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

 

 

aDNA 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.