In cancer sequencing, a new lingua franca

• Tier I: variants with strong clinical evidence for response or resistance to therapies that are FDA approved or included in professional guidelines for specific tumor types (e.g. BRAF V600E predicts response to vemurafenib in melanoma).
• Tier II: variants that are potentially clinically significant, but which may not yet be included in professional guidelines, or where an FDA-approved drug exists, but for a different tumor type. One example is the JAK inhibitor ruxolitinib, FDA approved for treating myelofibrosis, and which has shown potential in treating patients with acute lymphoblastic leukemia and mutations that activate the JAK-STAT pathway.
• Tier III: variants of unknown significance. This can include somatic variants in genes reported in the same or different cancer types with unknown clinical significance, and variants that have not been reported in any cancers. These variants should not have been seen in the general population with a significant allele frequency.
• Tier IV: variants that are benign or likely benign. Laboratories are not encouraged to report these mutations, says Dr. Li, unless requested by the referring physician.

The guideline suggests that laboratories report variants in descending order of importance—start with DEFCON 1, in other words. That way, says Dr. Li, physicians will know quickly what’s important and what they need to do next. It is, in some ways, a guided tour of variants. Especially for labs that do large panels, “You can’t just put all of them in a report and let the physicians figure out the significance,” Dr. Li says.

The working group found it wasn’t unusual for laboratories to report a mutation followed by extensive information about the FDA-approved drug(s) and clinical trials. “A lot of physicians found this not useful or even misleading,” Dr. Li says, adding that FDA-approved therapies or clinical trials described in the report should be carefully matched with patients’ genomic alterations and tumor types based on available clinical evidence. Since treatment or other patient management decisions are based on many pieces of medical information beyond genetic alterations, the report should not recommend specific therapies or clinical trials, she says, although general statements about availability of relevant trials or citing results of published trials is acceptable.

Deciding on the optimal number of tiers was the most time-consuming part of developing the guideline, says Dr. Lindeman. That may not come as a surprise to pathologists, but, he says, the oncologists in the working group may have been puzzled by the outsized effort. “They have two categories,” Dr. Lindeman explains: 1) treat. 2) don’t.

His laboratory is among those that have been using a five-tier system. “Some of my colleagues are a little grumpy that we’re going to change some things,” he says. “But I think they’re the right changes to make.”

That will mean deciding whether to reclassify each of the 16,000 cases that have been signed out to date, a daunting task that seems better suited to clerks in a Dickens novel toiling away at the Inns of Chancery. “I really don’t want to do it,” Dr. Lindeman admits. “But then it will throw our database off for scientific inquiry if we don’t. So we’re going to have to figure out a solution.”

The guideline also calls on laboratories to report significant negatives. In cancer sequencing, these can function like the absent character in a certain Beckett play—Godot never shows up, but he manages to drive the play’s action (such as it is) anyway.

Dr. Lindeman says he was acutely aware of this need as he oversaw this section of the guideline. “One of the things you see a lot in this field are reports that list all the mutations that were discovered. And the reader—an oncologist, surgeon, patient—is left to conclude that if something is not mentioned, it must not be there.”

There is a third possibility, he continues: The assay didn’t test that region, either through design or because that particular region didn’t work well in the assay run. So when an alteration is not found, he says, there’s a need for the report to make “some qualification that the assay was capable of detecting things in that area, and that it’s truly missing.”

The report should also make clear the frequency of sequences, or variant allele fraction, since it can have considerable impact on clinical care, he says.

With its emphasis on language, the guideline attempts to return genomics to a pre-Tower Babel. “Basically,” Dr. Li says, “this guideline provides a common language among pathologists, oncologists, and other health care providers.” Speaking in one tongue will help ensure patients benefit directly from genomic profiling. If test results are conveyed in ways others “can’t understand, then it doesn’t do the patient any good.”

The guideline also makes a point of telling laboratories to use “colloquial nomenclature” in their reports.

One example is the use of the cancer gene formerly known as MLL, or mixed-lineage leukemia, now called KMT2A. Since other publications—including many older ones—use the original name, the guideline recommends using the standard name but also suggests noting the previous name, “so there will be no confusion,” says Dr. Li.

Her own laboratory does this. “We even do it at the exon level,” she says, citing the example of NPM1, where the prognosis is good in AML patients with an exon 11 (formerly exon 12) insertion mutation. She and her colleagues report the current name but parenthetically note the old name, “so people will know it’s the same thing.”

Even the best guideline will fall short unless pathologists and oncologists talk about what’s in it, says Dr. Li.

