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Hematopoietic Neoplasms Mutation PCR Array

qBiomarker Somatic Mutation PCR Array: Human Hematopoietic Neoplasms
The Human Hematopoietic 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 hematopoietic neoplasms in the following genes: ABL1, CEBPA, CSF1R, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NPM1, NRAS, PTPN11, RUNX1, p53, and WT1. 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 Hematopoietic Neoplasm qBiomarker Somatic Mutation PCR Array, with its comprehensive content coverage, is designed for the study of mutations in the context of hematopoietic 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 76 DNA sequence mutation assays designed to detect the most frequent, functionally verified, and biologically significant mutations in human hematopoietic 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 41,000 hematopoietic 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.


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ABL1: 4 Assays
The mutations queried by these assays mostly lie in the protein kinase domain.

CEBPA: 7 Assays
The p.K304_Q305insL mutation lies in the DNA binding basic motif of the protein.

CSF1R: 1 Assay
This mutation near the C-terminus that corresponds to SNP variant rs1801271 abolishes the down-regulation of activated CSF1R.

FLT3: 3 Assays
The most frequently identified FLT3 mutations include point mutations, insertion and deletion mutations in the juxtamembrane and activation domains of the protein.

GATA1: 3 Assays
GATA1 plays an important role in erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin. Mutations in this gene have been associated with X-linked dyserythropoietic anemia and thrombocytopenia.

GATA2: 1 Assay
GATA2 is a negative regulator of hematopoietic stem cell and progenitor cell differentiation. This mutation lies within the second zinc finger domain and causes a gain-of-function that increases transactivation activity and enhances inhibition of PU.1 activity, a major regulator of myelopoiesis.

IDH1: 4 Assays
Most of these mutations abolish magnesium binding and alters the enzyme's activity to convert alpha-ketoglutarate into R(-)-2-hydroxyglutarate instead of isocitrate into alpha-ketoglutarate.

IDH2: 2 Assays
These mutations all lie in the substrate binding domain, and one (p.R140Q) is associated with D-2-hydroxyglutaric aciduria.

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: 3 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: 5 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.

MPL: 3 Assays
These mutations are predicted to lie at a junction between a transmembrane helix and a cytoplasmic domain.

NPM1: 5 Assays
NPM1 encodes a phosphoprotein that shuttles between the nucleus and the cytoplasm and is thought to be involved in regulation of the ARF/p53 pathway. A number of gene fusion events with NPM1 have been characterized, in particular the anaplastic lymphoma kinase gene on chromosome 2. Mutations in this gene are associated with acute myeloid leukemia.

NRAS: 15 Assays
The mutation assays include the most important NRAS mutations at codons 12, 13, and 61.

PTPN11: 11 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.

RUNX1: 2 Assays
RUNX is the alpha subunit of the core binding factor that is thought to be involved in normal hematopoiesis. Chromosomal translocations involving this gene have been associated with several types of leukemia.

TP53: 2 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.

WT1: 2 Assays
The WT1 transcription factor plays an essential role in normal urogenital system development. A small subset of patients with Wilm's tumors contains mutations in this gene.

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


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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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