Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue

Table 2

Assessment of fidelity of WGA of DNA extracted from breast cancer FFPE tissue. Amplification was performed by two methods: DOP and SCOMP. aCGH profiles of pre- (control) and post-amplification DNA samples were compared by correlation of raw aCGH data, segmentation and peaks of genomic alterations (means of three independent experiments).

	DOP versus control	SCOMP versus control	SCOMP versus control*	Control repeats
Correlation of nonsegmented profiles (Pearson)	𝑟=0.41 (<0.01)	𝑟=0.47 (<0.01)	𝑟=0.43 (<0.01)	𝑟=0.72
Gain/loss concordance of segmentation (% of genome length)	42.5% (<0.01)	68.5% (N/S)	67.8% (N/S)	78.6%
Peaks of amplified samples concordant to controls (% of all peaks)	72.2% (<0.01)	84.0% (N/S)	84.4% (N/S)	94.2%

Third column (*) represents the extended set of 6 SCOMP amplified samples. 𝑃 values in brackets are calculated for difference with control repeats by two-tailed exact Mann-Whitney 𝑈 test; N/S: not significant.