Affymetrix, Inc. (NASDAQ:AFFX) today announced the launch of the Affymetrix® MIP Copy Number Service, designed for cancer researchers using challenging FFPE samples. With the MIP Copy Number Service, scientists can now obtain high-quality allele-specific copy number data from FFPE samples. The service is available for research use only exclusively through the Affymetrix® Research Services Laboratory (ARSL).

DNA obtained from FFPE samples is often of insufficient quantity and too degraded for many array platforms, resulting in low sample pass rates. A recent article in the journal BMC Cancer 1 demonstrated that the MIP copy number assay generates high-quality data from ovarian FFPE samples with starting material as low as 75 nanograms (ng) and a sample pass rate greater than 90 percent. In a separate study in the journal Cancer Research 2, researchers used MIP technology to distinguish high copy number changes within specific grades of pediatric brain cancer, even with samples stored for more than 20 years.

The Affymetrix MIP Copy Number Service has been successfully used by leading cancer research institutes, including the M. D. Anderson Cancer Center, the University of California, San Francisco, and the Huntsman Cancer Institute at the University of Utah.

"Translational laboratories are having tremendous success using the Affymetrix ® MIP 330K Cancer Panel,” said Andy Last, Chief Commercial Officer of Affymetrix. “The broad dynamic range and high resolution of our MIP technology allows the identification of copy number values of 10 and higher, as demonstrated in the journal Cancer Research 2,” added Last. “Additionally, in the journal Cancer Genetics and Cytogenetics 3, the MIP assay identified both novel copy number aberrations (CNAs) and previously described CNAs in childhood leukemia samples.”

Previous studies have indicated that genomic instability is associated with tumor grade, tumor development, and disease progression. Because the MIP copy number application offers both allele and copy number data on a single platform, researchers now have a more comprehensive tool to evaluate risk factors for the early stages of cancer and disease relapse. Pairing allele information with copy number calls also enables a more in-depth analysis of cancer, including copy-neutral loss of heterozygosity, levels of normal-tumor contamination, and preferential allele amplification.

“Cancer researchers are unlocking the full potential of millions of archived FFPE samples using MIP copy number technology,” said Kevin King, President and CEO of Affymetrix. “Leading cancer researchers can now link copy number data with clinical data from these archived resources. This is the tremendous advantage of the MIP assay and will help researchers yield discoveries that could ultimately improve cancer diagnosis and categorization of patients, and thus lead to more targeted and individualized strategies for the treatment of cancer.”

For more information about the Affymetrix MIP Copy Number Service, please visit

1Press J. Z., et al. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer 8:17 (2008).

2Schiffman J. D., et al. Oncogenic BRAF mutation with CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas. Cancer Research 70(2):512-9 (2010).

3Schiffman J. D., et al. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia. Cancer Genetics and Cytogenetics 193(1):9-18 (2009).

About Affymetrix

Affymetrix technology is used by the world’s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government and nonprofit research institutes. More than 1,900 systems have been shipped around the world and more than 21,000 peer-reviewed papers have been published using the technology.

Affymetrix is headquartered in Santa Clara, Calif., and has manufacturing facilities in Cleveland, Ohio, and Singapore. The company has about 1,000 employees worldwide and maintains sales and distribution operations across Europe and Asia. For more information about Affymetrix, please visit

Forward-looking statements

All statements in this press release that are not historical are “forward-looking statements” within the meaning of Section 21E of the Securities Exchange Act as amended, including statements regarding Affymetrix’ “expectations,” “beliefs,” “hopes,” “intentions,” “strategies,” or the like. Such statements are subject to risks and uncertainties that could cause actual results to differ materially for Affymetrix from those projected. These and other risk factors are discussed in Affymetrix’ Form 10-K for the year ended December 31, 2009, and other SEC reports for subsequent quarterly periods.

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