patient's cancer at the time they are diagnosed at MSKCC, regardless of the disease stage. But, he acknowledged there are challenges with implementing such an approach.

First, as knowledge about the mutations that underlie lung cancer becomes more refined over time, patients who undergo what may be cutting-edge testing at diagnosis and survive one or two years, may find themselves requiring additional tests down the line as testing paradigms change.

Secondly, tumors can evolve in response to treatment, requiring additional genetic testing. "In some [patients] we see that they sometimes have a molecular transformation after an initially good [treatment] response, so we like to test them to see if [that is true] and learn more about the molecular changes in their cancer when they become resistant," Riely added.

Tissue samples and other challenges

All this testing, coupled with the fact that sampling tissue from the lung is technically difficult and yields smaller amounts of tumor tissue than biopsies of other tissues do, means that the more efficient clinicians can be in their testing the better.

According to MSKCC's Riely, the first main challenge to molecular testing in lung cancer is the question: "Are we getting enough tissue?"

"For decades, all you needed was a couple abnormal cells on a slide to diagnose non-small cell lung cancer, and that was sufficient to guide all therapy. … [Now we are] pushing everyone in getting adequate amounts of initial biopsy materials. But the corollary is that we keep coming up with more and more ways to use the tissue and more things to find out about it," Riely said.

MSKCC's mutation panel can be run all at once, but the center still tests all gene rearrangements separately using FISH.

Some research has suggested that the FDA-approved FISH test for ALK fusions may not be economically feasible as a broad screening tool for the larger lung cancer populations (PGx Reporter 3/21/2012) and may miss some patients who could benefit from treatment with crizotinib (PGx Reporter 12/19/2012).

Unlike many other groups, Wigle said he and his colleagues at Mayo Clinic start with immunohistochemistry for ALK fusion testing and only refer those patients with a certain degree of staining for confirmatory testing using FISH. But, he said, that protocol is outside the norm.

"The onus is on the science side to develop better, more efficient multiplexed testing to identify all the relevant molecular abnormalities," Riely said.

"We need to think carefully about how to do a test that gives us all the information we want," MGH's Heist added. "I think [the recent recommendations reflect] that there are FDA-approved drugs for [EGFR and ALK mutations], but all cancer patients should benefit from being eligible for clinical trials, and many of these trials are now genotype-specific, so just EGFR and ALK is really not adequate for what we are trying to do clinically for patients."

According to MGH's Sequist, as groups transition to next-gen sequencing, ALK and ROS fusion testing could be soon be included in that single technique, saving, or capitalizing on, valuable tissue.

However, Riely said he believes that health regulators would prefer that clinicians use only approved tests for each mutation, or group of mutations that are associated with a given targeted therapy.

"The FDA would like to approve each and every test that gets done in combination with a new targeted therapy," he said. "And although it's a laudable goal to ensure standardization of testing, it's a direct challenge to the actual clinical need, which is to do a multiplex test."

In a draft guidance, the FDA has indicated that tests that predict whether a patient will respond to a drug, a so-called companion diagnostic, need to be approved by the agency before they become commercially available. However, the agency has shown flexibility in accepting molecular diagnostics that may be used to guide treatment strategies, but aren't tied to a specific drug (ie. tests for CYP2C19 polymorphisms). While agency officials have acknowledged the need for advanced companion tests for cancer treatments that gauge many markers at once, industry players have yet to submit evidence that satisfies regulators. "There's nothing to stop us from doing multigene tests, it's just that we have to have the evidence that they're all important and all clinically valid for that drug," Elizabeth Mansfield, director of personalized medicine at FDA's Office of In Vitro Diagnostics, previously told PGx Reporter (PGx 1/2/2013).

Sequist said this companion diagnostics bottleneck is something that, as a field, doctors are going to have to negotiate going forward. "[If] the FDA continues to require a separate diagnostic test for each new drug they approve, that's not going to be sustainable in the long run because of limited tissue," she said.

The benefits of multiplex testing may yet begin to speak for themselves though, according to Byers. She said that MD Anderson is already seeing real clinical benefit to its broad testing approach. "I think one of the things that is really exciting for me and my colleagues is that as we do broader mutation testing, we are starting to find more of these [mutations] that we haven't had the technology or infrastructure to pick up before."

