NEW YORK – Precision oncology startup Claris GenomiX is searching for commercialization partners for its ColoType colorectal cancer subtyping test as the company looks to bring a line of tumor subtyping and therapy selection tests to market.
The Notre Dame, Indiana-based company and University of Notre Dame spinout is developing a pipeline of research-use-only assays and is pursuing partnerships to further develop them into laboratory-developed tests for clinical use, beginning with the 40-gene ColoType assay.
ColoType assesses a colorectal tumor based on the Consensus Molecular Subtypes model, which merges gene expression-based features of CRC tumors and their microenvironments from six different classification systems.
"We're in a strange state, where the research community has adopted this subtyping system, but there's no commercial diagnostic for executing it," said Claris Cofounder and CSO Steve Buechler.
ColoType is a targeted RNA-seq panel meant for use with solid tumor samples. Sequencing is done via Illumina AmpliSeq, and results are analyzed using algorithms developed by Buechler while employed by Notre Dame as a professor of applied computational mathematics and following his retirement from the university in 2020, resulting in continuous scores that measure the prevalence of each subtype in a tumor.
"It's a diagnostic used to provide more actionable intelligence for a medical oncologist to pick the best therapy regimen for their patients," said Claris Cofounder and CEO Jeff Sayre.
With ColoType, Claris is eyeing a small but competitive market in genetic-based personalized cancer therapy selection.
Exact Sciences, for instance, earlier this year announced plans to acquire Agilent subsidiary Resolution Bio, with the intent of developing that company's technology into specialty lab-based tests, leading with an NGS-based multi-cancer liquid biopsy therapy selection test.
Smaller precision oncology company Lucence uses a proprietary amplicon-based technology to broaden the number of meaningful targets for cancer screening and therapy selection by assaying both cell-free DNA and cell-free RNA.
Some governments are also taking note of these emerging technologies and launching nationwide precision oncology programs. Earlier this month, for example, the German Federal Ministry of Health announced a national-scale pilot project to evaluate the utility of genomic sequencing in improving diagnosis, therapy selection, and the clinical management of advanced cancer and rare disease patients.
"Tumor subtyping will advance the field meaningfully," said Min-Han Tan, founder and CEO of Lucence.
Tan cautioned, however, that advances would depend on proving the clinical utility of subtyping.
"Such [a] demonstration of clinical utility [will drive] quicker clinical adoption," he said.
Claris' Sayre said that given the company's small size (he and Buechler are currently the only employees), it would take a considerable amount of time to develop the assay as an LDT on its own.
But, he noted, a suitable partner with a certified lab "could bring this to market in 12 months or fewer, which would … allow our solution to start benefiting patients much sooner than if we tried to bring it to clinic ourselves."
Claris is also developing a suite of tests to guide therapy decisions in other cancers, specifically for patients with poor prognoses. Called ClarisInsight, the line of assays comprises tests for 15 cancer indications, including lung, breast, pancreatic, prostate, and liver.
Sayre said that Claris chose to focus specifically on the biology underlying poor prognosis cases because this is where precision oncology can provide the greatest benefit.
"If you look at breast cancer," he said, "it's the number one disease in terms of total cases diagnosed in a given year [among women]."
While cases, particularly if caught early, can be highly treatable, slightly fewer than 10 percent of breast cancer patients are considered to have a poor prognosis and thus significantly lower survival rates. The five-year survival rate for women in the US with non-metastatic breast cancer, for example, is approximately 91 percent. This falls to approximately 30 percent, however, for women in whom the cancer has spread to distant parts of the body.
"ClarisInsight targets these poor-prognosis cases," Sayre said. "And we believe that by providing diagnostics that can bring more insight into what's happening in the tumor biology and the tumor microenvironment, clinical oncologists will start really being able to help their patients and families."
The gene signatures used in the ClarisInsight assays stem from ongoing research into cancer molecular subtyping that Buechler and colleagues have been conducting over the past few years with collaborators at Notre Dame.
"Our goal has been to try to build on the success of consensus molecular subtyping in colorectal cancer to reproduce that in other cancer types," Buechler said.
In 2021, he and a colleague published a paper in NPJ Breast Cancer showing how the colorectal cancer Consensus Molecular Subtypes methodology could be adapted to subtyping breast cancer and is "pretty far along" in doing the same for lung cancer.
Claris hopes to commercialize both targeted RNA-seq and whole-transcriptome options of ClarisInsight tests as LDTs for lung cancer and breast cancers throughout 2024, leading with ClarisLung early in the year.
The University of Notre Dame holds the patent for the 40-gene ColoType assay and licenses it exclusively to Claris. Claris does not plan to seek patent protection for the whole-transcriptome versions of ColoType or the other ClarisInsight tests, but may patent some of the targeted RNA-seq tests.
"The true value of our discoveries and innovations lies in our proprietary computational methods," Sayre said. "To that point, we are in the process of patenting these methods. It is the technology that is at the foundation of our computing platform."
The company remains undecided on whether to pursue the same partnering strategy as with ColoType or to bring those tests to market independently.
The difference in deciding which strategy to adopt for which test, Sayre said, hinges broadly on timing — specifically how soon a test can be made market-ready and on how soon the company can establish its own CLIA-certified lab.
"Even if we had sufficient funding as of today," Sayre said via email, "it would take us at least 18 months to 24 months to be able to start offering ColoType as an LDT. In the meantime, we believe that there are one or two competitors, who already have CLIA-certified labs, that could beat us to market with their version of a [Consensus Molecular Subtyping] diagnostic for CRC."
Licensing decisions for the other ClarisInsight assays will be made on a case-by-case basis. As ClarisLung is the next assay closest to commercial readiness, Sayre said that the company may offer it for licensing, as with ColoType.
Regarding establishing the company's own lab facilities, Sayre commented that money is the limiting factor.
"With adequate capitalization, we are more than willing and capable of overseeing and managing the execution of our long-term plans," he said. "At a minimum, proper capitalization will allow us to establish our own lab and begin to grow our organization. Future ClarisInsight assays would then be offered and sold as in-house products."
Claris is considering a Series A funding round but has not yet found a funding partner. Buechler and Sayre currently provide the majority of Claris' funding, with the university serving as minority owner.