Optimized solution for cancer research

Rare mutation detection has extensive implications for cancer research. The accumulation of mutations in oncogenes or tumor suppressor genes is an important aspect of tumorigenesis. Acquisition of these mutations in a tiny subset of somatic cells can be sufficient for cancer initiation or progression.

Since these mutations are usually only present in a very small number of cells, they require an assay that delivers high signal-to-noise and low false-positive rates.

By combining TaqMan® fluorogenic 5’ nuclease chemistry with digital PCR methodology using the QuantStudio® 3D Digital PCR System, researchers are now able to detect low-frequency mutations. Custom TaqMan® SNP Genotyping Assays used in digital PCR usually provide great performance. Occasionally, these assays can benefit from additional optimization to seamlessly work with our QuantStudio® 3D Digital PCR System and achieve the high levels of performance required to detect and quantify mutations present at a very low frequency.

The QuantStudio® 3D rare mutation analysis solution includes a subset of wet lab–validated TaqMan® SNP Genotyping Assays to detect and quantify the most common cancer-related mutations (e.g., EGFR, BRAF, KRAS, PIK3CA, and JAK2). These assays were designed using the full bioinformatics power of the TaqMan® Assay design pipeline and were wet lab–validated specifically for our QuantStudio® 3D Digital PCR System. Researchers are now able to quantify rare mutants at a prevalence as low as 0.1% (Figure 1).

Overview of the QuantStudio® 3D rare mutation analysis solution
  • Optimized digital PCR performance—wet lab–validated TaqMan® assays targeting 38 somatic mutations for the QuantStudio® 3D Digital PCR System
  • High sensitivity—detect and quantify rare mutant prevalence as low as 0.1%
  • Cost-effective and convenient—single-tube format includes both wild type and mutant alleles with small and large reaction options
  • Streamlined analysis—advanced algorithms for better quantification of rare mutations
  • Guaranteed performance—wet lab–validated assay replaced or account credited if you are not satisfied
  • Custom design support—guidance available for additional Custom TaqMan® SNP Genotyping Assays for rare mutation analysis on the QuantStudio® 3D Digital PCR system that are not part of this wet lab–validated collection

Download the list of wet-lab validated TaqMan® SNP Genotyping Assays for digital PCR

Figure 1. Example of rare allele quantification of KRAS by digital PCR. The KRAS G12V mutation was detected with a Custom TaqMan® SNP Genotyping Assay optimized for digital PCR on the QuantStudio® 3D Digital PCR System. Each sample represents a fraction of mutant plasmid to wild-type genomic DNA. The 0.1% target represents mutant genomic DNA from a mutant cell line in a wild-type genomic DNA background. All samples were analyzed using QuantStudio® 3D AnalysisSuite Cloud Software with the relative quantification module. 
A) Targeted mutation rate of 10%. The mutation detection rate was 10.384% with a confidence interval of 8.235% - 13.076%
B) Targeted mutation rate of 1%. The mutation detection rate 1.393% with a confidence interval of 0.772% - 2.507%
C) Targeted mutation rate of 0.1%. The mutation detection rate was 0.142% with a confidence interval of 0.064% - 0.310%
D) Wild-type control sample

How to order the new TaqMan® Assays for rare mutation analysis
  1. Download and review the list of wet lab-validated Custom TaqMan® SNP Genotyping Assays for rare mutation analysis.
  2. Place an order for the 12-reaction size (P/N 4383547) directly with a sales representative.
  3. Place an order for the 450 reaction size (P/N 4332077) directly through our website.
  4. Require further assistance? Speak with a technical sales representative 1-800-955-6288, option 4.
Literature
QuantStudio® 3D Digital PCR System

QuantStudio® 3D Digital PCR System

Absolute quantification, using sealed-chip technology, for a reliable method and precise, sensitive data.

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