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CGC Genetics Adopts Illumina BeadXpress for Clinical Genetic Testing


By Justin Petrone

CGC Genetics will launch a genetic test in the second quarter of 2011 designed to identify diabetes and obesity risk.

Based on the Illumina BeadXpress system, the assay will become the ninth test to be deployed on the platform, and more are expected, according to CGC CEO Puri Tavares.

Tavares told BioArray News this week that the firm is currently performing a final validation of the diabetes and obesity panel. Once available, it will join the firm's existing assays, which include molecular diagnostics for Bardet-Biedl, Fraser, Noonan, and related syndromes; congenital hearing loss; craniosynostis; metabolic disorders; skeletal dysplasia; thrombophilia; and warfarin pharmacogenetics.

The Porto, Portugal-based testing company refers to its assays as "Array CGCs," and is one of a handful of firms to adopt the holographic microbead-based platform since the US Food and Drug Administration cleared the BeadXpress earlier this year (BAN 5/4/2010).

Other companies that have adopted the platform include Aliso Viejo, Calif.-based Ambry Genetics, which in August bought a unit to augment its high-throughput genotyping capabilities; Rockville, Md.-based BioReliance Genomics, which uses the BeadXpress to offer pharmacogenomic clinical trial services to drug developers; and Madison, Wis.-based EraGen Biosciences, which last year announced plans to transfer some of its assays to the BeadXpress.

An Illumina spokesperson told BioArray News that he could not discuss the firm's customers, but that the San Diego company has placed the BeadXpress in "several" Clinical Laboratory Improvement Amendments-compliant labs.

In addition, Illumina runs tests on the platform in its own CLIA lab.

Illumina acquired the technology platform that serves as the basis for BeadXpress when it bought CyVera in 2004. In 2007 it launched the system for custom genotyping, gene expression, methylation, and protein analysis.
According to Tavares, CGC chose Illumina's technology over that of its rivals' because the approach "relies on the capacity of assigning different panels for analysis based on clinical features of the diseases or disorders, such as groups of signs and symptoms, rather than just designing a chip for hundreds of thousands of unrelated SNPs."

The system's throughput was also a factor in CGC's decision to invest in the platform, which enables users to assay up to 384 SNPs at a time. These multiplex assays "allow a great flexibility in the organization of the test panels," Tavares said. "Depending on the pathologies we want to screen, groups of genes and mutations can be selected and organized in different tests."

CGC is also constantly upgrading its eponymous arrays. For example, the company recently expanded its panel for Noonan syndrome to include 80 mutations, 30 more than were offered when the test first became available last year.

"When we reorder our arrays we always update them," said Tavares.

While CGC refers to its assays as "arrays," they are not microarrays in the traditional sense. The firm offers array comparative genomic hybridization-based testing for constitutional abnormalities through a partnership with the Institute for Genomic Medicine at the University of Medicine and Dentistry of New Jersey in Newark.

Marvin Schwalb, associate director of the IGM, told BioArray News recently that its CGH service relies on custom-designed chips manufactured by Agilent Technologies. He also said that it is unlikely that CGC Genetics in the future will introduce new tests on traditional microarrays.

"Array CGCs simplify the diagnosis of complex diseases," Schwalb said. "The number of diseases that can't be handled by current platforms [including BeadXpress] is minute."

While CGC Genetics' Array CGCs do not rely on Illumina microarrays, they do use the company's GoldenGate genotyping assay, which can be run on Illumina's array platform and the BeadXpress.

According to Illumina, the GoldenGate assay uses a discriminatory DNA polymerase and ligase to SNP loci. The turnaround times for Illumina arrays and BeadXpress differ, though — another factor that Tavares said drove the firm to adopt BeadXpress.

As the BeadXpress' holographic beads are suspended in solution — "with gainful kinetics and handling procedures," Tavares noted — hybridization time typically takes three hours. By comparison, Illumina's Sentrix Array Matrix requires 16 hours, and total assay time on the company's Array Matrix is reduced to two from three days, she said.

Array CGCs comprise just a sliver of CGC's total portfolio. The company offers 1,500 genetic tests for prenatal screening and diagnosis, hematology, oncology, preventive medicine, common diseases, pharmacogenetics, and rare diseases, among others.

According to Tavares, CGC has chosen to apply Array CGC's to "different groups of diseases with overlapping symptoms or signs that can be tested in a single assay," allowing the firm to "reduce the turnaround time and costs that usually characterize conventional genetic testing."

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.