Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material

BMC Cancer

Table 5 pH of the hybridization buffer

Sample	Hyb. pH	Variance	StDev	DR	Max CGHseg	Correlation
FFPE tumor 2	6	0.07	0.04	1.4	0.6	0.98
FFPE tumor 2	6	0.08	0.04	1.6	0.7
FFPE tumor 2	7	0.09	0.04	1.5	0.7	0.97
FFPE tumor 2	7	0.08	0.05	1.2	0.6
FFPE tumor 2	8	0.08	0.04	1.3	0.6	0.94
FFPE tumor 2	8	0.10	0.05	1.7	0.8

Variance (Variance), standard deviation (StDev), dynamic range (DR), the highest log2 ratio calculated by CGH-segmentation (Max CGHseg), and Pearson Correlation (Correlation) for testing the effects of pH (Hyb. pH) of the hybridization buffer on a CGH profile of FFPE tumor #2. The log2 ratios associated with homozygous deletions vary widely since they depend heavily on dividing very small intensities by large intensities. This can have disproportionate impact on the dynamic ranges, therefore only the highest ratio is taken as a measurement for the dynamic range (Max CGHseg).

ISSN: 1471-2407