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Lymphoid Neoplasms Mutation PCR Array

Human
 
qBiomarker Somatic Mutation PCR Array: Human Lymphoid Neoplasms
The Human Lymphoid Neoplasm qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid, accurate, and comprehensive profiling of the top somatic mutations in human lymphoid neoplasms in the following genes: ABL1, ATM, BRAF, CDKN2A, CRLF2, CTNNB1/beta-catenin, EZH2, FBXW7, FGFR3, FLT3, HRAS, JAK2, KIT, KRAS, NOTCH1, NRAS, PIK3CA, PTPN11, 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 Lymphoid Neoplasm qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for the study of mutations in the context of lymphoid neoplasms 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 75 DNA sequence mutation assays designed to detect the most frequent, functionally verified, and biologically significant mutations in human lymphoid neoplasms. 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 4000 lymphoid neoplasm 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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ABL1: 3 Assays
The mutations queried by these assays mostly lie in the protein kinase domain.

ATM: 3 Assays
The most commonly detected ATM loss-of-function mutations occur in the FAT, FATC and the kinase domains.

BRAF: 2 Assays
There are two major classes of BRAF mutations. One class leads to increased BRAF kinase activity, such as the p. V600E mutation. The other class leads to impaired kinase activity, such as the p.G469A mutation.

CDKN2A: 1 Assay
The top CDKN2A loss-of-function mutations occur in the consensus ankyrin domain, which leads to inability to form stable complexes with its targets.

CRLF2: 1 Assay
This novel gain-of-function mutation synergizes with JAK2 R683 mutations to confer cytokine-independent growth to BaF3 pro-B cells.

CTNNB1: 4 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.

EZH2: 3 Assays
All detected mutations lie in the SET domain responsible for histone lysine methyltransferase activity.

FBXW7: 4 Assays
The mutations queried by these assays lay in either the third or fourth repeat of the protein's WD40 domain, typically involved in protein-protein interactions.

FGFR3: 2 Assays
The most frequently identified mutations occur in the kinase domain and non-kinase extracellular domains such as the hinge region and IgG-like domain. Some of the somatic mutations also correspond to congenital SNPs involved in genetic diseases.

FLT3: 2 Assays
The most frequently identified FLT3 mutations include point mutations, insertion and deletion mutations in the juxtamembrane and activation domains of the protein.

HRAS: 1 Assay
The most important HRAS mutation in lymphoid neoplasms occurs at codon 61.

JAK2: 3 Assays
Most of these mutations lie in protein kinase domain 1. One mutation (p.V615F) confers cytokine-independent growth to BaF3 pro-B cells. Mutations at R683 lead to constitutive tyrosine phosphorylation activity promoting cytokine hypersensitivity and are associated with susceptibility to Budd-Chiari syndrome.

KIT: 2 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.

NOTCH1: 8 Assays
Most of the represented mutations lie in predicted cytoplasmic domains.

NRAS: 14 Assays
The mutation assays include the most important NRAS mutations at codons 12, 13, and 61.

PIK3CA: 1 Assay
The most frequently occurring PIK3CA mutations mainly belong to two classes: gain-of-function kinase domain activating mutations and helical domain mutations that mimic activation by growth factors.

PTPN11: 4 Assays
The most frequently identified PTPN11 mutations include lesions affecting residues located in or close to the N-terminal SH2 domain/PTP-interacting surface and mutations that affect residues that control substrate specificity.

TP53: 11 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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