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Custom qBiomarker Copy Number PCR Arrays

For custom profiling of copy number variations and alterations

  • Custom copy number profiling for any real-time instrument
  • Wet bench-tested assays
  • Integrated multicopy reference assay for superior normalization
  • Complimentary, easy-to-use data analysis tool

Custom qBiomarker Copy Number PCR Arrays are designed to measure the number of copies for a genomic loci panel of your choice. Assays are available for every 200 base pairs covering the entire human genome. Custom qBiomarker Copy Number PCR Arrays are highly suitable for verification of single nucleotide polymorphism (SNP) array or array-comparative genomic hybridization (aCGH) data, and are available in plate or Rotor-Disc formats.

To order a Custom qBiomarker Copy Number PCR Array, please use this excel file.

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Cat No./ID: 337801
Custom qBiomarker Copy Number PCR Arrays
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Custom panels of copy number assays in 96-well, 384-well, or Rotor-Disc formats

Custom qBiomarker Copy Number PCR Arrays are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

Performance

 

When using real-time PCR to evaluate copy number changes in DNA samples, two elements are critical: real-time PCR assay performance, and reliable normalization of DNA input. Every qBiomarker Copy Number PCR Assay on a Custom qBiomarker Copy Number PCR Array is wet bench-tested for several characteristics affecting the accuracy of real-time PCR results: specificity, wide dynamic range, and uniformly high amplification efficiency. Laboratory verification of assay quality ensures that qBiomarker Copy Number PCR Assays deliver reliable results.

 

Indeed, qBiomarker Copy Number PCR Assays accurately identified aneuploidy in cell lines containing chromosomal aberrations previously identified by cytogenetic methods. Assays for AR and MECP2, which are both on the X chromosome, correctly quantified gene copy number in cell lines with 1, 3, and 4 copies of the X chromosome.

 

Custom qBiomarker Copy Number PCR Arrays use the qBiomarker Multicopy Reference Copy Number PCR Assay (MRef) to provide superior normalization of DNA input. Single-copy reference genes such as RNase P can yield unreliable normalization, as in cancer cell lines. By contrast, the MRef assay provides accurate normalization. Together, the laboratory verification of each qBiomarker Copy Number PCR Assay on the array and the superior DNA input normalization provided by the MRef assay ensure accurate, reliable results.

 

 

Principle

Each Custom qBiomarker Copy Number PCR Array contains a panel of qBiomarker Copy Number PCR Assays for GOIs or ROIs of your choice. Four replicates of each assay are included to increase the accuracy of copy number calls using statistical analysis. The arrays are available in 96-well plate, 384-well plate, and Rotor-Disc formats, all of which are designed to your specifications, to fit the needs of your experiment.

All qBiomarker Copy Number PCR Assays are designed in unique regions of the genome. A multicopy reference assay, the qBiomarker Multicopy Reference Copy Number PCR Assay (MRef) is included on each array, providing superior normalization for DNA input compared to single-copy reference genes. The reference assay recognizes a stable sequence that appears in the human genome over 40 times, and whose copy number is not affected or minimally affected by local genomic changes. Inclusion of this reference assay during testing allows use of the ΔΔCT method to accurately make copy number calls or relative copy number change calls for specific targets.

The simplicity of the qBiomarker Copy Number PCR Array format and operating procedure allows routine copy number profiling in any research laboratory with access to real-time PCR instruments.

Procedure

To complete the qBiomarker Copy Number PCR Array procedure, start with genomic DNA isolated from fresh or frozen samples, or DNA from FFPE sections (QIAGEN QIAamp DNA Mini Kit or FFPE Tissue Kit is recommended). Optionally, if DNA sample quantity is limited, DNA from fresh or frozen tissues can be uniformly amplified using QIAGEN REPLI-g UltraFast Kit. Then, mix your DNA with the appropriate qBiomarker SYBR® Green Mastermix and aliquot the mixture into each well of the same qBiomarker Copy Number PCR Array plate containing predispensed locus-specific primer assays. Real-time PCR is used to determine the copy number status of a particular sample using the ΔΔCT method by comparing the test sample with a reference genome. An optional DNA sample quality control step can be performed immediately before the detection array setup.

 

 

Applications

Custom qBiomarker Copy Number PCR Arrays are highly suited for accurate profiling of copy number alterations or variations in a custom panel of genes, such as for verification of single nucleotide polymorphism (SNP) array or array-comparative genomic hybridization (aCGH) data.

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Kit Handbooks (1)
For real-time PCR-based copy number alteration and variation analysis
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