OncoScan™ CNV Plus Assay for Research (Applied Biosystems™)

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 chromothripsis, 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 for researchers to understand high copy number mutations 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 64 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