Affymetrix Launches New OncoScan™ FFPE Assay Kit

Affymetrix, Inc. announced the launch of the new OncoScan™ FFPE Assay Kit, a whole-genome copy number assay for highly degraded FFPE solid tumor samples, at the Cancer Cytogenomics Microarray Consortium conference being held in Chicago this week.

Despite the growing need of cancer researchers and clinicians, obtaining high-quality, whole-genome copy number data from degraded FFPE-derived tumor DNA has remained extremely challenging due to the limitations of current methods such as FISH, array CGH, and next-generation sequencing technologies.

The new OncoScan FFPE Assay Kit, utilizing Affymetrix’ unique Molecular Inversion Probe (MIP) technology, is capable of analyzing small amounts of highly degraded DNA from FFPE samples quickly and affordably, providing a significant step forward in solid tumor cancer analysis.

This new product provides whole-genome copy number data with specifically enhanced high resolution in approximately 900 known cancer genes, loss of heterozygozity (LOH) across the whole genome as well as clinically relevant somatic mutation data − all from a single assay. An updated version of BioDiscovery’s Nexus software, OncoScan™ Nexus Express Software, enables copy number calls for hundreds of samples in minutes and will be included with the product.

The new kit was successfully tested earlier this year in leading cancer research institutes, including M. D. Anderson Cancer Center, Memorial Sloan Kettering Cancer Center, and ARUP Laboratories.

“We performed testing of the new OncoScan™ FFPE Assay Kit at ARUP on multiple solid tumor tissues, including melanoma, glioma, breast carcinoma, and liposarcoma,” commented Sarah South, Medical Director at ARUP Laboratories. “We used the recommended 80 ng of DNA from FFPE and were able to complete the assay over a 48-hour period. We were able to detect FISH-confirmed aberrations in several key cancer genes including ERBB2, MDM2, EGFR, and MYC suggesting that OncoScan FFPE Assay Kit can be considered a viable higher resolution and higher specificity alternative to FISH testing for confirmation of cancer gene aberrations in solid tumor tissue. Because OncoScan FFPE Assay Kit has whole-genome resolution, we also obtained valuable incremental copy number aberrations in these samples.”

Professor Torsten Pietsch, MD, PhD, Institute of Neuropathology, University of Bonn observed that based on his experience with a large cohort of FFPE brain tumor samples, “We believe that the OncoScan FFPE Assay Kit is a robust platform for the rapid discovery and validation of novel prognostic copy number signatures, that may also be useful in a clinical setting for the detection of specific gains in tumors as markers for patient stratification.”

“The significance of copy number aberrations is being established in an ever increasing number of genes; however, few studies have realized this potential for solid tumors because of the challenges of working with low-input FFPE samples,” said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. “OncoScan FFPE Assay Kit is a game changer for cancer laboratories that want to quickly and affordably analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data. In addition, the ability to detect a range of clinically relevant somatic mutations adds even more value to the assay and analysis.”

The technology has previously been made available via the OncoScan™ FFPE Express 2.0 Service from the Affymetrix Research Services Laboratory and has demonstrated an unparalleled success rate, with more than 70 publications in the last two years. The platform enables detection in highly degraded samples unlocking a wealth of stored information in FFPE archives of ten years and older.