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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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Acute Myeloid Leukemia (AML) qBiomarker Somatic Mutation PCR Array
Introduction
The Human Acute Myeloid Leukemia (AML) qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid, accurate and comprehensive profiling of recurrent frequent somatic mutations found in in human AML samples. Patients with AML, the most frequent hematological malignancy in adults, have highly variable prognoses and a high mortality rate. Mutations in a number of genes have been implicated in the pathogenesis of AML, including ASXL1, DNMT3A, FLT3, IDH1, IDH2, KIT, NPM1, NRAS, RUNX1, TET2 and WT1. Detection of somatic molecular abnormalities that may cause and maintain AML is crucial for patient sample stratification in translational research studies. These mutations also warrant extensive investigation to enhance the understanding of carcinogenesis and identify potential drug targets. With its comprehensive content coverage, this array is designed for studying mutations in the context of AML and has the potential for discovering and verifying AML biomarkers. The 83 real-time PCR DNA sequence assays included on the array detect the most frequent, functionally verified, and biologically significant mutations in AML. 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

ASXL1: 5 Assays
Most frequently observed mutations in this gene are C-terminal truncations that lose the interaction domain with RARA, the poly-serine region, and the atypical PHD-type domain. Other truncations also lose part of the NCOA1 interaction domain and a glycine-rich region.

DNMT3A: 2 Assays
Mutations are frequently observed in the domain conserved among S-adenosylmethionine-dependent methyltransferases superfamily members.

FLT3: 5 Assays
The most frequently identified FLT3 mutations include point mutations, insertion and deletion mutations in the juxtamembrane and activation domains of the protein.

IDH1: 5 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: 7 Assays
These mutations all lie in the substrate binding domain, and one (p.R140Q) is associated with D-2-hydroxyglutaric aciduria.

KIT: 24 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.

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

RUNX1: 7 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.

TET2: 2 Assays
The most common variants of this gene are C-terminal truncations missing its two glutamine-rich regions, all of its metal binding site residues, and a phosphoserine and a phosphotyrosine site.

WT1: 4 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.

Related Biologies
Leukemia
Gene Resource List
Format
pdf
FileSize
137KB
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Name qBiomarker™ Somatic Mutation PCR Array Human Acute Myeloid Leukemia (SMH-045AA)

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