Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues

Table 2 Comparison of array CGH genome profiles before and after Bst amplification

		Number of clones	Normal gene content	Gene amplification	Gene deletion
*NSCLC 8 (2.9)**
Before Bst MDA		16277	12779	3450	48
Comparing after to before MDA	Matching clones	13725 (84.3%)	12592 (91.75%)	1131 (8.24%)	2 (<0.01%)
	Clones that changed	2552 (15.7%)	187 (7.3%)	2319 (90.9%)	46 (1.8%)
	% of abnormal clones before MDA			67.22%	95.83%
*NSCLC 9 (2.1)**
Before Bst MDA		23942	13538	9483	922
Comparing after to before MDA	Matching clones	13960 (58.3%)	13231 (94.8%)	729 (5.2%)	0 (0%)
	Clones that changed	9982 (41.7%)	307 (3.1%)	8754 (87.7%)	922 (9.2%)
	% of abnormal clones before MDA			92.31%	100%

Data from each of the four array CGH experiments (NSCLC 8 & 9 before and after Bst amplification) was normalized and replicate data points with standard deviation of log₂ ratio > 0.075 were excluded. Following, data was analyzed with aCGH-Smooth software, which identifies breakpoints and areas of gene amplification and deletion. The numbers presented refer to clones that were evaluable both before and after Bst amplification for each of the tumors. * Highest ratio of un-amplified sample/reference.

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