Somatic Mutation Profiling

MassARRAY^® System—a proven method for somatic mutation profiling 

Somatic mutation profiling has the potential to quickly identify which signaling pathways drive proliferation of a particular tumor type. Mutation profiling of patients may also be a useful clinical research tool in oncology.

The MassARRAY System has been used in a number of published research studies for somatic mutation
profiling. In one study, a group of clinical researchers at the Dana Farber Cancer Institute designed a mutation
panel to enable large scale screening of cancer samples with increased clinical sensitivity. The panel was
used to screen >1,000 human tumor samples from 17 types of solid tumors. Relevant mutations were confirmed in 30% of the samples. Novel mutations were detected due to the higher sensitivity of this method. EGFR (Epidermal Growth Factor Receptor) mutations were detected in ~9% of the total DNA population¹. In a follow-up study, the platform was used to screen 400+ mutations in >30 oncogenes and tumor suppressors against ~900 clinical samples of which >35% had at least one of the mutations².

View an online Customer Seminar Showcase "Profiling Critical Cancer Genes in Clinical Tumor Samples" to learn more how somatic mutation profiling has enabled research initiatives.

 

Capabilities of the MassARRAY System 

• A highly sensitive method for screening low abundant mutations
• A highly adaptable method to run a varied numbers of samples or mutations
• Pre-designed, optimized panels such as the OncoCarta™ Panel
• A highly flexible method for researchers to design custom assays to any region

OncoCarta Panel—a pre-designed panel for mutation profiling

The OncoCarta Panel provides a useful tool for targeted discovery and validation of tumor samples, as well as cell line characterization for drug discovery and development. The OncoCarta™ Panel v1.0* offers:

• A comprehensive screen of 19 oncogenes and 238 mutations in EGFR, KRAS, BRAF, and more
• Analysis of solid tumor samples with as little as 10% mutation frequencies
• Demonstrated use in paraffin-embedded tissueand a variety of other sample material³

For more information, view on OncoCarta webinar. 

Assays by Sequenom™—A custom service program for your assay needs

Assays by Sequenom allows you to have assays for somatic mutation analysis designed to your preferred gene, pathway, or disease of investigation. All assays are designed using Sequenom's Assay Design tools with 2-3 rounds of optimization to provide you with 100% working assays. The assays are then run on the MassARRAY Analyzer system by one of our scientists to verify PCR and primer extension. Visit our Assay Explorer™ database to generate your custom wish list, or search through pre-designed assays that may be of interest to your research needs.

Designing your own somatic mutation assays for highly sensitive and accurate analysis 

Sequenom’s application noteprovides important guidelines for custom assay design, that were also used in the development of the OncoCarta Panel. These guidelines improve low abundant signal detection and reduce the likelihood of overlapping signals.  Using these guidelines, researchers can readily design custom somatic mutation assays to any gene or genomic region of interest.  In addition, the application note discusses methods for assay validation including testing with control samples or synthetic templates. 

References

1. Thomas, R.K. et al. High-throughput oncogene mutation profiling in human cancer. Nature Genetics. 39, 283-294 (2007).
2. MacConaill, L. et al. Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples, PLoS ONE, (2009) 4(11) 1-7.
3. Pearce, M., et al. Mutation profiling in tumor samples using the Sequenom OncoCarta™ Panel. Nature Methods, June 2009, vii.
4. Pearce, M. and Ehrich, M. Somatic Mutation Analysis in Tumor Samples using the Sequenom MassARRAY® System. Nature Methods, May 2010.