OncoScan™ CNV Assay


Catalog number: 902695


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 chromotripsis. The assay has the same copy number coverage as the OncoScan CNV Plus Assay but does not include somatic mutation coverage. 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 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
  • 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 identificat ion 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•

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
• Nexus Express Software, for copy number and somatic mutation calls for tens to hundreds of samples


Array Format:

Genechip probe array

Array Type:

Cytogenetics & Copy Number

Number of Arrays:

48 arrays

Number of Markers:

over 220,000 SNPs

Product Size:

24 samples

Nexus Express Software, B allele frequency view
Data courtesy of Dr. Sarah South, ARUP Laboratories, Utah

Multi-Sample Whole-Genome View