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OncoScan® Assays Services

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Discover new biomarkers for diagnosis, prognostics, or predictive research by looking at whole genome copy number changes

Part # Description Unit Size
OncoScan® CNV FFPE Services
OncoScan® FFPE Services
FFPE DNA Extraction Services

Tumors usually arise from normal cells with tissue-specific acquired mutations or aberrations in their genomic materials. Copy number variation (CNV) is one of the most important somatic aberrations (Beroukhim R., et al. The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899-905 (2010)). As it turns out, cancer top classes are dominated by either mutations (M class)-quality of a gene, or copy number changes (C class)-quantity of a gene. Cancer is driven by either mutation (M class) or copy number (C class) (Ciriello G., et al. Emerging landscape of oncogenic signatures across human cancers. Nature Genetics 45(10):1127-1133 (2013)).

In order to fully maximize cancer discoveries from formalin fixed, paraffin embedded (FFPE) samples, one will have to look at both copy number and somatic mutations in FFPE samples. With OncoScan services, you can easily assess the copy number status in your samples. We offer two outstanding options:

  • OncoScan CNV FFPE Services: high-resolution, genome-wide copy number profiling
  • OncoScan FFPE Services: same outstanding copy number coverage as OncoScan CNV Services, plus a somatic mutation panel of 74 mutation in 9 genes (BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS, and TP53).

This robust solution offers

  • Unbeatable whole-genome copy number coverage for large and small copy number changes
    • Additional data as compared to targeted gene panels
      • Whole-genome coverage vs. targeted-coverage
      • Ability to detect large aberration (Mb scale) that are missed by targeted panels
    • High-resolution (50-125 kb) copy number detection in priority cancer genes
      • Integrated analysis of whole-genome copy number changes and copy-neutral loss of heterozygosity (LOH)
      • Linear dynamic range: 0-60 copies
  • High-quality data from 80 ng of input DNA
  • Rapid data analysis
    • Visualize copy number data for hundreds of samples in minutes
    • We partnered with BioDiscovery, an industry-leading software provider, to enable a more comprehensive data analysis solution. Learn more about Nexus Copy Number™ Software at

Convenience and quality

Experience the convenience of the Affymetrix Research Services Laboratory (ARSL)-just send in your DNA. ARSL has processed thousands of the most challenging FFPE samples with a pass rate of greater than 92 percent, and our lab has the quality systems in place to handle your project with the highest standard of care and excellence. Take advantage of our expertise and receive data of the highest quality with the OncoScan FFPE and CNV FFPE Services.


Minimum sample volume 40 µL
Recommended concentration 5 ng/µL
Recommended quantification method PicoGreen®
Turnaround times
(from sample acceptance)
4-6 weeks depending on the size of the study
Please inquire for more information

Learn how scientists are using OncoScan CNV assays

  • Evidence of clinical utility of copy number in solid tumors using the OncoScan┬« FFPE Assay Kit
  • Copy number alterations and breast cancer: retrospective results from archived FFPE samples based on OncoScan® solution
  • Whole-genome copy number analysis in stratification and differential diagnosis of brain tumor patients: experiences in more than 600 FFPE brain tumor biopsies


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


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Molecular inversion probes: a novel microarray technology and its application in cancer research (pdf, 2.2 MB)


MIP CN sample data set (zip, 710 MB)

MIP CN 334K Marker List (zip, 2.83 MB)

MIP technology reveals important copy number changes in pediatric cancers (pdf, 1.06 MB)

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