Affymetrix Launches DNA Copy Number Service for Difficult FFPE Samples in Cancer Research

Affymetrix, Inc. announces the launch of the Affymetrix® MIP Copy Number Service, designed for cancer researchers using challenging FFPE samples. The MIP Copy Number Service allows scientists to 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 Cancer1 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 Research2, 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 Research2,” added Last. “Additionally, in the journal Cancer Genetics and Cytogenetics3, 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.”