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qBiomarker Somatic Mutation PCR Arrays

For rapid and accurate profiling of the somatic DNA mutation status of gene panels

  • Pathway- or disease-focused profiling of somatic mutation status
  • Simple real-time PCR procedure
  • High sensitivity and wide dynamic range
  • Designed for routine use on most PCR instruments
  • Master mix included

qBiomarker Somatic Mutation PCR Arrays are translational research tools that allow rapid and accurate profiling of the somatic mutation status for important genes related to a biological pathway or disease. Mutations are selected from comprehensive somatic mutation databases (e.g., COSMIC) and peer-reviewed scientific literature based on their clinical or functional relevance and frequency of occurrence.

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qBiomarker Somatic Mutation PCR Arrays are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.


Performance

qBiomarker Somatic Mutation PCR Arrays show a high degree of sensitivity even with formalin-fixed paraffin-embedded (FFPE) samples (see figures "High degree of sensitivity" and "Sensitivity of qBiomarker Somatic Mutation PCR Arrays with FFPE samples").

qBiomarker Somatic Mutation PCR Arrays have utility in the detection of mutations in cell lines or research samples, which is critical for toxicological, drug development, and cancer studies (see figure "Profiling of common cancer cell lines for somatic mutation status").

Principle
Real-time PCR is the most sensitive and reliable method for the detection of DNA mutations. By combining allele-specific amplification and hydrolysis probe detection, qBiomarker Somatic Mutation real-time PCR assays have been developed which can detect as few as 1% somatic mutations in the background of wild-type genomic DNA. Allele-specific amplification is achieved by Amplification Refractory Mutation System (ARMS) technology, which is based on the discrimination by Taq polymerase between a match and a mismatch at the 3’ end of the PCR primer (see figure "Principle of ARMS technology").
Procedure

Simply mix the DNA template with the ready-to-use PCR mastermix, aliquot equal volumes to each well of the same plate, and then run the real-time PCR cycling program. qBiomarker Somatic Mutation PCR Arrays are compatible with all ABI, Bio-Rad, Eppendorf, Roche, and Stratagene instruments.

qBiomarker Somatic Mutation PCR Arrays are available in 96-well and 384-well plates and are used to detect mutations related to a disease state or pathway, plus gene copy number controls for normalization. Each qBiomarker Somatic Mutation PCR Array also includes control elements for general PCR performance.

Easy-to-use data analysis

Data can be analyzed using the available Excel-based data analysis templates. Data analysis is based on either the ∆∆CT or Average ∆CT method.

Arrays are available in a variety of formats, all with mastermix included:

qBiomarker Somatic Mutation PCR Array Format A: Fluoroscein, 96-well; for Bio-Rad iCycler, iQ5, MyiQ, and MyiQ2 instruments
qBiomarker Somatic Mutation PCR Array Format A: ROX, 96-well; for ABI Standard 96-well Blocks (5700, 7000, 7300, 7500, 7900HT, ViiA 7); Bio-Rad Chromo 4 (MJ Research); Stratagene Mx3005p, Mx3000p; Eppendorf ep realplex 2/2S, and 4/4S instruments
qBiomarker Somatic Mutation PCR Array Format C: ROX, 96-well; for ABI 7500 FAST 96-well Block, 7900HT FAST 96-Well Block, StepOnePlus, and ViiA 7 FAST 96-well Block instruments
qBiomarker Somatic Mutation PCR Array Format D: ROX, 96-well; for Bio-Rad CFX96, Opticon and Opticon 2 (MJ Research); Stratagene Mx4000 instruments
qBiomarker Somatic Mutation PCR Array Format E: ROX, 384-well; for ABI 7900HT 384-well Block, ViiA 7 384-well Block; Bio-Rad CFX384 instruments
qBiomarker Somatic Mutation PCR Array Format F: ROX, 96-well; for Roche LightCycler 480 96-well Block instruments
qBiomarker Somatic Mutation PCR Array Format G : ROX, 384-well; for Roche LightCycler 480 96-well Block instruments
Applications

qBiomarker Somatic Mutation PCR Arrays are highly suited for the rapid and accurate profiling of mutations for a pathway- or disease-focused set of genes and key downstream and associated signaling genes.

