Thermo Fisher Scientific OncoScan CNV Assay for Research

Applied Biosystems™ OncoScan™ CNV Assay for Research

The OncoScan CNV Assay is a whole-genome copy number microarray-based assay that enables the detection of relevant copy number variations (CNVs) such as copy number gain and loss, loss of heterozygosity (LOH), copy neutral loss of heterozygosity (cnLOH), ploidy, allele-specific changes, break point determination, mosaicism, clonal heterogeneity, and chromothripsis.

This assay provides reagents for sample preparation from formalin-fixed paraffin-embedded (FFPE) tumor samples and microarray hybridization and staining. It is designed to cover the entire genome as well as known cancer drivers, enabling the generation of in-depth copy number data from as little as 80 ng of DNA per sample.

Key Features

• Whole-genome copy number analysis: Detect deletions, duplications, LOH, cnLOH, break points, ploidy, mosaicism, and unbalanced translocations not well characterized by short-read or targeted sequencing.
• Comprehensive coverage: Analyze genes with established and emerging significance in cancer and tumor progression.
• Complete flexibility: Detect chromosomal arm aberrations, focal changes, LOH, and cnLOH in a single assay, reducing cost and time.
• Robust performance: Standardized results from lot to lot and operator to operator.
• Low sample input & fast results: Obtain results in 72 hours from only 80 ng of FFPE-derived DNA.
• Rapid analysis: Free software provides intuitive data visualizations for hundreds of samples in minutes.
• High-resolution detection: Identify copy number variations from 50–125 kb to large (Mb) scale in priority cancer genes.

Coverage and Performance

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

Analysis Software

Data analysis is free and easy using one of the available tools:

• Chromosome Analysis Suite (ChAS): Ideal for copy number calls for a few samples.

Specifications