Learning as much as possible about a cancer can help physicians and patients decide on the best course of action to treat the disease. Increasingly, they are turning to molecular diagnostics for help.
The number of such diagnostics has multiplied, particularly in oncology. Molecular diagnostics could allow a clinician to differentiate a breast cancer patient who will have a recurrence of the disease from one who will not, or to distinguish a cancer that originated in the thyroid from one that began in the lung.
"Cancer is definitely the iconic genetic disease that we acquire because every single one so far has been found to be due to some molecular genetic change in the normal tissue that converts it to cancer," says David Henner, chief medical officer at Pathwork Diagnostics. "As cancer develops — becomes more aggressive, becomes metastatic — there are further molecular changes that can occur, that then further define the cancer. I think molecular diagnostics are going to be increasingly important in cancer."
There are a number of molecular diagnostics for cancer on the market, and more are coming. Physicians are beginning to order tests and there are indications that some molecular diagnostics may be cost-effective. The technologies that many tests are based on — microarrays and PCR — may soon be shaken up as sequencing enters the clinical market.
The molecular diagnostic field began to grow rapidly about 10 years ago with a number of tests emerging based on gene expression signatures.
Both Agendia's MammaPrint and Genomic Health's OncotypeDx launched in 2005. MammaPrint tests the expression of 70 genes using Agilent arrays to determine a patient's risk of breast cancer recurrence, while OncotypeDx examines a set of 21 genes using RT-PCR to ascertain recurrence risk and chemotherapy benefit for patients with ER-positive breast cancer. Other tests have since come online to detect cancer, to determine the origin of unknown cancers, to determine molecular subtypes of various cancers, and more.
The MammaPrint test grew out of work at the Netherlands Cancer Institute that compared the gene expression profiles of women with breast cancer who had disease recurrences to those with breast cancer who did not. "They went through the whole human genome. They kept cutting it down," says Doug Bradley, vice president of global marketing at Agendia. "They went to 5,000 genes ... down to 230 genes and, from there, they went to 70 genes and rank-ordered them as the most prognostic genes for predicting cancer recurrence based upon those women that had recurrences." A similar process was used to develop the 18 gene signature that is part of Agendia's ColoPrint test, he adds.
The 21 genes involved in the OncotypeDx test came out of a pool of candidate genes that were associated with recurrence risk. That pool was whittled down to 16 cancer genes and five reference genes, says Calvin Chao, senior director of medical affairs at Genomic Health. The cancer genes include ones involved in proliferation and invasion, an estrogen group, a Her2 group, and three independent cancer genes, Chao adds. The reference genes help normalize the expression data.
Genomic Health similarly developed a recurrence test for colon cancer, which launched in 2010, and is in the process of developing a prostate cancer test to distinguish among men with aggressive versus indolent disease.
Pathwork Diagnostics' set of genes to determine a cancer's origin is a bit different. "The basic premise of the test is that every tissue in every cancer type has a different set of gene expression," Pathwork's Henner says. Many of those genes are likely carried over from the original normal tissue. So the researchers selected genes, like thyroid transcription factor, that distinguish different tissues.
The tests are then run using a number of technologies, commonly microarrays and PCR. Sequencing, however, is becoming an attractive alternative, and is the basis of Foundation Medicine's molecular subtyping test. "Microarrays have several different advantages; one is that you can use as many genes as you want because essentially, the whole genome is on the chip," Henner says.
"You can do assays like this with PCR, but they become limited to — at the most — less than a hundred genes, and that does reduce your accuracy of being able to distinguish among different tissue types, so there are some trade-offs there," he adds.
Indeed, Magnus Sjogren, chief medical officer at Diagenic, says his company's BCtect — which includes 96 genes for the early detection of breast cancer — is run using RT-PCR. "We decided early on that RT-PCR is a more robust and suitable technology for a gene expression-based test when you do not have hundreds or thousands of genes in your signature," he says.
Genomic Health's Chao adds that PCR allows for quantitative, rather than qualitative, results. "RT-PCR methodology is very important because it allows us to give very precise quantitative gene expression of these 16 cancer genes and allows us to then mathematically calculate the recurrence score using that algorithm with precision," he says.
Once the signatures are measured, they are usually fed into algorithms to determine the recurrence risk, tissue of origin, or other measures.
In the US, molecular diagnostic tests may be offered as either laboratory-developed tests in labs certified under the auspices of the Centers for Medicare and Medicaid's Clinical Laboratory Improvement Amendments — or CLIA — or as tests cleared or cleared by the Food and Drug Administration.
And companies take different paths.Genomic Health's OncotypeDX is offered under CLIA, and the test is only run at the company's certified, central lab. Chao says that the lab is also certified by the College of American Pathologists and has licenses from the state of California, and others.
Other tests have been cleared by FDA under its 510(k) process. Agendia's MammaPrint was cleared by FDA in 2007 and Pathwork Diagnostics' Tissue of Origin test was cleared in 2008 for frozen tissue, and in 2010 for use on FFPE samples. "FDA had access to and reviewed of all of our processes for developing the test: all of our quality processes, all of our verification and validation studies to show that the test works and that it is reproducible," Pathwork's Henner says.
