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New ACMG Guidelines Have 'Raised Bar' for Cyto Chips, Array Makers Say


By Justin Petrone

The four largest array vendors this week welcomed the American College of Medical Genetics' new recommendations on how best to design and interpret chromosomal microarrays used by clinical cytogeneticists.

In addition to welcoming the recommendations, Affymetrix, Agilent Technologies, Illumina, and Roche NimbleGen said their products already exceed the new guidelines, and seem keen on using them as a launchpad for reaching customers.

"The ACMG guidelines have appropriately raised the bar for array manufacturers with regard to recommending coverage and performance requirements," said Richard Shippy, director of strategic marketing for clinical applications at Affymetrix.

He said the recommendations should benefit cytogenetics due to their focus on an "overall higher level of product quality and diligence in the analytical validation." Shippy also said Affy's new CytoScan HD research product, launched this month, already "exceeds the performance outlined by the ACMG guidance" (see related story, this issue).

The ACMG made its new recommendations available in a pair of papers in the current issue of Genetics in Medicine. The first paper concerns design and performance characteristics of arrays meant to detect constitutional abnormalities; while the second aims to help clinical labs evaluate copy-number variants (BAN 7/19/2011).

While the recommendations were developed by an ACMG working committee, the organization also consulted members of the cytogenetics community, and later gave manufacturers the ability to provide input before they were finally published.

Some vendors did comment on the final draft, while others did not.

An Illumina spokesperson said the company has been working with ACMG "for years," which included "reviewing and providing comments directly regarding this document."

The spokesperson added that several of Illumina's customers had "central roles in the creation of this and other [ACMG] guidelines [and] documents."

Meantime, Anniek De Witte, CGH microarray product manager at Agilent, said that the company did not provide any comments on the recommendations because it already felt its comparative genomic-hybridization arrays met the new guidelines.

"We saw a draft of the document but we didn’t have any direct input … since the recommendations aligned very well with how Agilent CGH microarrays have always been designed and validated," De Witte told BioArray News.

De Witte said that the firm saw several of the new recommendations as particularly significant. For instance, the guidelines state that including SNP probes is a desirable feature of a clinical genomic microarray, and added that Agilent last year began selling CGH+SNP microarrays that can detect copy-neutral loss-of-heterozygosity and uniparental disomy (BAN 9/14/2010).

ACMG's new guidelines also encourage manufacturers to provide software that enables performing laboratories to customize their analysis. De Witte said that Agilent's new CytoGenomics software, launched earlier this month, addresses this need.

"It gives each individual lab the flexibility to set up their own parameters and thresholds that they are comfortable with and have validated," she noted (BAN 7/5/2011).

Representing Roche NimbleGen, Emily Rorem, director of international clinical product management, noted ACMG's resolution thresholds.

"As stated in the recommendations, the primary goal of these assays is to provide a system that will reliably detect copy-number alterations at a resolution which exceeds traditional technologies," Rorem told BioArray News.

Particularly, she described as "significant" ACMG's recognition of "the importance of exceeding a maximum resolution of 400 kilobases for the identification of small clinically relevant copy number variations" and "allowing laboratories to visualize all microarray data without the application of filters."

Rorem said that Roche NimbleGen believes the new recommendations for analytically validating cytogenetic microarrays for FDA approval are "very consistent with our current submission plans and reflect the requirements of cytogenetic laboratories needs for a relevant and robust workflow."

Rorem said that, like Affy, Agilent, and Illumina, Roche NimbleGen has pledged to take its system through the US Food and Drug Administration clearance process (BAN 7/20/2010).

All of the firms pledged to follow ACMG's recommendations.

"The recommendations align very well with how Agilent CGH microarrays have always been designed and validated in the past," said De Witte. "Now that there are formal recommendations we will follow these closely."

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

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