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Acute Myeloid Leukemia Mutation PCR Array

Human
 
qBiomarker Somatic Mutation PCR Array: Human Acute Myeloid Leukemia
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.

The qBiomarker Somatic Mutation PCR Arrays & Assays 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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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.

 

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. Genomics of acute myeloid leukemia: the next generation. Riva L, Luzi L, Pelicci PG. Front Oncol. 2012;2:40. PMID:22666660
  2. Myeloid malignancies: mutations, models and management. Murati AA, Brecqueville MM, Devillier RR, Mozziconacci MJ, Gelsi-Boyer VV, Birnbaum DD. BMC Cancer. 2012 Jul 23;12(1):304. PMID:22823977
  3. The origin and evolution of mutations in acute myeloid leukemia. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, Dipersio JF, Ding L, Mardis ER, Wilson RK. Cell. 2012 Jul 20;150(2):264-78.PMID:22817890
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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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