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Affymetrix, CollabRx Deal Adds Copy Number Interpretation to Clinical Research Labs' Analytical Workflows


NEW YORK (GenomeWeb) — A new agreement between Affymetrix and CollabRx that will allow clinical research labs to interpret microarray data within the architecture of CollabRx's Gene Variant Annotation Service showcases two market trends, according Gavin Gordon, CollabRx's vice president of business development and strategic alliances.

The first is the desire of clinical research labs that offer cancer genetic sequencing tests to add copy number information to their services. The second is the tendency of platform vendors to work with companies like CollabRx to enhance the analytical, interpretive component of their offerings.

Gordon told BioArray News this week that while many of the clinical research laboratories have adopted its cloud-based analytical tools to guide the interpretation of next-generation sequencing-generated DNA mutation data, they are also interested in adding copy number analysis to their workups of oncology cases, and are using Affymetrix's OncoScan FFPE and CytoScan Cytogenetics Suite products to obtain that information.

Affymetrix's OncoScan FFPE Assay Kit allows users to obtain copy number information on about 900 cancer genes from formalin-fixed, paraffin-embedded tumor samples. The firm's CytoScan HD Array includes 750,000 SNPs and enables breakpoint estimation, loss of heterozygosity determination, regions identical-by-descent, maternal contamination, and low-level mosaicism, according to the firm.

"Our customers are either already working with Affymetrix or they are looking at moving to its platform for copy number," Gordon said, noting that there are several beta customers, including academic institutions and clinical research labs, that are already using the integrated platforms.

San Francisco-based CollabRx has announced a number of deals with clinical research labs in recent months that planned to use its GVA Service to interpret their oncology-focused clinical genetic sequencing tests. Earlier this month, the data analytics company inked such an agreement with The Jackson Laboratory. Other partnerships with Cellnetix, Cyvenio, and Quest Diagnostics have been discussed.

According to Padma Sundar, director of product marketing at Affymetrix, some labs that are using sequencing panels for mutation detection are also using the company's OncoScan FFPE Assay Kit to obtain copy number information from solid tumors and CytoScan Cytogenetics Suite assays to gain copy number data in hematological malignancies.

Sundar pointed to multiple recent publications that "highlight the potential actionability of several amplifications and deletions based on currently available drugs" as evidence of this trend, referencing one Nature Genetics study that appeared last September, and a second Nature Biotechnology paper that was published in November.

"CollabRx is already being widely used by labs for generating results on somatic mutations from NGS studies and they will add copy number to that at no incremental cost to the clinical researchers," Sundar told BioArray News.

Sundar added that the company's deal with CollabRx should add "significant value by providing the clinical relevance of … copy number changes" generated by its platforms. "This should drive demand for copy number studies, and therefore for our OncoScan FFPE Assay Kits and CytoScan Cytogenetics Suite," she said.

From Gordon's perspective, the deal reflects vendors' interest in adding analytical components to their offerings by partnering with companies like CollabRx. He cited a similar deal with Life Technologies that allows users of Life Tech's cancer panels to use the GVA Service to interpret their findings.

CollabRx announced its multiyear partnership with Life Tech, now part of Thermo Fisher Scientific, in October 2012. That deal called for the "development and commercialization of CollabRx's technology and content resources to be used in conjunction with Life Technologies' global cancer diagnostics development and its laboratory developed test services business," according to a statement at the time.

"A lot of vendor companies want to get more involved with the analytical and interpretive side of the workflow," said Gordon.

He also characterized CollabRx's recent partnership as "just the beginning" of its collaboration with Affymetrix. "This is a high-level, strategic partnership that includes joint business development and joint marketing activities," he said.

Affymetrix had "other choices in our space," he noted, and it seems that the firm sees the deal as a vindication of its offering.

"We have experts on staff, a real knowledge base, and a lot of credibility there," said Gordon. He also noted that the firm's IT service is "a scalable, fully automated, sophisticated IT platform that processes data as it comes in," adding that, when necessary, CollabRx "just adds more space to the cloud."