It’s not unusual, she says, for oncologists to request NGS without specifying which genes they’re most interested in. “When laboratories look at a result, we don’t want to be biased to a specific mutation, but we do check a patient’s history.” When there are conflicts between sequencing results and a pathology diagnosis, or with what the oncologist might be looking for, dialogue is the remedy. “When everything is typical, that’s easy. When it’s atypical, that’s when we need multidisciplinary discussion.” She recalls the example of a patient with an unusually tricky diagnosis; NGS eventually identified a fusion gene that led to a different diagnosis and treatment plan. The patient continues to do well, she says, but that success hinged on continual conversations between the geneticist, pathologist, and oncologist.

At Children’s Hospital of Philadelphia, Dr. Li notes, the genomic data is considerable. All patients with cancer undergo genomic profiling at diagnosis or at relapse, including mutation and point mutation, copy number changes, and fusions. The comprehensive report isn’t simply filed away into the medical record. The laboratory professionals meet weekly and monthly to discuss results with pathologists, oncologists, and radiologists. The regular meetings have an educational purpose as well as a clinical one. “Even for our oncologists, they don’t always go to the lab and don’t always know exactly what we do,” she says.

The meetings also reinforce an important notion for pathologists: The information they provide, while critical, is only one part of patient care, Dr. Li says. “We may not know about a patient’s cardiac or GI condition, which may influence treatment.”

Though the four-tier system anchors the guideline, it’s prefaced by nearly four pages of information about databases.

As Dr. Li puts it, “If you don’t understand those databases, you may misuse them.” Pathologists need to understand how they’re aggregated and their limitations, to avoid overinterpretation of annotation variants as well as to avoid missing rare but important somatic variants.

If laboratories aren’t using databases, Dr. Lindeman says, “they’re tying one hand behind their back, if not both.” (Insert joke about Irish step-dancing here.) The heavy emphasis early in the guideline was not an accident. “It may be that we hit people over the head a little bit, because we think it’s really important,” he says.

The reasons are obvious to Dr. Lindeman. At Brigham and Women’s, “we would be in trouble if we didn’t have our database of alterations and interpretations,” he says. The database helps him and his colleagues learn from each case and apply that knowledge to subsequent cases. Ditto for other databases that share knowledge more broadly. His institution, he says, is large by academic standards. With their 16,000 samples, “We can rely on what we’ve seen before.

“But,” he asks, “if you’re a smaller center, and maybe you’ve sequenced only a couple hundred, where do you get that breadth of experience to know what you’re looking at?” For any lab that has the personnel and resources to build its own database, “by all means do,” says Dr. Lindeman. But even then, “I think it would be a good idea to tap into what’s out there anyway.”

The guideline also acknowledges the brisk dynamics of NGS. Whatever experts know now is likely to change and be crowded by new, sometimes conflicting, and often messy updates. Those who try to keep up may feel like they’re swiping through medicine’s version of a Tinder account.

The guideline makes the sensible recommendation that laboratories figure out how to continually evaluate variants—then concedes this is a “monumental task.” Even as NGS becomes more affordable, and spreads to smaller labs, the upkeep, so to speak, might be difficult—like buying a Porsche, then being done in by the oil changes and other routine maintenance.

Smaller laboratories should consider reaching out to others with more experience, Dr. Li suggests. They should also participate in somatic variant NGS proficiency testing programs, as well as in ongoing QI and QC.

Dr. Lindeman offers observations in lieu of fail-safe answers. “It’s hard to keep up,” he says, conceding that even his own relatively large practice works hard to do its best. “We keep each other on our toes, and we go to meetings and read.” Perhaps an academic educational listserv would work, he muses, or a shared database. “But I don’t have an easy answer.” There simply may not be one, not with 20,000 genes. “People say, ‘Well, which ones are important?’ Well, every one is important,” he says. “They wouldn’t be there if they weren’t.”

Apostolia-Maria Tsimberidou, MD, PhD, a guideline coauthor and professor, Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston (where she also pioneered the personalized medicine department, in 2007), says she’s hopeful the guideline will help tame the data she and her fellow oncologists receive.

“There are many companies that do this testing, many institutions, many laboratories,” with vast differences in how results are interpreted and reported, says Dr. Tsimberidou, who is the current chair of ASCO’s clinical research committee.

For oncologists, the next step after receiving sequencing results is to ask about clinical implications. That question is as natural and inevitable as drawing one’s next breath. It’s also “the most crucial one,” she says, “because patients’ clinical outcomes depend on the efficacy of the treatments they receive using the sequencing results.”

