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qBiomarker Copy Number PCR Arrays

The qBiomarker Copy Number PCR Arrays are designed to measure the number of copies for a panel of genomic loci that are associated with signaling pathways or diseases. The PCR Arrays detect either germline (Copy Number Variations - CNV) or acquired changes (Copy Number Alterations - CNA) in copy number. The genomic loci are selected from comprehensive curated databases (such as the DGV database) and literature reviews based on their clinical or functional relevance and frequency of occurrence.

qBiomarker Copy Number PCR Arrays:

Diseases/Disorders Associated with CNA Diseases/Disorders Associated with CNV
Breast Cancer Alzheimer's disease New!!
Lung Cancer Schizophrenia New!!
Ovarian Cancer Intellectual Disability
Prostate Cancer Birth Defects
Gastric Cancer  
Pancreatic Cancer  
Pathway High Content Arrays*
Kinases & Phosphatases Oncogene & Tumor Suppressor Panel 384HC
WNT Signaling Pathway Autism Spectrum Disorders 384HC New!!
* Available as 384-well plates ONLY
Create Your Own - Custom Copy Number PCR Arrays

Why qBiomarker Copy Number PCR Arrays?

  • Pathway Focused: Profile copy number changes of important loci relevant to signaling pathways or disease
  • Superior Normalization: Integrated multi-copy reference assay for improved copy number determination
  • Simple and Accurate: qPCR procedure provides high sensitivity and wide dynamic range.
  • Designed for Routine Use: Copy number profiling to any lab with a real-time PCR instrument.

How qBiomarker Copy Number PCR Arrays/Assays Work

The procedure involves isolating genomic DNA (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 Copy Number PCR Arrays or Assays, and data analysis (using the qBiomarker Copy Number Data Analysis). An optional DNA sample QC step immediately before the detection array or assay setup allows the user to qualify the DNA samples.

To complete the Copy Number PCR Array procedure, start with genomic DNA isolated from fresh tissues, or DNA from FFPE sections. Then, mix your DNA with the included ready-to-use qBiomarker SYBR Green Mastermixes and aliquot the mixture into each well of the same plate containing pre-dispensed locus-specific primer assays. By performing real-time PCR, the copy number status of a particular sample is determined by comparing the allele specific Ct values between your test sample and a wild-type control sample (see qBiomarker Copy Number Data Analysis section for detailed principles).

Each PCR array contains a panel of SYBR® Green primer assays for a stringently selected set of pathway or disease focused copy number assays, and the qBiomarker Mutli-copy Reference Assay. The PCR Arrays are available in 96-well or 384-well plate formats; containing four technical replicates of each assay (see plate layouts below). qBiomarker Copy Number Assays and qBiomarker mastermixes have been pre-optimized hand-in-hand for SYBR® Green real-time PCR detection. 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.

Layout of Focused qBiomarker Copy Number PCR Arrays (23 locus/gene & 95 locus/gene formats)

Each qBiomarker Copy Number PCR Array contains primer assays for specific loci within the genome. The 96-well arrays have 23 locus -specific assays that are in technical quadruplicate (each assay is a different shade of blue in the top figure. In addition to the locus-specific assays, every array has the qBiomarker Multi-copy Reference Assay (purple wells) for normalization of input DNA. The 23 locus arrays are also available on 384-well plates, where the 96-well pattern is printed four times on the 384 well-plate. The 95-locus/gene arrays are only available for 384-well plates. The 95-locus specific assays are also "arrayed" in technical quadruplicate as shown in the lower plate above. The qBiomarker Multi-copy Reference Assay is also included in technical quadruplicate (shown in purple). The layout of the assays is different between the 23- and 95-locus arrays with detailed loading instructions described in the user manual.

The qBiomarker Copy Number PCR Arrays & Assays are intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

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Copy Number PCR Arrays
Custom Arrays
Copy Number Assays
Multicopy Reference Assay
qBiomarker Mastermix
Data Analysis