OncoScan™ FFPE Assay Kit

Catalog number: 902293

Applied Biosystems™  Related applications: Microarray Analysis

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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

The 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 OncoScanNexus 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.


Array Format: Genechip probe array
Array Type: Cytogenetics & Copy Number
Number of Arrays: 48 arrays/24 samples
Product Size: 24 samples


Manuals & protocols