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Three Cancer Genome Characterization Centers Select Agilent’s Microarray Platform to Profile Cancers

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The National Cancer Institute (NCI) has announced grant recipients for its coveted Cancer Genome Atlas pilot project, including three institutions using microarray platforms from Agilent Technologies Inc.: the University of North CarolinaDana-Farber Cancer Institute and Memorial Sloan-Kettering Cancer Center

These institutions were among seven that were awarded a combined $35 million over three years in NCI grants as Cancer Genome Characterization Centers (CGCC) that are designed to implement the Atlas project.

All three institutions will rely on Agilent’s genomics solution, comprising microarrays, reagents, hardware and data analysis tools.

As part of the NCI initiative, each CGCC is expected to process a minimum of 1,000 clinical samples per year.

The CGCC initiative emphasizes high-throughput, high-resolution technologies to detect genomic, epigenomic and transcriptome aberrations, including alterations in DNA segment copy numbers, translocations, loss of heterozygosity, altered DNA methylation patterns and changes in gene expression, all of which may play a role in cancer.

The pilot project will explore the benefits of a systematic approach for analyzing specific types and subtypes of tumors.

"The University of North Carolina group, based in the Lineberger Comprehensive Cancer Center, will perform genome-wide gene expression profiling and microRNA expression profiling, both using Agilent DNA oligo microarrays," explained UNC Chapel Hill’s Charles M. Perou, Ph.D., assistant professor, Department of Genetics.

"The UNC group chose the Agilent platform because of its flexibility in gene content, which allows researchers to change any feature, or gene, at any time."

"As new genes, microRNAs or gene splice forms are discovered, they can easily and seamlessly be included into the next phase of microarrays."

"The Agilent platform provides proven sensitivity and specificity for each feature," he added.

"Along with streamlined protocols and hardware that will allow us to achieve the demanding high-throughput needs of the Cancer Genome Atlas project."

The Cancer Genome Characterization Center at Harvard Medical School is composed of Raju Kucherlapati, Isaac Kohane, Peter Park and Samuel Aronson of the Harvard Partners Center for Genetics and Genomics; George Church and Jonathan Seidman of the Harvard Medical School; and Lynda Chin, M.D., a researcher with the Dana-Farber Cancer Institute

"The goal of this center is to identify novel genes important in initiation and progression of cancer by quantitating DNA and RNA dosage using arrayCGH, or Comparative Genomic Hybridization, and a novel, highly sensitive method called polony sequencing," said Chin.

"We chose CGH as a key tool because genomic alterations have proven to be a productive entry point for discovery of cancer-relevant genes," she added.

"We selected the Agilent platform because of its excellent signal-to-noise detection when hybridized with full-complexity genomic DNA."

"We fully expect that future researchers will build on this work, using the same CGH platform."

"It is gratifying that Agilent microarrays are playing such a major role in this vital program," said Agilent director of genomics marketing Kevin Meldrum.

"The utility of microarrays has expanded beyond gene expression to applications such as CGH, DNA Methylation, and miRNA."

"We’re enabling these studies as well as developing our microarray technology by optimizing the balance between density, sensitivity and flexibility with our platform."

"It’s rewarding to know that these leading researchers and the NCI appreciate the value of this approach."