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Affymetrix microarray

Obtaining genome-wide copy number variation (CNV) and loss-of-heterozygosity (LOH) profiles from solid tumor samples represents a significant challenge due to the difficulty of working with limited amounts of DNA from highly degraded FFPE samples.

A simple whole-genome scanning approach avoids the traditional single locus, low-resolution bottleneck of FISH and PCR. Although next-generation sequencing technologies have shown their usefulness for mutation discovery, the requirement for target enrichment and deep coverage in order to obtain copy number information from heterogeneous FFPE samples remains a significant challenge.

OncoScan™ FFPE Assay Kit

NOTE:

Affymetrix strongly recommends using the QIAamp DNA FFPE Tissue Kit protocol for purifying DNA from FFPE blocks that will be used in OncoScan™ Assay. For improved DNA yields, Affymetrix also recommends a modification to the QIAamp DNA FFPE Tissue Kit protocol. The modified procedure adds a heating step at 98°C for 15 minutes to improve the tissue digestion process to release DNA from tissue sections.

See recommended extraction procedure