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qBiomarker Assay PreAMP Mix

For locus-specific preamplification prior to real-time PCR to support ultrasensitive cancer mutation detection
  • Nested preamplification improves sensitivity and decreases false positives
  • PCR-based protocol is accessible to most laboratories
  • Integrated, complimentary data analysis simplifies mutation calling
The qBiomarker Assay PreAMP Mix enables preamplification of DNA from small amounts of intact or degraded DNA prior to analysis with qBiomarker Somatic Mutation PCR Assays. The kit contains a locus-specific primer mix which, together with the qBiomarker PreAMP PCR Mastermix, uses PCR preamplification to amplify a specific locus with minimal bias for analysis with the qBiomarker Somatic Mutation PCR Assays.
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  • Cat. no. (e.g., SI00299551, QT01342509)
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  • CpG loci identification numbers (CG#) (e.g., CG17753661)

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qBiomarker Assay PreAMP Mix
100 µl PreAMP mix for specific loci — enough for 250 reactions
337042 Varies
$93.90
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Principle
For successful somatic mutation detection, experimental methods must detect the DNA molecules with mutations of interest in samples that may contain a vast excess of DNA molecules with the wildtype sequence at the same locus. Based off of this principle, there are two factors that affect these experiments: the inherent percentage of mutant DNA in a sample, and the sensitivity of the method. In the case of cancer, a specific mutation may be found in a small percentage of the tumor, which is a characteristic of tumor heterogeneity. Additionally, different types of samples and sample sources affect this ratio of mutant to wildtype DNA as well as the number of DNA molecules that can be assayed. A method's sensitivity directly reflects how few mutant DNA molecules can be detected within a given amount of wildtype DNA.

Sample types common in cancer research, including formalin-fixed paraffin embedded (FFPE) samples, serum samples, fine needle biopsies, and sorted cells frequently contain only small amounts of amplifiable DNA. Genomic DNA in FFPE samples is fragmented, for example, while DNA in serum samples is heavily diluted. In the case of fine needle biopsies or sorted cells, these samples have small numbers of cells that will yield limited amounts of genomic DNA. Amplifying genomic DNA enables more accurate detection of the mutations in DNA from these sample types.

The qBiomarker PreAMP system uses nested PCR preamplification to improve sensitivity and decrease false positives. In a 12-cycle PCR reaction, the loci of interest are amplified and are ready to be analyzed with qBiomarker Somatic Mutation PCR Assays and Arrays. The qBiomarker Assay PreAMP Mix contains primers to amplify any specific locus covered by the qBiomarker Somatic Mutation PCR Assays — a collection of 1200+ assays for more than 100 genes. In combination with the qBiomarker PreAMP Synthesis Kit, the mix enables the analysis of mutations in a specific locus using qBiomarker Somatic Mutation PCR Assays.
Procedure
DNA is first isolated from FFPE, serum, or small samples using the appropriate QIAamp or DNeasy kit. The qBiomarker PreAMP Synthesis Kit and qBiomarker Assay PreAMP Mix are then used to preamplify the DNA using locus-specific primers. qBiomarker Somatic Mutation Assays are used for mutation detection, and CT values are uploaded into the GeneGlobe Data Analysis tool for data analysis and mutation calls.
Applications

The qBiomarker Assay PreAMP Mix is highly suited for preamplification of genomic DNA from samples with low amounts of amplifiable DNA for exclusive use with qBiomarker Somatic Mutation PCR Assays. Recommended sample types include:

  • FFPE samples
  • Plasma, serum, urine, or other cell-free body fluids
  • Laser capture microdissection samples
  • Fine needle biopsies
  • FACS-sorted cells

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Handbooks & Protocols (2)
For screening disease-focused mutation panels by PCR
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For real-time PCR-based, pathway- or disease-focused, somatic mutation profiling
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Instrument Technical Documents (1)
For screening disease-focused mutation panels by PCR
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Kit Handbooks (1)
For real-time PCR-based, pathway- or disease-focused, somatic mutation profiling
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