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Instrument Technical Documents (2)
For screening disease-focused mutation panels by PCR
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For gene expression and genomic analysis
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Kit Handbooks (1)
For real-time PCR-based, pathway- or disease-focused somatic mutation profiling
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Download Files (1)
Data analysis file for qBiomarker™ Somatic Mutation PCR Array Human DNA QC Pathway- FFPE Samples
Catalog number- 337021
Pathway number- SMH-999

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References
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FGFR Pathway qBiomarker Somatic Mutation PCR Array
Introduction
The fibroblast growth factor receptors (FGFRs) are receptors that bind fibroblast growth factors (FGFs), members of the largest family of growth factor ligands. The FGFRs and their downstream signaling cascades have been implicated in a diverse range of cellular processes including proliferation, apoptosis, survival, chemotaxis, cell adhesion, and differentiation. The importance of proper FGFR signaling is evident from genetic studies in human and mouse models demonstrating disruption of FGF signaling by mutations cause a variety of disorders including skeletal diseases, infertility, and cancer. The Human FGFR Pathway qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid and accurate profiling of the somatic mutation status of FGFR genes and key genes in the FGFR signaling pathways: AKT, BRAF, KRAS, HRAS, NRAS, MEK1, PIK3CA, and PTEN. The utility of individual and multiple somatic mutation status information in identifying key signaling transduction disruptions has been demonstrated in numerous research studies. For example, the mutation status of the EGFR and KRAS genes can predict the physiological response to certain drugs targeting these molecules. The FGFR Pathway qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for studying mutations in the context of the FGFR pathway and has the potential for discovering drug target biomarkers for a variety of human diseases involving the FGFR signaling pathway and downstream effectors. This array covers 85 DNA sequence mutation assays designed to detect the most frequent, functionally verified, and biologically most significant mutations in the FGFR pathways. These mutations were chosen from curated, comprehensive somatic mutation databases and peerreviewed scientific literature. The simplicity of the product format and operating procedure allows routine somatic mutation profiling in any research laboratory with access to real-time PCR instruments.
Gene List

FGFR genes (FGFR1, FGFR2, FGFR3):
15 mutation assays are included for FGFR1, 2 and 3 in this panel. These assays detect the most frequently identified
kinase domain mutations and non-kinase domain (e.g. extracellular domains such as the hinge region and IgG-like
domain) mutations. Some of the somatic mutations included have congenital correlates that are involved in genetic
diseases.

AKT gene:
The mutation assay detects the best known AKT1 mutation, c.49G>A, p.E17K. This is a PH domain mutation that
results in constitutive targeting of AKT1 to plasma membrane.

BRAF gene:
Two classes of mutation assays are included. One class covers mutations that lead to increased BRAF kinase
activity, such as the p.V600 mutations. The other class detects mutations that lead to impaired kinase activity, such
as the p.G464V, p.G466V, and p.G469A mutations.

KRAS gene:
16 KRAS mutation assays provide comprehensive analysis capacity for the most frequently occurring mutations in
KRAS codon positions 12, 13, and 61. Mutations at these positions result in reduced intrinsic GTPase activity and/or
cause KRAS to become unresponsive to RasGAP. The p.Q22K mutation assay is also included.

HRAS gene:
Similar to KRAS mutation assays, the 13 HRAS mutation assays on this panel aim to cover the most important
HRAS mutations identified in cancers at codon 12, 13, and 61 positions.

NRAS gene:
12 NRAS mutation assays are included on the panel to cover codon positions 12, 13, and 61.

MEK1 gene:
4 assays for mutations with significance in cancer were included on this panel. These mutations cluster in MEK1 Nterminal negative regulatory domain and an adjacent domain, and are all activating mutations (i.e. lead to upregulated intrinsic MEK1 kinase activity).

PIK3CA (phosphatidylinositol 3-kinase catalytic subunit) gene:
The mutation assays covered on this panel can detect 7 of the most frequently occurring PIK3CA mutations that
belong to two classes: p.H1047 mutations, which are activating, kinase domain mutations; and mutations in P539-
E545 region, which are helical domain mutations that mimic activation by growth factors.

PTEN gene:
Included on the panel are 6 most commonly detected PTEN loss-of-function mutations that are due to either
truncation (p.R233* and p.R130*) or point mutation-caused phosphatase inactivation (p.R130 and p.R173
mutations).

Related Biologies
Growth Factors
Gene Resource List
Format
pdf
FileSize
136KB
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Name qBiomarker™ Somatic Mutation PCR Array Human FGFR Pathway (SMH-005AA)

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