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Roche NimbleGen Plans to Debut CNV Arrays for Genome-Wide Association Studies

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By Justin Petrone

Citing "rapid adoption" of arrays with copy number variation content for use in genome-wide association studies, Roche NimbleGen said it plans to launch a menu of new CNV chips early next month.

The firm intends to debut a 2.1-million feature array and a chip with three 720,000-feature arrays containing CNVs that could be implicated in a "broad range of common and complex diseases," including autism, schizophrenia, autoimmune diseases, and HIV susceptibility, spokesperson Kary Staples told BioArray News last week.

"With the emergence of high-resolution maps of CNVs, their impact on disease phenotypes has become a key research focus," Staples said. "Life-science researchers are rapidly adopting the use of CNV arrays for large-scale genome-wide association studies."

According to Vanessa Ott, Roche NimbleGen's CNV array product manager, the new chips will contain targeted content culled from several sources. These include the Centre for Applied Genomics-hosted Database of Genomic Variants, a curated catalogue of structural variation in the human genome; and the Genome Structural Variation Consortium's CNV discovery project, which used Roche's 2.1-million-feature arrays to create a high-resolution map of human CNVs based on the analysis of 20 European and 20 African HapMap samples.

The arrays will also include CNV content from Asian samples identified using Roche NimbleGen's CGH 2.1M whole-genome tiling arrays. In July, Roche announced a partnership with the Korean Centers for Disease Control and Prevention and Seoul-based service provider Macrogen to characterize CNVs related to common diseases, such as diabetes, in the Korean population (see BAN 7/7/2009).

According to Roche NimbleGen, 99 percent of the CNVs on its new arrays will be represented by at least five probes, and 84 percent will be represented by at least 10 probes. The arrays also provide "backbone coverage of the entire human genome to enable detection of novel CNVs down to approximately 5-kilobase resolution," Roche said.

Ott told BioArray News last week that Roche decided to include CNVs from different ethnic populations because "recent data suggest that there are CNVs specific to [them], and it is our goal to include all of this CNV content on our arrays."

Ott added that all of Roche's CNV arrays are customizable. "We have customers who use our catalog array designs as a starting point, and tweak the designs to include their own targeted regions of interest – including CNVs, disease-associated regions, et cetera," she said.

Roche NimbleGen will continue to update its CNV array designs as new sequence and CNV content becomes available, including data from the 1000 Genomes Project, Ott said. The Madison, Wis.-based company plans to introduce "higher-resolution arrays" next year that could enable it to "continue to update the targeted CNV content, and also maintain sufficient backbone probes on the array to detect rare variants," she added.

According to Ott, Roche anticipates future increases in feature density and believes the flexibility of its array design process and its maskless array synthesis technology will enable it to update its CNV array designs to "keep pace with the discovery of new sequence and CNV content."

Looking at CNVs

Most array vendors want to sell new CNV content drawn from a variety of sources. For instance, Agilent Technologies this year launched three chips tailored to survey CNV content as part of GWA studies (see BAN 4/7/2009).

Affymetrix and Illumina have pledged to include more CNV content on their next- generation SNP-genotyping platforms. Affy said it plans to launch catalog and custom genotyping assays for use on its GeneTitan system in the fourth quarter. Illumina began selling its first next-gen array, the HumanOmni1-Quad BeadChip, in May, and the firm has promised to add more to menu as new SNP and CNV content becomes available (see BAN 5/19/2009).

For its part, Roche NimbleGen is making more CNV content available to the market because it is seeing a "dramatic increase" in inquiries from researchers interested in investigating CNVs, Ott said.

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She said that this rise in interest is fueled by several factors. First are, "published reports showing association of CNVs with human diseases such as autism, schizophrenia, and mental retardation." Another factor is the "emergence of high-resolution maps of common CNVs," such as the Genome Structural Variation Consortium's CNV discovery project.

Additionally, Ott said that GWAS using current SNP arrays are "only explaining a small percentage of complex disease phenotype, leading researchers to look more closely at the role of common and rare CNVs in complex disease."

Agilent, Roche's most direct competitor in the CNV array market, sees things similarly. In March, the company launched its 2x400K CNV array, which was designed to cover the known CNV regions from the Database of Genomic Variants. In April, the Santa Clara, Calif.-based firm followed with its Human CNV Association 2x105K microarray, based on a Wellcome Trust Case Control Consortium design. In June, the company rounded out its CNV array menu with a million-probe chip suited for discovery.

All CNV arrays were produced in the firm's higher-density SurePrint G3 format, which it debuted earlier this year (see BAN 3/3/2009).

Last month, Dione Bailey, Agilent's product manager of CGH and CNV microarrays, told BioArray News that the firm views its current menu of G3 CNV arrays complete. Agilent does, though, have plans to create more CNV arrays going forward.

"We have plans to launch for additional arrays over the next 12 to 16 months as we expand our platform," Bailey said. "Right now, in terms of the new G3 platform though, this line is complete."

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