Both Agendia and Pathwork Diagnostics also have CLIA certification for their labs.
Currently, Agendia is offering its BluePrint, TheraPrint, and TargetPrint tests — its molecular sub-typing, ER/PR/HER2 expression, and alternative therapy tests, respectively — as laboratory-developed tests, though Bradley notes that the company has filed with FDA for clearance for BluePrint and TheraPrint.
FDA has signaled its interest in regulating some diagnostic tests offered under CLIA by issuing draft guidances.
Tests like Foundation Medicine's, which is sequencing-based, add a whole new wrinkle to the regulation issue. "We've had discussions with FDA," says Foundation's Chief Operating Officer Kevin Krenitsky. "FDA wants to be informed about this, they know this technology is coming. I think it is pretty clear to say FDA isn't ready for this yet. There's no question about that. There is still relatively vigorous debate going on as to whether FDA is going to regulate LDTs [laboratory-developed tests] or whether they are not."
To the clinic
Some molecular diagnostic testing companies are beginning to get feedback on the adoption of their oncology tests by physicians, how the tests are affecting clinical care, and whether the tests are cost-effective.
Physicians are starting to order such tests to help them treat their patients' cancer. Genomic Health performs 250 assays to 300 assays per day in its central lab, and has received samples from more than 60 countries, Chao says. Further, he adds that OncotypeDx has been incorporated into a number of clinical guidelines for breast cancer, including those from the American Society of Clinical Oncology, the National Comprehensive Cancer Network, and St. Gallen.
Foundation Medicine has quietly offered its test since last October — it is launching the test at the ASCO annual meeting in Chicago this month — and it has been seeing about 25 tests to 35 tests come in each week. "The uptake and adoption of the test has been pretty dramatic as far as what we expected," Krenitsky says, adding that the company expected about three or four tests a week to come in prior to the launch.
The type of samples that can be analyzed also makes a difference in ordering. After the version of Agendia's MammaPrint came out in January that could examine FFPE samples rather than fresh samples, the company saw an uptick in adoption. "That's made a huge difference. We're doubling our sales now as a result of switching our test," Bradley says. The sample no longer has to be taken and sent at the time of biopsy. It can be sent later, after the patient has met with an oncologist.
Companies also say they are finding that their tests are changing how physicians practice medicine. "You can imagine if you offer a test result and it didn't change any decisions. It could be theoretically wonderful, but it doesn't have a practical application unless you are changing decisions," Genomic Health's Chao says.
In a meta-analysis of seven studies, his company found that OncotypeDx results change 37 percent of treatment decisions for breast cancer patients, Chao says. Most of those decisions — 33 percent of that 37 percent — were made against the administration of chemotherapy and a small fraction — 4 percent — were made to administer chemotherapy. "That's an important 4 percent ... because these are women that would have otherwise been reassured by their physicians not to need chemotherapy based on clinical parameters, but then it is discovered that they have a much higher risk," Chao says. For the colon cancer test, which also looks at disease recurrence, the company has seen 30 percent of treatment decisions change, he adds.
Similarly, Pathwork's Henner says that his company's Tissue of Origin test has led about half of physicians to change their leading diagnosis for patients with cancer of uncertain diagnosis, and about 65 percent to change their treatment plan. In about a third of cases, the leading diagnosis was unchanged, though Henner says physicians then might have more confidence in their diagnosis. "Even in some of those patients, there is a change in the therapy as the doctor is more certain about what they are dealing with," he adds.
If molecular diagnostics are being adopted and are helping doctors make treatment decisions that are better suited to patients' cancers, one hope is that they will save money. "You can imagine for every patient that decides that she is going to avoid chemotherapy based upon the confidence received from the OncotypeDx assay, those are costs that are not incurred by the healthcare system," Chao says. "That's not just the cost of the drug but the cost of all the side effects, the complications, the drugs needed to treat some complications, doctor's office visits, and occasional hospitalizations that occur because of the toxicity of the drugs." In the US, Chao's company has determined that its test offers a net cost savings of roughly $2,000 per patient.
Pathwork Diagnostics has done similar studies, finding that its test is also cost effective. "Our tests costs about $40,000 for every added life-year," Henner says. "Now, it sounds like a lot, but it is much smaller that most quality-adjusted life-year benefits that you get from most new drugs, usually several hundred thousand dollars for an extra life-year, so we were pleased with that."
Of course, the technology is changing rapidly. "We're looking at [sequencing]. We're all looking at it," Pathwork's Henner says. "Every laboratory that is working with microarray or PCR is looking at when will the next-gen sequencing systems be ready for routine clinical tests."
As of now, though, some are using it as a discovery or confirmation tool. "We see sequencing currently as a discovery tool and would most likely use that in a new discovery study. It will take some time before we see that in the clinic," Diagenic's Sjogren adds.
Chao notes that Genomic Health has used sequencing tools to do a validation of the genes included in its test.
In the future, however, sequencing may become the testing platform of choice, and companies say their tests can make the transition.
Sequencing may have a lot to offer the molecular diagnostic field. "I think the world has been moving in this direction for a long time," Foundation's Krenitsky says.