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Agilent Adds WTCCC-Designed CNV Chip to Menu


Last month, Agilent Technologies introduced the second catalog array in its growing menu of copy number variation-themed chips — an effort to reach customers who are interested in surveying CNVs in genome-wide association studies.

The Human CNV Association 2x105K microarray is designed for studying associations between genomic CNVs and disease. It follows the company's launch of the 2x400K CNV array, which was designed to cover known CNV regions from the Database of Genomic Variants.

The array is based on a design by the Wellcome Trust Case Control Consortium, which is currently conducting a study of CNVs and their relationships to a number of widespread disorders.

The new chip is configured with two microarrays per slide, with each array containing 105,000 probes. The firm claims that, compared to existing arrays, the design of this array will enable more calls with fewer data points because of targeted content in "high-confidence" CNV regions.

Last August, the WTCCC selected Agilent to manufacture CNV microarrays for the second phase of its study to identify genetic variants influencing disease susceptibility in a variety of rare and common diseases. Using CNV data from the WT-hosted Genome Structural Variation Consortium plus content that overlaps with the content of the Affymetrix SNP 6.0 array, the WTCCC identified a set of 11,000 disease-related loci that it used for the new Agilent arrays. To date, the consortium has run 20,000 samples on the new arrays.

By launching this chip, Agilent is making the WTCCC design available to anybody who wants to run it. "A lot of groups are tied into what the WTCCC is doing," says Dione Bailey, Agilent's CGH and CNV array product manager.

Bailey says that customers have requested access to the WTCCC array for use in similar association studies. "It is a targeted design in that the WTCCC did upfront screening to select regions in the population that they were interested in and focused on these sets in these diseases," she says.

Justin Petrone

Microarray Notes

In a paper published in PNAS, Affymetrix, Genentech, and Stanford University's Genome Technology Center describe a new array-based resequencing assay that they used to sequence a total of 2,350 megabases with a false positive rate of one in 500,000 base pairs.

The Baylor College of Medicine's Medical Genetics Laboratories will use Illumina's Infinium high-density microarrays to study genomic imprinting and its role in developmental diseases such as Prader-Willi syndrome, Angelman syndrome, and others.

CGC Genetics, a medical genetics lab firm that provides microarray-based genetic diagnostic tests and was one of 13 companies to receive cease-and-desist letters from the State of California, recently gained a Clinical Laboratory License from the state.


Amount NIH will grant For Data Analysis ¬Methods for Its Roadmap initiative Genotype-Tissue Expression Project

Funded Grants

$167,294/FY 2008
DNA Microarray Analysis of Neuronal Excitability
Grantee: Donald Cooper, University of Texas Southwestern Medical Center
Began: May 15, 2005; Ends: Apr. 30, 2010

This project will combine DNA microarrays and patch-clamp electrophysiology to characterize gene expression patterns of neurons in the rodent brain in response to repeated psychomotor stimulant injections. Cooper will look for "voltage and ligand-gated ion-channel genes that are subject to modulation by psychostimulants in the accumbens, subiculum and prefrontal cortical neurons."

$1,757,977/FY 2008
Prenatal Cytogenetic Diagnosis by Array-based Copy Number Analysis
Grantee: Ronald Wapner, Columbia University Medical Center
Began: Jun. 8, 2007; Ends: May 31, 2012

This study will compare the accuracy and efficacy of array CGH to conventional cytogenetics. Wapner will look at 4,000 patients: the first 1,750 will undergo routine testing to compare the technique's ability to identify aneuploidy and, with the rest, he'll tackle the potential of aCGH to find subtle cytogenetic abnormalities.