Thermo Fisher Scientific OncoScan CNV Plus Assay for Research

Applied Biosystems™ OncoScan™ CNV Plus Assay for Research

The OncoScan CNV Plus 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, breakpoint determination, mosaicism, clonal heterogeneity, and chromothripsis, as well as a panel of driver somatic mutations.

It provides reagents for sample preparation from formalin-fixed paraffin-embedded (FFPE) tumor samples and for microarray hybridization and staining. Designed to cover the entire genome as well as known cancer drivers, this assay is part of a comprehensive workflow for researchers to understand high copy number mutations and somatic mutation data from as little as 80 ng of DNA per sample.

Key Features

• Whole-genome copy number analysis: Detect deletions, duplications, LOH, cnLOH, breakpoint determination, ploidy, mosaicism, and unbalanced translocations not well characterized by short-read or targeted sequencing.
• Somatic mutation panel: Covers 64 mutations in 9 genes (BRAF, EGFR, IDH1/2, KRAS, NRAS, PIK3CA, PTEN, TP53).
• Comprehensive coverage: Whole-genome analysis of genes significant in cancer progression and emerging targets, minimizing revalidation burden.
• Complete flexibility: Detect chromosomal arm aberrations, focal changes, LOH, and cnLOH in a single assay, reducing cost and time.
• Robust performance: Standardized results across lots and operators.
• Low sample input and fast results: Obtain results in 72 hours from only 80 ng of FFPE-derived DNA.
• Rapid analysis: Free software provides intuitive data visualization for hundreds of samples in minutes.
• High-resolution detection: Accurate identification of CNVs from 50–125 kb to megabase scale in key cancer genes.

Coverage and Performance

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

Analysis Software

Data analysis is free and supported by the following tools:

• Chromosome Analysis Suite (ChAS): For copy number calls in a few samples
• Somatic Mutation Viewer 1.1: For somatic mutation calls in a few samples

Specifications