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Myelodysplastic Syndromes Mutation PCR Array

qBiomarker Somatic Mutation PCR Array: Human Myelodysplastic Syndromes
The Human Myelodysplastic Syndromes (MDS) qBiomarker Somatic Mutation PCR Array is a translational research tool that allows rapid, accurate and comprehensive profiling of recurrent somatic mutations in human MDS samples. MDS and related disorders (myelodysplasia) comprise a group of myeloid neoplasms characterized by deregulated, dysplastic blood cell production. Mutations in a number of genes have been implicated in the pathogenesis of MDS, including ASXL1, CBL, DNMT3A, EZH2, IDH1, IDH2, NRAS, RUNX1, TET2, TP53, and the more recently identified mutations in the RNA splicing machinery components SF3B1, SRSF2 and U2AF35. Detection of somatic molecular abnormalities that may cause and maintain MDS 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 MDS and has the potential for discovering and verifying MDS biomarkers. The 83 real-time PCR DNA sequence assays included on the array detect the most frequent, functionally verified, and biologically significant mutations in MDS. 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.

CBL: 4 Assays
The most frequently occurring mutations in this gene reside in its RING-type, or zinc finger-like, domain in an Asp/Glu-rich (acidic) region likely involved in its ubiquitination activity. Other mutations include p.R420Q and p.K382E, which impair CBL-mediated degradation of cell-surface receptors in a dominant-negative fashion, and p.Y371H, which should reduce tyrosine phosphorylation by the insulin receptor.

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

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

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.

NRAS: 14 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.

SF3B1: 6 Assays
The most frequently occurring mutations in this gene reside in any one of its 11 HEAT repeats. These domains are possibly protein-protein interaction surfaces or involved in intracellular transport processes.

SRSF2: 3 Assays
Mutations frequently occur at a proline residue in amino acid position 95.

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.

TP53: 19 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.

U2AF35: 4 Assays
Mutations frequently occur at two residues each in different zinc fingers (C3H1-type domains) likely involved in RNA binding.

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. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts.Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium.N Engl J Med. 2011 Oct 13;365(15):1384-95. PMID:21995386
  2. Frequent pathway mutations of splicing machinery in myelodysplasia. Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S. Nature. 2011 Sep 11;478(7367):64-9. PMID:21909114
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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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