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OncoScan® FFPE Assay Kit

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Genome-wide copy number in 48 hours

Part # Description Unit Size
OncoScan® FFPE Assay Kit
Sufficient for 24 samples   
OncoScan® Training Kit
Sufficient for 18 samples   

Finally, the ability to deliver whole-genome analysis from FFPE samples quickly, accurately, and cost-effectively

Obtaining genome-wide copy number and loss-of-heterozygosity (LOH) profiles from solid tumor samples is 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 utility in mutation discovery, the requirement for target enrichment and high-depth coverage in order to obtain copy number information from heterogeneous FFPE samples remains a significant challenge.

Why is genome-wide copy number important in the analysis of solid tumors?

  • The significance of copy number aberrations is being established in an ever increasing number of genes
  • The number and the type of aberration have been shown to be prognostic as well as diagnostic
  • Increasing evidence of the occurrence of chromothripsis in multiple solid tumors with potential prognostic and predictive significance
  • Treatment response may be monitored by detecting aberrations in sub-clones and assessing clonal evolution
  • Combining whole-genome copy number, LOH, and somatic mutation data enables a deeper understanding of the disease

Data courtesy of Dr. Sarah South, ARUP Laboratories, Utah

"We performed beta testing of the new OncoScan FFPE Assay Kit at ARUP. During beta testing, we ran 38 FFPE samples from multiple solid tumor tissues, including glioma, breast carcinoma, and liposarcoma, which contained FISH-confirmed aberrations. The age of the samples ranged from 6 months to 3 years since fixation. We used the recommended 80 ng of DNA from FFPE and were able to complete the OncoScan assay over a 48-hour period. 98% of the samples passed QC, and we were able to detect clear gains, losses, and LOH, including copy-neutral mosaic LOH in all the passing samples. Because OncoScan FFPE Assay Kit has whole-genome coverage, we were not only able to detect the FISH-confirmed aberrations in several cancer genes including ERBB2, MDM2, EGFR, and MYC but also obtained incremental copy number aberrations in these samples, many of which were expected aberrations for the tissue type. Our results suggest that OncoScan FFPE Assay Kit may be considered a viable higher resolution and higher specificity alternative to FISH testing for confirmation of cancer gene aberrations in solid tumor tissue."

Sarah South, PhD, Medical Director, Cytogenetics,
Genomic Microarray and Genetic Processing Laboratories,
ARUP Laboratories, Utah

The new OncoScan FFPE Assay Kit delivers an entirely new perspective on the cancer genome from even the most challenging solid tumor samples.

  • Low sample input, fast results – from only 80 ng of FFPE-derived DNA to results in 48 hours
  • One assay, multiple views – whole-genome copy number, loss of heterozygosity (LOH), and key somatic mutations analysis
  • High-resolution copy number detection in ~900 cancer genes
  • Rapid analysis – from data to copy number calls for hundreds of samples in minutes using OncoScan® Nexus Express Software

Exceptional assay delivering exceptional performance

The OncoScan assay utilizes Molecular Inversion Probe (MIP) technology, which has been optimized for highly degraded FFPE samples (probe interrogation site of just 40 base pairs). Assay performance has been extensively validated with archived FFPE samples (10 years or older) and has been shown to be compatible with all major solid tumor tissue types.

One assay – many powerful data types

Genome-wide copy number and LOH, high resolution on cancer genes, plus somatic mutations, all from a single assay

  • 50-100 kb copy number resolution in ~900 cancer genes
  • 300 kb genome-wide copy number resolution outside of the cancer genes
  • Genome-wide LOH detection including copy-neutral LOH detection
  • High dynamic range of 10+ copies
  • Demonstrated concordance with FISH-confirmed amplifications in key cancer genes including ERBB2 (Her2), EGFR, MDM2, MYC, and FGFR1
  • Actionable somatic mutations

Rapid data analysis enables cost-effective signature discovery

From data to copy number calls for hundreds of samples in minutes using OncoScan® Nexus Express Software

OncoScan FFPE Assay Kit includes:

  • OncoScan® Reagents – Molecular Inversion Probe (MIP) probe panel amplifies the precise target DNA of interest
  • OncoScan® Array – 2 universal tag arrays capture the amplified target DNA for a single color readout on GeneChip® Scanner 3000 or GeneChip® Scanner 3000Dx v.2, installed in over 2,000 labs globally
  • OncoScan® data analysis – The OncoScan Console Software is used to run the TuScan algorithm . The TuScan algorithm developed for the analysis of solid tumor cancer samples and OncoScan® Nexus Express Software allow rapid, easy-to-use data analysis and visualization


For Research Use Only. Not for use in diagnostic procedures.

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