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Greenwood Genetics Center Transitions to Affymetrix's CytoScan Dx Citing Benefits to Clinicians, Labs

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NEW YORK (GenomeWeb) – When Greenwood Genetics Center announced last week that it is now offering Affymetrix's US Food and Drug Administration-cleared CytoScan Dx Assay to its clinicians for chromosomal microarray analysis, it became the first laboratory in the US to do so.

Though the Greenwood, SC-based center already offers a laboratory-developed test based on Affymetrix's research use only CytoScan HD product, the addition of the CytoScan Dx Assay appeals to users for multiple reasons, according to Alka Chaubey, director of the center's cytogenetics laboratory.

"It has added a layer of regulatory assurance," Chaubey told BioArray News this week. "And this greater reliability affects reimbursement from payors," she said.

Indeed, to the best of her recollection, Chaubey said that each time a claim related to CytoScan HD has been denied in the past, it has been because payors regard the high-resolution chromosomal microarray as an investigational screening tool and not a medical device.

"Now we can say that the assay is not investigational," Chaubey said. She noted that Blue Cross/Blue Shield of South Carolina in April already altered its policies to support the reimbursement of the CytoScan Dx Assay. "The regulatory assurance for this test really has benefits for patients, clinicians, and labs," Chaubey said.

Though GGC introduced the CytoScan Dx Assay last week, the test has been cleared for clinical use since January. Still, it took time for Affymetrix to begin selling the 2.6-million-marker array, accompanying reagents, and analysis tools to customers, and the assay itself launched toward the end of the second quarter.

Chaubey said that GGC had to undergo a verification process to introduce the CytoScan Dx Assay as a clinical test, which included the training of a technician, an internal validation, and additional oversight from Affymetrix.

Of all labs that use CytoScan HD as a component of LDTs, GGC was perhaps best positioned to transition to the CytoScan Dx Assay because of the role the center played in the generation of the data that formed part of Affymetrix's submission to the FDA.

Chaubey discussed GGC's role in securing FDA clearance for Affymetrix's test with BioArray News earlier this year. It included participating in a multisite reproducibility demonstration, conducting analytical validation of variations identified by the CytoScan Dx Assay, and providing the majority of the 960 samples used for the clinical validation component of the study.

Though GGC is now offering the CytoScan Dx assay, it will continue to also offer its CytoScan HD-based LDT, in part because the indications connected with FDA clearance are for the detection of copy number variants associated with developmental delay, intellectual disability, congenital anomalies, and dysmorphic features.

Clinicians affiliated with the center, which maintains satellite offices in three other South Carolina cities and processes about 1,500 CMA cases per year, have been "very interested" in transitioning to the test, Chaubey said. At the same time, they can only order the assay if their patients exhibit the specific phenotypes indicated by the FDA.

"If a patient presents with suspected autism, we will still have to run the CytoScan HD, but if the patient presents with autism and developmental delay and/or a congenital anomaly, then the clinician can order CytoScan Dx," she said.

This has created a "slight learning curve" for GGC's clinicians, she said, and ensured that the center will continue to offer CytoScan HD "for all other phenotypes not indicated."

While GGC's clinicians are eager to move to the test, given its added assurance and positive reimbursement prospects, it also comes with a slightly greater expense. Though Chaubey would not quote a price differential between CytoScan HD and the CytoScan Dx Assay, she said that there is a "little bit of a cost increase" because the assay is part of a closed system, meaning that some components that GGC used to obtain independently are now obtained directly through Affymetrix as part of the CytoScan Dx Assay kit.

However, this cost is not passed along to patients or payors, she stressed.

"It won't cost patients any more than it used to," Chaubey said of the CytoScan Dx Assay. "It will cost the laboratory slightly more and, in general, Affymetrix does try to keep the transition to CytoScan Dx cost-neutral," she said.

However, as more laboratories introduce the CytoScan Dx Assay, there is an additional value to the test over CytoScan HD. Chaubey noted that since LDTs based on CytoScan HD are validated and run according to the decision of each provider, different labs have different thresholds for calling copy number changes and reporting results back to clinicians and patients.

Since the CytoScan Dx Assay provides a closed system, with set thresholds and data analysis procedures, this lab-to-lab variation should disappear once more labs adopt the assay. "The CytoScan Dx Assay provides a standard method of analysis, so there should be more uniformity in getting reports back to patients," said Chaubey. "For this reason and others, the clinicians are very interested in this test."

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