Byers and her team are now starting to see successful stories of patients with obscure or unexpected mutations that match to targeted drugs. "There have been a couple of examples recently where a mutation that has not really even been described in lung cancer before is found in a patient and they are put on a drug … and that patient has had a great response," she said.

"I think this is truly an exciting era in the care of patients with lung cancer," Riely added. "We are seeing new markers or new targets for drug therapy coming out almost yearly, and we are seeing more and more exciting results of targeted treatments for patients with individual lesions."

"But there are a number of challenges," he said. "Tissue limitation is one. [But] also, as people who design clinical trials, we need to design smaller and smaller trials that prove the point that a new drug is effective for a given molecular target even when we at a major cancer institute would only have three patients a year with that target."

Wigle said that while the Mayo Clinic is currently still focused on single-gene testing as a first-line reflex, the future will likely see a shift to broader sequencing-based testing, but not before some significant hurdles are overcome.

"We started a couple years ago having people show up in the clinic and slapping a one-terabyte hard drive on the desk, saying 'what does this mean for my treatment?'" he said. "So it's clear that patients are actively seeking this information out and we are being asked to help interpret it."

"Or, people are coming to us and they've failed first-line therapy and don't have an EGFR or ALK mutation," and they want to know what they can do, he added.

For some patients, he noted, the Mayo Clinic offers a "limited basis" program called the Lung Cancer Individualized Medicine Clinic, through which the center does exome, or even in some cases whole-genome, sequencing for patients who have strong interest and for whom researchers believe there may be clinical relevance in additional analysis.

"I think it would be overstepping things to say we've altered anyone's treatment on the basis of that," Wigle said. "But it's certainly very interesting."

According to Wigle, with mutations outside of EGFR and ALK, often all clinicians can currently do is match patients early with a clinical trial. "We try to do that in situations where it may be relevant, but the number of mutations you are going to find versus the number of drugs or trials is still a pretty stark imbalance right now," he said.

However, he added, as technology advances there will inevitably come a point where enrichment or targeting strategies no longer make sense over broad genome profiling, even if the number of approved targeted treatments is still low.

Plusses and minuses

According to Sequist, there are "plusses and minuses" to broad testing methods. "Right now, we don't have 750 drugs for lung cancer, but we can test 750 genes," she said.

"With our first foray into the gene testing, we were more looking for the predominant driver mutations — things like EGFR or ALK — but there are probably a lot of other layers of modulation of those drivers, so that's one thing we'll be looking at with some of these other cancer genes when we move to sequencing," she added.

According to Byers, another issue is pursuing coverage for greater and greater multiplex testing. "Sometimes we'd like to do even more mutational profiling in patients — even beyond the platform we routinely use here. But if you want to go to more extensive sequencing, you have to consider: Is that going to get paid for? And is it going to balance how likely it is to help versus the out-of-pocket costs," she said.

"Of course," she said, "that is going to change because the technology is getting less and less expensive."

In addition to MGH, MD Anderson, and MSKCC, Vanderbilt Ingram Cancer Center is also developing a sequencing-based system for testing lung cancer patients, according to Leora Horn, clinical director of the center's thoracic oncology program. She said in an email that Vanderbilt currently does multiplex testing that includes EGFR, KRAS, PTEN, PIK3CA, NRAS, MEK1, AKT1, BRAF, HER2, and then separate testing for ALK, ROS1, and RET rearrangements.

Other groups, like the University of Washington, have recently adopted sequencing panels, like MD Anderson's, for use across a variety of cancers, including lung cancer. UW's OncoPlex sequencing service targets hotspot regions and exons of 194 genes and has become standard of care for the university hospital, with additional FISH testing for ALK and other gene rearrangements for patients with lung cancer, as well as other cancers (CSN 2/27/2013).

Arguably, large centers like these oversee only a fraction of cancer patients in the US. But according to Sequist, the innovation at academic centers is rapidly moving into other parts of the oncology community.

"From my observations [and] from speaking with doctors around the country, I have the sense that a lot of practitioners are ordering multiple tests on patients. Some of the centers have the ability to do multiplex testing, but many others are using a send-out service," she said.

"Mainly, I do think this idea of not testing one gene and waiting to see if it comes back positive or negative before testing the next, it's really caught on … [and] it's a more efficient use of time and tissue to test multiple things at once," she added.

Sequist said that she anticipates a lot of academic centers will switch to sequencing during the next couple of years and more multiplex testing will likely continue to then roll out to the larger thoracic oncology community as well.

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