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Soft Tissue Tumors (including GIST) Mutation PCR Array

Human
 
qBiomarker Somatic Mutation PCR Array: Human Soft Tissue Tumors (including GIST)
The Human Soft Tissue Tumors (including GIST) qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid, accurate, and comprehensive profiling of the top somatic mutations in human soft tissue tumor samples in the following genes: APC, BRAF, CTNNB1/beta-catenin, HRAS, KIT, KRAS, NF2, NRAS, PDGFRA, SMARCB1, and p53. These mutations warrant extensive investigation to enhance the understanding of carcinogenesis and identify potential drug targets. Numerous research studies have demonstrated the utility of individual and multiple somatic mutation status information in identifying key signaling transduction disruptions. For example, the mutation status of the EGFR and KRAS genes can predict the physiological response to certain drugs targeting these molecules. The Human Soft Tissue Tumor qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for the study of mutations in the context of soft tissue tumors (including GIST) and has the potential for discovery and verification of drug target biomarkers for this cancer type and other cancer types in which these mutations have been identified. This array includes 83 DNA sequence mutation assays designed to detect the most frequent, functionally verified, and biologically significant mutations in human soft tissue tumors. These mutations were chosen from curated, comprehensive somatic mutation databases and peer-reviewed scientific literature, and represent the most frequently recurring somatic mutations compiled from over 4800 soft tissue tumor samples (including 3100 GIST samples). 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.

 

Assay Functional Annotations How It Works References Resources
 
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APC: 3 Assays
The most commonly detected APC inactivation mutations are mainly composed of truncation mutations (due to nonsense mutations and frameshift mutations) and point mutations between codons 1250 and 1578.

BRAF: 1 Assay
The most important BRAF mutation in soft tissue tumors leads to increased kinase activity, the p. V600E mutation.

CTNNB1: 7 Assays
The most frequently detected CTNNB1/beta-catenin mutations result in abnormal signaling in the WNT signaling pathway. The mutated codons are mainly several serine/threonine residues targeted for phosphorylation by GSK-3beta.

HRAS: 5 Assays
The mutation assays include the most important HRAS mutations identified in cancers at codons 12, 13, and 61.

KIT: 27 Assays
The most frequently identified KIT gain-of-function mutations include the D816V point mutation, the exon 11 (juxtamembrane domain) deletion and point mutations, an exon 9 insertion mutation, and exon 13 point mutations.

KRAS: 6 Assays
The mutation assays include the most frequently occurring mutations in KRAS codons 12, 13, and 61. Mutations at these positions result in reduced intrinsic GTPase activity and/or cause KRAS to become unresponsive to RasGAP.

NF2: 6 Assays
NF2 is similar to some members of the ERM (ezrin, radixin, moesin) family of proteins and links cell-surface proteins with cytoskeletal components and proteins involved in cytoskeletal dynamics. Mutations in this gene are associated with neurofibromatosis type II which is characterized by nervous system and skin tumors and ocular abnormalities.

NRAS: 3 Assays
The mutation assays include the most important NRAS mutations at codons 12, 13, and 61.

PDGFRA: 15 Assays
The most frequently identified PDGFRA gain-of-function mutations include deletion, point mutation, and deletion-insertion mutations in regions p.D842-S847 and p.R554-E571 as well as the point mutations p.N659Y and p.T674I.

SMARCB1: 5 Assays
SMARCB1, as part of a complex, relieves repressive chromatin structures, allowing the transcriptional machinery to more effectively access its targets. Mutations in this tumor suppressor gene have been associated with malignant rhabdoid tumors.

TP53: 5 Assays
The most frequently detected somatic mutations in TP53 are largely composed of DNA-binding domain mutations which disrupt either DNA binding or protein structure.

View a table of the mutations, associated COSMIC IDs and assay numbers, by clicking “Mutation Table” above on the right.

 

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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