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Receptor Tyrosine Kinase (Panel II) Mutation PCR Array

qBiomarker Somatic Mutation PCR Array: Human Receptor Tyrosine Kinase (RTK) Pathways (Panel II)
The Human Receptor Tyrosine Kinase (RTK) Pathways qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid and accurate profiling of the somatic mutation status for several receptor tyrosine kinase pathways. Components in the RTK pathways are frequently mutated in human cancers, and therefore warrant extensive investigation to enhance the understanding of carcinogenesis. Panel II contains mutation assays for 8 key genes in the shared downstream PI3K and Ras-MAPK 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 RTK Pathways qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for studying mutations in the context of these pathways and has the potential for discovering drug target biomarkers for a variety of human cancers involving these pathways and downstream effectors. Panel II includes 86 DNA sequence mutation assays designed to detect the most frequent, functionally verified, and biologically significant mutations in the downstream PI3K and Ras-MAPK pathways. 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.

Panel I and Panel II are available in two separate 96-well format plates, or are available in a combined 384-well format (2 samples per plate).

The qBiomarker Somatic Mutation PCR Arrays are intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.


Assay Functional Annotations How It Works References Resources
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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.L597 and 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 >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:
13 NRAS mutation assays are included on the panel to cover codon positions 12, 13, and 61, as well as mutation

MEK1 gene:
4 assays for mutations with significance in cancer were included on the 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 17 most frequently occurring PIK3CA mutations that mainly
belong to two classes: T1025-G1049 region mutations, which are activating, kinase domain mutations; and
mutations in the P539-E545 region, which are helical domain mutations that mimic activation by growth factors.

PTEN gene:
Included on the panel are 11 most commonly detected PTEN loss-of-function mutations that are due to either early
stop codon truncation or point mutation-caused phosphatase inactivation (p.R130 and p.R173 mutations).


Assay Functional Annotations How It Works References Resources

Overview of the qBiomarker Somatic Mutation PCR Array / Assay Protocol

Overview of the qBiomarker Somatic Mutation PCR Array / Assay Protocol.
The procedure involves DNA extraction (QIAGEN QIAamp DNA Mini Kit or FFPE Tissue Kit is recommended), an optional amplification (QIAGEN REPLI-g kit or REPLI-g UltraFast kit is recommended) step for DNA isolated from fresh samples, qPCR detection on qBiomarker Somatic Mutation PCR Arrays or Assays, and data analysis (using the qBiomarker Somatic Mutation Data Analysis Template). An optional DNA sample QC step immediately before the detection array or assay setup allows the user to qualify the DNA samples.

Principle of Mutant Discrimination with ARMS®

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Assay Functional Annotations How It Works References Resources
  1. The PKB/AKT pathway in cancer.Carnero A. Curr Pharm Des. 2010 Jan; 16(1):34-44
  2. BRAF, a target in melanoma: implications for solid tumor drug development. Flaherty KT, McArthur G. Cancer. 2010 Jul 13. [Epub ahead of print]
  3. Clinical relevance of KRAS in human cancers. Jancík S, Drábek J, Radzioch D, Hajdúch M. J Biomed Biotechnol. 2010; 2010:150960.
  4. Oncogenic Ras in tumour progression and metastasis. Giehl K. Biol Chem. 2005 Mar; 386(3):193-205
  5. MEK1 mutations confer resistance to MEK and B-RAF inhibition. Emery CM, Vijayendran KG, Zipser MC, Sawyer AM, Niu L, Kim JJ, Hatton C, Chopra R, Oberholzer PA, Karpova MB, MacConaill LE, Zhang J, Gray NS, Sellers WR, Dummer R, Garraway LA. Proc Natl Acad Sci U S A. 2009 Dec 1; 106(48):20411-6
  6. PIK3CA mutations in human solid tumors: role in sensitivity to various therapeutic approaches. Ligresti G, Militello L, Steelman LS, Cavallaro A, Basile F, Nicoletti F, Stivala F, McCubrey JA, Libra M. Cell Cycle. 2009 May 1; 8(9):1352-8
  7. Oncogenic mutations as predictive factors in colorectal cancer. Ličvre A, Blons H, Laurent-Puig P. Oncogene. 2010 May 27; 29(21):3033-43
  8.  PI(3)King Apart PTEN's Role in Cancer. Zhang S, Yu D. Clin Cancer Res. 2010 Jul 8. [Epub ahead of print]
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Assay Functional Annotations How It Works References Resources

User Manual qBiomarker Somatic Mutation PCR Array System (PDF)
Data Analysis qBiomarker Somatic Mutation PCR Array Data Analysis Software
Application Data Detection Limits, Cancer Pathways
FAQ Frequently Asked Questions about Somatic Mutation Assays and Arrays
Webinar qBiomarker Somatic Mutation Analysis: Real-World Application Data
Slide Presentation> Presentation about qBiomarker Somatic Mutation Assays and Arrays (PDF)
Scientific Poster A Novel Tool for Pathway-Focused Cancer Mutation Profiling (PDF)
Presented at American Association for Cancer Research 2011
White Paper Rapid and accurate cancer somatic mutation profiling with the qBiomarker Somatic Mutation PCR Array (PDF)
Product Profile For screening biology-focused panels of gene mutations (PDF)

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