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Startup iKaryos Debuts Affy SNP Array-Based Cancer Testing Service

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By Justin Petrone

Three-month-old molecular testing firm iKaryos Diagnostics this week began offering an array-based whole-genome analysis of cancer samples.

The new service, called Virtual Karyotype, uses Affymetrix SNP-genotyping arrays to provide oncologists and pathologists with copy-number and loss-of-heterozygosity information to help guide patient treatment.

Oncologists and pathologists currently use more traditional technologies like fluorescent in situ hybridization to observe copy number and LOH in patients, iKaryos said in a statement. By having wider access to this information, specialists will, for example, be able to determine how aggressive a particular tumor is, or if it is likely to recur, the privately held firm said.

According to company officials, iKaryos, based in Omaha, Neb., was specifically founded to commercialize the service, which is being offered in collaboration with Creighton University and Creighton Medical Laboratories, also in Omaha.

Jill Hagenkord, co-founder and iKaryos' chief medical officer, said this week that she and co-founder Federico Monzan began offering the service in April through Creighton Medical Labs, where both are molecular pathologists. The company is now working to attract more pathologists and oncologists to use the Virtual Karyotype service, which is being offered as a laboratory-developed clinical test through Creighton's Clinical Laboratory Improvement Acts-compliant facilities.

According to Hagenkord, iKaryos has a fee-for-service relationship with Creighton, and an agreement concerning intellectual property rights. She declined to further discuss IP issues. She also said that iKaryos uses a variety of Affymetrix catalog SNP arrays that are selected according to the density required to identify clinically actionable abnormalities.

The use of SNP arrays in cancer testing is relatively new, Hagenkord cited the successful adoption of array technology in the constitutional abnormality testing arena over the past few years as an example of where services like iKaryos could be heading.

"It's analogous to [the] constitutional genetic abnormalities market," Hagerkord told BioArray News this week. She noted that Spokane, Wash.-based Signature Genomic Laboratories was among the first companies to begin offering array-based constitutional testing in 2004, but that there are now "over 60 labs in the US offering array-based cytogenetic testing for constitutional disorders because it's become the standard of care." According to Hagerkord, "cancer testing is the next obvious market for array-based karyotyping.

"iKaryos is the business development and marketing arm of our academic laboratory," said Hagenkord, who is also the medical director of the molecular pathology and clinical genomics laboratories at Creighton. She said that customers can send iKaryos a frozen or formalin-fixed, paraffin-embedded tumor sample, and iKaryos will extract and process the data, digitize the results, and then use software tools to recreate and query the tumor's genome. The company then conducts an analysis of the results, and provides customers with a report they can use to make treatment decisions.

"We can tell you that this is a renal tumor that is more likely to recur than most renal tumors, or how aggressive a tumor is, or what a particular abnormality means for different cancers," said Hagenkord.

CEO Robert Klein told BioArray News this week that iKaryos is targeting oncologists and pathologists using existing cytogenetics methods. He noted that the company will be exhibiting at the Association for Molecular Pathologists meeting in Orlando, Fla., this week and is currently weighing different sales approaches to reach potential clients.

"We offer a signed-out pathology report with actionable information that's given to the ordering physicians," said Klein, describing the Virtual Karyotype. "Oncologists and pathologists live and die by copy-number changes. These are well established in the literature and we provide the type of information that pathologists and oncologists already understand," he said. "They know how to interpret the copy number changes we are reporting. We also have large database we can query that has a large amount of information from previously run samples," he added.

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According to Klein, the market for array-based cancer diagnostics could be "huge," but, as a startup, it is up to iKaryos to create the market. "We are in a position where it is incumbent on us to spread the word that there is a better way to do cancer diagnostics," he said.

As most oncologists and pathologists are relying on conventional cytogenetic methods to obtain the kind of information that iKaryos provides, the firm is positioning itself as providing a complementary or, in some cases, replacement technology to what is in the market today.

"This is competitive with the rival technologies that are out there," Klein said. He declined to provide pricing information, but said a FISH panel would cost more than what iKaryos charges for its services.

In terms of expansion, Klein said that iKaryos is focused on its current offering though it has "other applications in the works." He also said that due to regulatory issues, the service will be offered solely through iKaryos' lab, though it is possible that the firm might open other branches in the future.

Hagenkord said that while the company is currently small, it is easy for iKaryos to take on an increased work load as it sells its service to more pathologists and oncologists. "The nice thing about this assay is that it was intended for genome-wide association studies, so it's actually very scalable," Hagenkord said. "You can raise your throughput without adding personnel. Being able to offer interpretation is the only limiting factor," Hagenkord added, but said that iKaryos already has staff that can pick up projects on an as-needed basis.

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