About 80% of all cancers are affected by both somatic mutations and copy number (CN) changes . The ability to detect CN changes such as copy number variations (CNVs) is critical to fully profile solid tumors. Accurate CN profiling, which can be used as an indicator of disease progression, may lead to better analytical management .
The Applied Biosystems™ OncoScan™ CNV and CNV Plus Assays can accurately identify CN changes and allelic imbalances, including loss of heterozygosity (LOH), copy-neutral LOH (cnLOH), and chromothripsis across the entire genome in solid tumors.
- OncoScan CNV Assay — high-density CN coverage across 900 cancer genes and standard coverage across the whole genome
- OncoScan CNV Plus Assay — same CN coverage as the OncoScan CNV Assay plus a somatic mutation panel covering 64 mutations in 9 genes
Historically, it is difficult to obtain genome-wide CN and LOH profiles from solid tumor samples due to limited amounts of DNA derived from samples which have been formalin-fixed, paraffin embedded (FFPE). Molecular inversion probe (MIP) powers the OncoScan CNV and CNV Plus assays, driving high specificity to genomic loci without the need for high DNA inputs or shotgun library preparation.  In addition, each probe in the assay has been validated with qPCR to help ensure the probe pools accuracy.
While the OncoScan workflow looks more complex than most array-based protocols, once mastered, it can generate reliable in-depth CN and somatic mutation data. The Global Product Support team at Thermo Fisher Scientific has created a list of helpful tips to overcome any challenges you may encounter when trying to catch critical CN changes. Whether you are a first-time or an experienced user, we hope you’ll find these recommendations useful for improving workflow and achieving optimal data collection.
Below summarizes the master tips to ensure optimal workflow. Please refer to the technical note, Recommendations for improving the OncoScan workflow for optimal results, for more information.
Figure 1. Recommendations to improve the OncoScan workflow for more consistent results
Tip 1: Be alert at package arrival and properly handle and store all reagents
- For robust performance, proper and timely handling of reagents and storage is the key. That includes checking reagent temperature and packing conditions and storing all reagents appropriately. It’s crucial to avoid using any reagents that have not been properly stored.
Tip 2: Proper Instrument maintenance is crucial for success
- Well maintain and routinely calibrate all equipment. One important tip is to bleach fluidics weekly or after every 4 runs (whichever occurs first) to avoid reduced signal on OncoScan arrays.
Tip 3: Keep all reagents on ice at all times
- Throughout the workflow, it is imperative to keep all reagents on ice. Make sure the reagents are added to chilled PCR plates.
Tip 4: Avoid cross-contamination by identifying possible sources
- To reduce the risk of sample and de-oxynucleoside triphosphate (dNTP) contamination, follow the best practices recommended in the user manual. Those recommendations include separating the workplace into pre-PCR and post-PCR areas and changing gloves between the AT and GC mixing steps.
Tip 5: Perform all in-process QC steps
- For optimal results, perform all 3 in-process QC steps recommended in the user manual.
- Ciriello G, Miller M, Aksoy B, et al. (2013) Emerging landscape of oncogenic signatures across human cancers. Nat Genet 45:1127–1133. https://doi.org/10.1038/ng.2762.
- Wang Y, Cottman M, Schiffman JD. (2012) Molecular inversion probes: a novel microarray technology and its application in cancer research. Cancer Genet 205(7–8):341–355. https://doi.org/10.1016/j.cancergen.2012.06.005.
- Chastain EC. (2014) Target hybrid capture methods. In: Kulkarni S, Pfeifer J (eds). Clinical Genomics, 1st edn. Academic Press, New York, 37–55.