Figure 1: QuantiGene Plex DNA Assay in SKBR3, normal skin fibroblast, and MDA-231 cells. The ratio of SKBR3 to control copies was ~7. Two other genes on chromosome 17 were amplified and one gene was not. Control genes on chromosomes 1, 5, and 8 in SKBR3 breast cancer cells and control cell lines did not show any DNA copy number amplification.
QuantiGene Plex DNA CNV Assay Data & 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|
| 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.
The QuantiGene Plex DNA Assay offers reproducible and reliable results from a variety of starting materials. In this example, purified genomic DNA as well as lysates from seed and leaves were prepared from the same transgenic lettuce plant. The samples were assessed using the QuantiGene Plex DNA Assay with a panel of 10 targets. After normalization to gene 10, the results indicated the same ratio of gene copy number for each of these genes in all three samples.
Figure 3: Results of the QuantiGene Plex DNA Assay with different sample sources, including purified genomic DNA (gDNA) as well as lysates from seeds (seed) and leaves (leaf) of a transgenic lettuce plant. Normalized data with gene 10 are shown to indicate the relative DNA ratio.
Drug metabolism panel – DNA copy number
The QuantiGene Plex DNA Assay offers single-copy number discrimination for accurate classification of copy number variation in drug metabolism studies. The assay can be used as a companion to Affymetrix DMET™ Arrays or to validate array data. In this case, a nine plex assay was used to quantify six target genes, SULT1A1, GSTM1, CYP2D6, CYP2A6, GSTT1, and UGT2B17, normalized using three genes (RPPH1, SNAP25, and PMP22) in 20 Coriell samples (nine Asian, six Yoruba, and five Caucasians) and one ParagonDx sample (Caucasian). The results were analyzed using the background-subtracted average MFI value of target and control genes. The target genes’ MFI value was normalized by the geometric mean of the three control genes’ MFI. The control genes are considered to be N=1. In the data shown, F: female; M: male; J/M: Japanese male; J/F: Japanese female; C/M: Chinese male; and C/F: Chinese female.
For Research Use Only. Not for use in diagnostic procedures.