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Foundation Medicine, MSKCC to Develop Sequencing-based Blood Cancer Test from DNA, RNA

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Foundation Medicine and Memorial Sloan-Kettering Cancer Center are developing a sequencing-based test for hematologic cancers from both DNA and RNA that they plan to launch by the end of the year.

The test will be used to match patients to clinical trials.

Foundation CEO Michael Pellini told Clinical Sequencing News that the test will be based on the firm's technology, methods, and computational algorithms, while Memorial Sloan-Kettering will contribute clinical and genomic expertise in hematologic malignancies. Foundation plans to commercialize the test both in the US and internationally.

Ross Levine, both a physician and researcher at MSKCC studying the genetics of hematologic malignancies, told CSN that one of the center's long-term goals is to "get a state of the art genomic test into clinical practice for patients with hematologic tumors," and the collaboration with Foundation "allows us to help move that forward."

Foundation currently markets a sequencing test for solid tumors, FoundationOne, which targets 236 cancer-related genes plus 47 introns from 19 genes that are known to be rearranged or altered in cancer.

The test for hematologic cancers will differ in that it will include both targeted DNA and targeted RNA sequencing. While details about how many and which genes to include are still being worked out, Levine said the test may ultimately be larger than the 236-gene FoundationOne panel. Cost also has not yet been determined, but the list price for FoundationOne is $5,800, which Foundation bills to patients' insurance companies or directly to the patient if uninsured.

DNA and RNA

One unique aspect of the hematologic test, said Levine, is that it will incorporate RNA sequencing. "In all cancers, but particularly hematologic cancers, there [are] a lot of examples of translocations and events that lead to fusion genes and rearrangements that are difficult to detect with lower-throughput DNA sequencing and even targeted sequencing," he said. "By contrast, with RNA, [these alterations] are more feasible to detect because you can detect a fusion between two genes that are expressed together that you wouldn't otherwise detect," he said.

The FoundationOne test does not incorporate RNA sequencing, so in order to identify gene fusions, Pellini said that the test uses "techniques that capture DNA spanning the entire rearranged introns of 19 genes fused in human cancer."

However, because there are so many more gene fusions in hematologic cancers, this technique would not be as efficient, he said. He added that because RNA sequencing is more efficient at identifying gene fusions, Foundation may consider incorporating RNA sequencing into a future version of its FoundationOne test.

The DNA sequencing portion will identify somatic mutations such as point mutations, small insertions and deletions, while the RNA sequencing portion "can really detect translocations and fusions, which are clinically relevant and actionable, in a way that current DNA platforms in a clinical setting are not able to do," Levine said.

Collaboration vs. in-house development

Levine said that once developed, the test would be used at MSKCC both clinically and also for research projects. One aspect of the collaboration is that Foundation will be involved in some research projects at MSKCC. That was "a critical and essential aspect for us," Levine said.

In particular, Levine said that one important project will be studying how to use genomic information — "what patients, what information makes sense in what context, and understanding how to use [the genomic information]," as well as "linking genomic information to clinical outcomes."

MSKCC's diagnostic molecular pathology laboratory is currently developing a number of different targeted cancer panels in-house, including one for acute myeloid leukemia (CSN 10/17/2012).

Many of the panels being developed internally at MSKCC are smaller, more focused panels, such as a 30-gene AML panel. But the test being co-developed by Foundation and MSKCC will likely encompass hundreds of genes, said Levine.

The details of how many genes and which genes are still being worked out, but Levine said that it could ultimately be a larger panel than the 236-gene FoundationOne test.

Levine said that MSCKCC's in-house efforts will continue, but the collaboration with Foundation will help move the test "very rapidly into the clinic." Getting the test into the clinic this calendar year will only be possible through collaboration, he added.

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