Figure 2

FFPE DNA characterization by QFI-PCR and fluorescence-based assays from 165 tumor DNA samples. (A) Distribution of FFPE DNA quantification using QFI-PCR and the fluorescence-based Qubit dsDNA HS assay from 5 ng bulk DNA input as determined by NanoDrop spectrophotometry. A total of 27 samples were undetected by fluorescence assay (<0.1 ng/μl, equivalent to 2% ‘functional’ DNA templates; shown as open circles); these samples produced between 0.03 and 2.5% QFI using qPCR. Five samples were undetected by QFI-PCR and produced between 2.4 to 4.0% of the spectrophotometrically determined DNA concentration using Qubit. Five samples were undetected using both methods (not shown in figure). (B) A scatterplot of QFI-PCR and Qubit relative DNA quantification revealed a linear trend for templates with at least 3% QFI (R = 0.66; N = 86). No correlation, however, was observed for the poorest quality samples (R = 0.07; N = 42; shown as open circles).