Applied Biosystems™

OncoScan™ CNV Plus Assay

Catalog number:  902293

 Related applications: Microarray Analysis

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Description

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, break point determination, mosaicism, clonal heterogeneity, and chromotripsis, as well as a panel of driver somatic mutations. It provides the reagents for sample preparation from formalin-fixed paraffin-embedded (FFPE) tumor samples and microarray hybridization and staining. Designed to cover the entire genome as well as known cancer drivers, this assay is part of a comprehensive workflow that enables the generation of in-depth copy number and somatic mutation data from as little as 80 ng of DNA per sample.

Key features of the OncoScan CNV Assay include:
Whole-genome copy number analysis—detect structural variants such as deletions, duplications, LOH, cnLOH, break point determination, ploidy, mosaicism and unbalanced translocations that are not well characterized by short read sequencing or targeted sequencing
Somatic mutation panel—covering 74 mutations in 9 genes (BRAF, EGFR, IDH1 and 2, KRAS, NRAS, PIK3CA, PTEN, and TP53)
Comprehensive coverage—whole-genome analysis of genes with established significance and importance in cancer and tumor progression as well as those with emerging evidence, helping to "future-proof" the technology investment and minimize revalidation burden
Complete flexibility—detect chromosomal arm aberrations, focal changes, LOH, and cnLOH in a single assay, helping reduce costs and processing times
Robust performance—obtain standardized results from lot to lot and operator to operator
Low sample input and fast results—get 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 copy number detection in priority cancer genes—accurate identification of very small (50–125 kb) to large (Mb) copy number variations

Coverage and performance
• 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
• Known driver somatic mutations

Analysis software
Data analysis is free of charge and easy using one of the three available softwares:
Chromosome Analysis Suite (ChAS), for copy number calls for a few samples
• Somatic Mutation Viewer 1.1, for somatic mutation calls for a few samples
Nexus Express Software, for copy number and somatic mutation calls for tens to hundreds of samples

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

Specifications

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

Contents & storage

• OncoScan CNV Plus Array (Cat. No. 902292)
• OncoScan CNV Plus Reagent Kit (Cat. No. 902294)

Documents

Manuals & protocols