Affymetrix | Panomics Solutions
Quantitative Biology Delivered.

QuantiGene DNA Multiplex Assay: Overview

The QuantiGene Plex DNA Assay provides DIRECT from lysate measurement of 3 to 33 target DNAs per well with excellent copy number discrimination. 

Unique Benefits

  • Quantitatively measure multiple DNA targets simultaneously with unparalleled accuracy and precision
  • Excellent copy number discrimination using clinically proven branched DNA (bDNA) signal amplification technology
    • Direct quantitation of target DNA - avoid biases associated with DNA isolation and PCR amplification
    • No assay optimization required
    • High precision - coefficient of variation (CV) of less than 15% for entire process (sample isolation to results)
    • Distinguish single-copy differences in DNA copy number - linear assay with low CVs

Accurate results in a variety of samples

  • Compatible with plant and animal tissues, FFPE tissue sections, whole blood, cultured cells, isolated DNA and more

Validated panels

  • Each panel is functionally validated


  • Validation of CNVs from chromosomal regions identified by comparative genomic hybridization (CGH) experiments
  • Validation and testing of disease biomarkers (e.g. cancer, neurology, autoimmune disease, etc.)
  • Targeted drug metabolism testing (e.g., DMET™ studies)
  • Animal and plant breeding
  • Identification of transgenic, knockout animals and plants
  • Animal and plant zygosity testing
  • Genetic authenticity testing (cell lines, animal and plant tissues, foods, etc.)
    Viral, fungal, and bacterial testing

Single Copy Gene Resolution

QuantiGene Plex DNA Assays can distinguish as little as 20 percent differences in DNA copy number and have the ability to quantitate single copy number variations.
The application below shows single-copy gene resolution and the ability to discriminate single-copy differences at the lower end of the linear range of the assay. The QuantiGene Plex DNA Assay has a 3 log linear working range and can detect up to hundreds of DNA copies.

Figure 1: Human BAC fibroblast growth factor receptor 1 (FGFR1) DNA (from 1.3 pg [0.5 copies] to 18.2 pg [7 copies]) was spiked into a constant amount of mouse genomic DNA (180 ng or 30,000 cell equivalents, based on 6 pg mouse DNA/cell). The copy number equivalents of FGFR1 were quantified using the QuantiGene DNA Assay. From 0.5 to 6 FGFR1 DNA copy equivalents per cell were easily distinguished.

Assay Specifications

  Limit of Detection   ≤ 10,000 copies/assay wella
  Limit of Quantitation   ≤ 20,000 copies/assay wellb
  Linear Dynamic Range   ≥ 2.5 logsc
  Assay CV   ≤ 15% intra-assay;≤ 20% inter-assay
  Compatible Sample Types   Cultured cells, bacteria, whole blood,
  PAXgene blood or dried blood spots,
  fresh/frozen tissues(human, animal or plant),
  FFPE samples, purified DNA
  Assay Format   96-well plated
  Targets/well   3 - 33
  Automation Compatible

a Defined as signal greater than background plus three standard deviations of the background.
b Defined as the signal just above the lowest signal that obtains an 80-120% spike recovery.
c Defined as the assay window that consistently achieves a 80-120% accuracy of fold change.
d Contact Affymetrix for information on a 384-well version.
e Batch or full automation using standard automation equipment. Contact Technical Support for protocol details and assistance in setting up your automation system.