Tumor Sequencing Test Brings Personalized Treatment Options to More Patients

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Genomics researcher Michael Berger

Summary

A powerful diagnostic test, MSK-IMPACT™ gives our doctors an unparalleled amount of information about individual people’s cancers to guide their treatment.

A new genome-sequencing test developed at Memorial Sloan Kettering allows our doctors to quickly find out whether a patient’s tumor carries clinically useful mutations — including aberrations that make cancers vulnerable to particular drugs — and to match individual patients with available therapies or clinical trials that will most benefit them.

Until now, genomic testing of tumors has been done routinely only in certain cancers. For most cancers, the available tests have been limited to analyzing one or a handful of genes at a time, and within each gene, only the most common mutations could be detected.

The new test, called MSK-IMPACT™, makes the analysis far more comprehensive and can be used on any type of solid tumor, irrespective of where in the body the cancer is thought to have arisen. (A similar genomic test for blood cancers was recently co-developed by Memorial Sloan Kettering scientists and Foundation Medicine, a biotech company.)

“It’s an incredibly powerful test,” Memorial Sloan Kettering’s Department of Pathology Chair David S. Klimstra says of the MSK-IMPACT technology. He expects it will enable our physicians to rapidly extend the promise of precision medicine to many patients with difficult-to-treat cancers, including both common and rare tumor types.

Intensified Tumor Testing

“We are able to look at hundreds of genes in multiple patients simultaneously and collect an enormous amount of information about each of these genes,” adds genomics researcher Michael Berger, who developed MSK-IMPACT in the Department of Pathology. Marc Ladanyi, Chief of the Molecular Diagnostics Service, led the clinical validation of the test together with molecular pathologist Marcia Arcila, and bioinformatician Donovan Cheng.

The bulk of the tests will be done for patients with advanced disease, for whom results can help guide treatment choices. The assay will also be offered on a research basis in the newly launched Marie-Josée and Henry R. Kravis Center for Molecular Oncology.

Effective Sequencing

The MSK-IMPACT test is based on next-generation sequencing — cutting-edge technology that allows cancer genomes to be profiled very quickly and with great sensitivity. Next-generation sequencing makes it possible to analyze more types of genetic abnormalities than conventional DNA sequencing technologies. “For example, we can tell if a gene has been mutated or deleted, or if there are additional copies of it,” Dr. Berger says.

Until recently, this technology had mainly been used in the context of research studies, in which tumor samples of the highest quality are chosen. “The samples we deal with in the clinic are different and much more difficult to analyze,” Dr. Berger explains. “They may contain a mix of various tumor cells and noncancerous cells, and the cells’ DNA might be degraded.”

In developing MSK-IMPACT, Dr. Berger and his co-workers, with support from the Farmer Family Foundation, meticulously enhanced the next-generation sequencing protocols and computational methods for the clinical diagnostic laboratory setting, where many tissue samples need to be processed and analyzed simultaneously.

Actionable Targets

Rather than sequencing a tumor’s whole genome, or the entire part of the genome that codes for proteins, MSK-IMPACT analyzes 341 of the most important cancer genes, which are captured and sequenced on an instrument called Illumina HiSeqTM. This targeted sequencing approach makes the analysis of tumor tissue more feasible and effective and increases the chance of finding clinically relevant gene changes.

“All important regions of these 341 genes are sequenced, rather than the more focused analysis of only the most frequently altered regions, or mutational ‘hot spots,’ allowed by earlier technology,” explains Dr. Klimstra. “This gives us a much more comprehensive picture of the full spectrum of genetic changes in a person’s cancer.”

The 341 genes covered by the test are ones that have been shown to play a role in the development or behavior of tumors. They represent all “actionable targets” — genes that can either be targeted with drugs or provide clinically relevant information about the disease if they are altered. Dr. Berger says the test will be updated periodically as new actionable targets are discovered.

A Wealth of Information

So what can the MSK-IMPACT test tell doctors about their patients’ diseases? A lot, according to Dr. Klimstra. “In fact,” he says, “the test will likely generate more molecular information about tumors than we will know what to do with initially.”

The 341 genes were selected by drawing connections between the genomic profiles and clinical data of past patients. For example, changes in some of the genes have been shown to indicate that a tumor is more likely to respond to a particular drug, while other gene changes may predict that a certain therapy will be of little or no benefit.

“The interaction of different altered genes can also be important in predicting the behavior of the tumor,” Dr. Klimstra says, “which is another reason why we needed a test to evaluate many genes simultaneously.”

In some cases, finding a specific mutation in a tumor can lead to a new clinical trial in which a patient is offered an experimental drug that may be the best treatment option for his or her disease, but that would not have been considered if the mutation had not been found. Other times doctors may spare a patient intensive treatment with standard drugs such as chemotherapy, if test results show that the therapy is likely not to be beneficial.

But Dr. Klimstra emphasizes that many gene changes detected by the test will not be immediately actionable. “If a mutation has rarely been observed in a disease and has not been studied, we may suspect it’s important, but we don’t know what would happen if we were to target it,” he says. “That’s why an important aspect of MSK-IMPACT is to gather data for research to help future patients.”

Basket Trials

Patients with an actionable mutation that has not yet been studied in their tumor type may be eligible for treatment in a new type of clinical study called a basket trial. Traditional clinical trials focus on a particular cancer type, which is typically defined based on where in the body the cancer originated. Basket trials, however, focus on specific gene changes and may enroll patients with many different types of cancer whose tumors carry similar mutations.

Memorial Sloan Kettering investigators are currently undertaking an intensive research effort to learn what kinds of mutations different tumors have, and how these mutations impact patients’ responses to various kinds of treatment. Dr. Berger and his colleagues are working to develop genomic tests for research on banked tumor samples, as well as other clinical tests to detect mutations MSK-IMPACT might miss.