Sometimes the next step is clear, but not always. The majority of molecular abnormalities that turn up in sequencing are not “targetable,” she notes. In practice, there’s a gap between identification of the driver molecular alteration(s) and available drugs that inhibit the function of these alterations. Nonetheless, she says, “Some investigators propose that even if preclinical data exist, we should match the molecular abnormality with a drug because on the package insert, preclinical data demonstrate that targeted agents inhibit certain alterations.” While this might seem reasonable in theory, she says, “we cannot extrapolate that this information is relevant in humans, unless clinical trials in patients with cancer have demonstrated that a targeted agent has antitumor activity.”

Experience has taught Dr. Tsimberidou that dictums are unhelpful, or worse. Every patient’s tumor has unique characteristics requiring treatment based on the personalized medicine approach. “What oncologists need in the report is an accurate description of the molecular abnormalities and their function.” When pathologists indicate treatment, however, that can add complexity, says Dr. Tsimberidou, who shares reports with her patients. Some reports list a recommended treatment based on an animal study or limited information about a patient’s tumor. In other reports, the recommended treatments are contraindicated based on other clinical information or coexisting molecular alterations.

“We’ve been asked not to be too prescriptive,” Dr. Lindeman acknowledges. He’s seen it in others’ reports, where laboratories recommend a particular drug. “Sometimes patients don’t qualify for that drug,” he says. He cites the case of a report, from another lab, that recommended a treatment that was contraindicated because the patient was diabetic. “So now my colleague in oncology had to spend a considerable amount of time explaining to the patient that even though the report said they should get the drug, they can’t.”

On the other hand, it’s useful when pathologists disclose test limitations up front. “Then we can exercise our own personal experience about the clinical significance of the findings and discuss results with the lab,” Dr. Tsimberidou says.

Adds Dr. Lindeman, “I haven’t encountered too many oncologists who don’t want to know when something isn’t working.” But keep it brief. “We’re writing this report for people who are very busy and don’t have a lot of time. They would like to have a very quick and simple explanation.” For those who find themselves writing three pages, know that it’s going to be a wasted effort, he says, like turning out the lights in a burning building.

Laboratories might consider trying an old newspaper technique, using so-called inverted pyramid style to cram the key details on top. “The first page should convey everything the physician needs to know in order to treat,” says Dr. Lindeman. “If they have to go to page two for that, it’s a problem.” That doesn’t mean there can’t be a page two, but use it for noncritical information, such as additional technical details and regulatory requirements.

With an oncologist’s preference for action, Dr. Tsimberidou speaks in the same breath about the strengths of the guideline and the next steps she’d like to see taken.

“Molecular abnormalities are crucial,” she says. “But oncologists also have to take into account other mechanisms of carcinogenesis, including immune markers, epigenetics, and proteomics.”

The guideline covers none of these, of course. “So we look to the four tiers we now have,” she continues, “and we ask, what is the level of evidence for acting on a mutation?” But even with the clearly defined tiers of evidence, “We still have much to sort through. Variants of unknown significance are informative but perplexing,” she says. If such a variant is the only molecular alteration available, patients are eligible for clinical trials with targeted agents; there are no other available treatments. “We discuss these data with the patient, and we may offer experimental treatment.”

“Looking at one molecular abnormality alone is, I think, inadequate,” she adds. The guideline drives home a related point, however. “We need to prospectively collect these data, assess what is clinically significant and what is not, and report them,” particularly to improve treatment in such subsets of patients.

Continuing to look ahead, Dr. Tsimberidou sees the guideline as a snapshot of sorts, a picture of what to do now while developing a long-term plan. “There are so many other challenges in the implementation of personalized medicine,” she says. She points to a reported case of a patient with multiple myeloma who had a subclone that was not monitored and was not eliminated with treatment; the subclone, it turned out, expanded, causing disease progression, and the patient died. “It’s important to have sequential molecular profiling,” she says. Likewise, she adds, it’s important to consider how molecular abnormalities can differ between original tumor and metastatic sites.

Dr. Tsimberidou recognizes the costs involved in doing additional sequencing. And she understands that for this to happen, cell-free DNA testing will have to advance.

Even then, oncologists will be limited by the portfolio of drugs available and their costs. And when the appropriate drug is available, she says, oftentimes its use is delayed for months while she negotiates approval with insurers. It’s a sobering ritual. “You hope the patient, who has no other treatment options, will still be alive to receive it.”

She pauses for a breath. There’s so much more to say. But the guideline, she says, “Is a step forward.”
[hr]

Karen Titus is CAP TODAY contributing editor and co-managing editor.