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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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PDGFR Pathway qBiomarker Somatic Mutation PCR Array
Introduction
Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) have served as prototypes for growth factor and receptor tyrosine kinase (RTK) function for more than two decades, and are implicated in a range of diseases. While autocrine activation of PDGF signaling is involved in certain gliomas, sarcomas, and leukemias, paracrine PDGF signaling has been frequently observed in epithelial cancers, where it triggers stromal recruitment and has been implicated in epithelial-mesenchymal transition, thereby affecting tumor growth, angiogenesis, invasion, and metastasis. Mutations in the PDGFR-A gene constitute one major class of genetic alterations that lead to gastrointestinal stromal tumors (GIST), one of the most common mesenchymal tumors of the gastrointestinal tract. Mutations in the PDGFR-A gene are the targets of drug therapies and other agents. Specific PDGFR-A gene mutations appear to confer differential drug sensitivity. Activation of the PDGFR pathway involves key downstream mediators, including mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and phospholipase-? pathways. These downstream components are also possible targets of inhibition. The Human PDGFR Pathway qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid and accurate profiling of the somatic mutation status of the PDGFR-A gene and additional key genes in the PDGFR signaling pathway / network: AKT, BRAF, KRAS, HRAS, NRAS, MEK1, PIK3CA, and PTEN. Gene components were selected based on their frequency of mutation in human cancers. 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 PDGFR Pathway qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for studying mutations in the context of the PDGFR pathway and has the potential for discovering and verifying drug target biomarkers for a variety of human cancers involving the PDGFR 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 PDGFR pathway. These mutations were chosen from curated, comprehensive somatic mutation databases and peer-reviewed 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
PDGFR-A gene:
22 mutation assays are included for PDGFR-A in this panel. These assays detect the most frequently identified PDGFR-A gain-of-function mutations, including deletion, point mutation, and deletion-insertion mutations in regions p.D842_S847, and p.R554_E571, and the point mutations p.N659Y and p.T674I.

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:
15 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.

HRAS gene:
Similar to KRAS mutation assays, the >10 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, as well as mutation p.A18T.

MEK1 gene:
4 assays for mutations with verified clinical significance in cancer were included on this panel. These mutations cluster in MEK1 N-terminal negative regulatory domain and an adjacent domain, and are all activating mutations (i.e. lead to up-regulated 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).

Gene Resource List
Format
pdf
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Name qBiomarker Somatic Mutation PCR Array for PDGFR Pathway (SMH-004AA)

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