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Cynvenio Looks to Add Cell-free DNA Analysis to Circulating Tumor Cell Platform

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NEW YORK (GenomeWeb) — Cynvenio Biosystems, which offers both research and clinical liquid biopsy services that quantify and sequence circulating tumor cells to identify cancer mutations, is researching how its method could also be used to analyze circulating cell-free DNA.

Cynvenio received CLIA certification in mid-2013 for its lab, and has since been offering its LiquidBiopsy service to clinical and research customers. LiquidBiopsy involves isolating and quantifying circulating tumor cells from a patient's blood sample and using commercial hotspot panels like Ion Torrent's AmpliSeq to sequence DNA extracted from those cells to detect cancer-associated mutations.

The company also markets a breast cancer-specific LDT, ClearID, which does the same, but specifically in the context of breast cancer management. It also offers research customers both CTC sequencing and PCR-based analyses.

In a phone call with CSN this week, Cynvenio's Chief Scientific Officer Paul Dempsey said that as the company's CTC analysis business has been progressing, Cynvenio has also begun research to apply its sequencing approach to analyze cancer mutations in circulating cell-free DNA.

Cynvenio's CTC isolation is enabled by an automated platform that processes blood samples using antibodies to filter CTCs out of a patient's blood, yielding isolated CTC pellets. However, the company realized early on that it could also apply its sequencing approach to cell-free DNA, Dempsey said.

"The approach we developed in the CTC space involves a pre-analytic step that is compatible with a number of different analytes in a blood draw," he explained. "So we knew we could look at those two templates in the same sample."

In subsequent research, Cynvenio has been working to establish how cfDNA and CTCs compare in terms of things like mutation prevalence and background noise, to try to establish the potential utility of cfDNA relative to, and potentially in combination with CTC analysis.

In a poster presented earlier this year at the annual meeting of the American Association for Cancer Research, Cynvenio scientists compared their analysis pipeline applied to both CTCs and cfDNA in parallel.

"The main thing that we talked about in that poster was that that the noise characteristics are very different for these two templates," Dempsey said. "That's important if you are going to be building a clinical test around something. It means you have to incorporate either a way to get rid of the noise — or a threshold to accommodate it — which makes it less sensitive."

In the study, Cynvenio researchers compared the prevalence and variance of SNVs in normal cell-free DNA and in DNA extracted from EpCaM-selected cells, to mimic its CTC analysis pipeline. The group found an almost seven-fold higher incidence of false positives in cfDNA compared to DNA from circulating cells in these healthy donor samples.

The inter-sample variance in cell-free DNA false positives was also 50 times higher than that seen for EpCaM-selected cell samples.

"Although informative results are possible with [cell-free] DNA, it is much 'noisier' in sequence-based tests than is DNA from freshly isolated cells. This noise results in a high false positive rate and highly variant changes in the test sensitivity," the authors concluded.
Despite these caveats, Dempsey said, the research has also suggested that the two sample types might be able to complement each other, especially if cfDNA and circulating tumor cells reflect different aspects of disease biology, as many researchers expect.

"For me, I think it's very exciting to have a way to measure multiple aspects of disease from a single sample, to be able to elaborate on the static readout of a tissue biopsy," he added.

Beyond this initial study focused on comparing the two templates in the context of healthy samples, Cynvenio is also analyzing cfDNA in clinical samples from cancer patients it has collected through its CLIA lab business, Dempsey said. This work has not been published yet.

So far, this is all on the research side, he said, but the company plans to integrate cfDNA into its CLIA activities in the near future.

Meanwhile, Cynvenio now has about a year behind it of offering its CTC services clinically. Dempsey said that though the lab only markets one cancer-specific service, ClearID, for breast cancer, it has also tested other cancer types in the clinical setting.

"We've had success in prostate and colorectal cancer," Dempsey said. "But the medical community has different needs in each of these [areas] so tailoring to each is an ongoing process."

Earlier this month Cynvenio also announced it had launched an early access program for its LiquidBiopsy Rare Cell Isolation Platform, with the Mayo Clinic Cancer Center and the Norris Comprehensive Cancer Center at the University of Southern California.

These users are adopting the platform for research only, Dempsey said. But in the background, Cynvenio is working toward a smaller, more adaptable iteration of its technology, for which it intends to seek clearance by the US Food and Drug Administration for clinical use.

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