Next-Generation Sequencing Platform Efficiently Detects MSI Status

A next-generation sequencing (NGS) approach for the detection of microsatellite instability-high (MSI-high) status for immunotherapy treatment candidacy may be more efficient and cost-effective compared with the current approach, according to results published in Cancer Medicine.

Last May, the Food and Drug Administration (FDA) approved Keytruda (pembrolizumab) to be the first treatment indicated for a common biomarker — solid tumors identified as MSI-high or mismatch repair deficient. This was big news considering most drug approvals and their indications are geared toward the location of the tumor’s origin.

MSI status is a feature of cancer’s genetic code that contains abnormal cells as a result of defects that occur in the way DNA repairs itself.

“Really what is happening is that there are changes at the genetic level within the cancer that lead to a massive number of a special type of mutations, insertions and deletions,” explained David Spetzler, M.S., Ph.D., M.B.A., president and chief scientific officer at Caris Life Sciences, which manufactures the assay to identify MSI status.

These cells become so abnormal, though, that the immune system calls upon the body’s natural defenses and detects the cancer. As a result, MSI-high tumors respond far more readily to immunotherapy.

“If you can unleash the immune system, which is what the PD-L1 checkpoint inhibitors do, then those types of cancers are highly susceptible to that immune cell death mediated pathway,” Spetzler said in an interview with CURE.

Therefore, it became important to produce an effective way to identify this biomarker, especially since it is somewhat rare.

“When we are talking specifically about MSI, the incidence rate across all cancer types is sitting at about 3 percent of late-stage patients. Some of the lineages are even more rare than that,” said Spetzler. “So, it becomes very inefficient to run multiple tests looking for something that may only show up a small fraction of percent of the time, whereas, if you can include MSI in a panel, where you are looking much more broadly, then you are going to get everything all at once.”

The NGS assay takes a piece of the tumor, for which DNA is extracted from the cells, to look for a variety of mutations. Spetzler noted the test also takes an added step of evaluating changes in RNA — which act as a messenger carrying instructions from DNA for controlling the synthesis of proteins – and protein levels.

Spetzler noted the test also has one very specific benefit to patients. “The assay that we developed has an additional advantage to the patients in terms of not needing normal tissue to compare it back to,” he said. “And so, anytime you can avoid having to do additional collections from patients, that is of course of benefit.”

To evaluate the assay’s efficacy, researchers identified 2,189 matched cases that spanned across 26 cancer types, of which the majority were colorectal cancer (1,108 cases), to compare mismatch repair status identified by Caris’s NGS platform or by the current industry standard of PCR fragment analysis.

The NGS assay had 100 percent sensitivity and 99.9 percent specificity of MSI detection compared with the standard testing. Similarly, across all 26 tumor types, the assay had sensitivity of 95.8 percent and specificity of 99.4 percent.

Overall, the NGS assay identified MSI-H cases in 23 different tumor types.

Because MSI status is crucial in directing, or not directing, patients to be treated with immune checkpoint inhibitors, the researchers also compared MSI status to other known biomarkers, tumor mutation burden and PD-L1 expression, across 11,348 cases.

“The general theory is that if you have a lot of mutated proteins on the specific cancer, then that is a good target for the immune system and tumor mutation burden is another independent indicator of that potential situation,” Spetzler said.

The researchers identified 3 percent of cases with MSI-H status, 7.7 percent with tumor mutation burden and 25.4 percent with PD-L1 expression. Among MSI-H cases, 30 percent were tumor mutation burden-low and 26 percent were PD-L1-positive, and only 0.6 percent of cases were positive for all three biomarkers. Of note, this overlap varied by cancer type.

As a next step, Spetzler said the company needs to develop a companion diagnostic.

“We are trying to broadly understand the patient population that is going to potentially experience a benefit from immunotherapy,” Spetzler said. “It was an interesting study because it creates opportunities for patients today as well as laying the groundwork for more opportunities in the future.”