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Insight's PCR-Based ALK Test Development Moves Forward with NCI's Help

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Originally published April 9.

Insight Genetics is on track to advance the development program for its PCR-based diagnostic for gauging ALK fusion transcripts after being selected by the National Cancer Institute to participate in its Clinical Assay Development Program.

Earlier this month, Insight Genetics announced that the NCI had chosen the firm to participate in the CADP, through which the institute provides companies assistance with certain aspects of an assay development program, such as external validation, pre-investigational device exemption meetings with the US Food and Drug Administration, and statistical analyses?.

Insight will use NCI's help through the CADP to advance development of its ALK Screen test, which the company says detects "known and unknown" ALK mutations and fusions associated with various cancers, particularly non-small cell lung cancer, and has certain advantages over fluorescence in situ hybridization- or immunohistochemistry-based ALK tests. Specifically, Insight VP of R&D David Hout told PGx Reporter that the company will use the CADP to move forward a head-to-head comparison of its qPCR ALK Screen against the gold standard, Abbott's Vysis ALK Break Apart FISH probe test.

Hout noted that Insight hasn't yet done extensive head-to-head comparisons between the Insight PCR test and the Abbott FISH test. However, data from such a study will be critical to driving adoption and establishing reimbursement for Insight's test, since it will compete with the current standard of care.

In comparison to FISH tests, Insight has highlighted the superior turnaround time and sample handling capacity of its PCR test. Hout noted that Abbott's test returns results in about one week and can analyze 30 to 40 specimens per run. Comparatively, Insight's test has a turnaround time of 24 hours and can handle 100 specimens at a time. "We're scaling up to increase that number," Hout noted.

"One of the selling features of using a PCR-based approach as opposed to a FISH approach is that we only need a couple of slivers from a tumor biopsy FFPE tissue," Hout added. "So, the amount of tissue that goes into the assay is minimal. We can also run numerous assays from just one or two slivers from a patient's FFPE sample. So, again, minimal tissue is needed to repeat runs of the assay" in case of an error. Noting that FISH-based tests have "sensitivity issues," Hout further highlighted that a PCR-based test would pick up all ALK fusions and mutations, not just those known in the literature.

The CADP support from NCI comes after Insight received a $1.5 million Phase II SBIR grant from the institute to develop the Insight ALK Screen. The company is using these funds to test a large number of clinical specimens in a Phase II study and establish the ability of its ALK Screen to accurately gauge which specimens harbor ALK fusions and mutations.

According to Hout, Insight has already tested a large number of formalin-fixed paraffin-embedded tissue samples with academic collaborators to study the ALK screen.

"The situation with ALK is that the prevalence [of the rearrangements] is so low [in lung cancer] that we have to screen a large number of lung cancer patients to identify those who are ALK positive," Hout noted. Approximately 3 percent to 5 percent of NSCLC patients have tumors that are ALK positive. "But we have been doing this in preparation for our SBIR Phase II awards so we can do some reproducibility studies, as well as [do studies] in our collaboration with Qiagen," he said.

Once the ALK Screen test is developed, Insight has a collaboration with Qiagen to advance a companion diagnostic that would run on Qiagen's Rotor-Gene Q real-time PCR system. At this point, Insight doesn't yet have a drug with which to marry its companion ALK test though.

An obvious partner for Insight would be Pfizer, which currently markets the only FDA-approved ALK inhibitor, Xalkori, for NSCLC patients who harbor ALK rearrangements. The FDA in 2011 approved Xalkori, as well as a companion test, Abbott's FISH test. Since then, Pfizer has said it is investigating RT-PCR platforms and looked into NanoString's platform to improve companion testing for Xalkori. The company has also conducted studies to explore next-generation sequencing approaches to identify mutations in those that may become resistant to the drug (PGx Reporter 12/19/2012; 3/27/2013)

Hout said that Insight is also looking into companion diagnostics partnerships with drug firms developing next-generation ALK inhibitors, but he did not provide further details. Ariad, Novartis, Synta, and Xcovery are also developing ALK-inhibitor treatments.

In the meantime, Insight is planning to provide ALK Screen as a lab-developed test through GE subsidiary Clarient Diagnostic Services. Last year, Clarient garnered a worldwide, non-exclusive license from Insight Genetics enabling it to develop a PCR-based genetic test that gauges ALK expression (PGx Story 6/6/2012).

According to Hout, Clarient hasn't made a significant push to sell Insight's test because it is trying to iron out reimbursement for it. However, once it does become available as an LDT, the PCR test can be used by doctors to initially screen patients for ALK fusions and mutations and then confirm the finding with Abbott's test. FDA guidelines require physicians to use results from an agency-approved companion diagnostic kit when determining whether a patient will respond to a particular drug. Currently, Abbott's FISH test is the only FDA- approved ALK rearrangement test.

However, if Insight is able to garner FDA approval for its test in the coming years, Clarient would have to obtain a license from Qiagen to sell the ALK companion test, Hout explained.

Hout said that Insight is very close to achieving research-use only status for ALK Screen. Later this year, the company will seek CE mark for ALK Screen, enabling it to launch the test in the European market.

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