Genotyping FFPE analysis

Archival Formalin-Fixed Paraffin-Embedded (FFPE) samples hold an abundance of invaluable information for human cancer studies. Because these samples generally yield highly degraded DNA and RNA, they perform poorly in most whole-genome genotyping and expression studies. This issue has been recently solved for genotyping and expression studies that require the use of microarrays. We have tested these new products and we are now proud and confident to offer genotyping and expression workflows adapted for FFPE samples.

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


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

Illumina beadchip

Employing a streamlined workflow, all of Illumina's custom, semi-custom, and commercially available arrays can be used to genotype FFPE samples. This workflow utilizes the Infinium FFPE DNA Restoration Solution, which simplifies the upfront sample processing by identifying samples of sufficient quality and repairing the damaged DNA in the samples for downstream genotyping.

Omni Arrays - With six different BeadChips featuring a variety of content and formats, the Omni family of microarrays gives researchers the flexibility to study the widest range of genetic variation - no matter the study size or budget.

Core Arrays - Designed to make large-scale whole genome genotyping affordable, these customizable human genotyping arrays include an informative backbone of tag SNPs (single nucleotide polymorphisms), enabling researchers to tailor studies to specific populations or research goals.