Validation of quantitative PCR assay
|
Marker |
Cytogenetic location |
Test DNA |
Reference DNA |
Test/reference DNA copy number ratio |
Fluorescence Ratio from cDNA microarray |
Relative DNA copy number by quantitative PCRa,b |
|
F8C |
Xq28 |
45, XO |
46, XX |
0.5 |
0.5 |
0.4 |
|
F8C |
Xq28 |
46, XX |
46, XX |
1.0 |
1.0 |
1.0 |
|
F8C |
Xq28 |
47, XXX |
46, XX |
1.5 |
1.3 |
1.6 |
|
F8C |
Xq28 |
48, XXXX |
46, XX |
2.0 |
1.5 |
1.8 |
|
F8C |
Xq28 |
49, XXXXX |
46, XX |
2.5 |
1.8 |
2.1 |
a
DNA copy number determination by quantitative PCR (S. Gelmini et al., 1997, Clin Chem 43, 752-8) was performed using a TaqMan instrument (ABI), with PE Applied Biosystems TaqMan PCR reagents and protocols. Gene-specific primers and fluorogenic probes were designed from 3’UTR DNA sequences using PrimerExpress (ABI) software. Relative gene copy numbers were derived using the formula 2DCT where DCT is the difference in amplification cycles required to detect amplification product from equal starting concentrations of normal genomic DNA compared to tumor genomic DNA (R.M. Pitti et al., 1998, Nature 396, 699-703). All assays were performed in duplicate; mean values are reported. bQuantitative PCR results were normalized to beta tubulin, which was known to be present in equal DNA copy number for all non-tumor samples.