Figure 3.

SNP and segmental copy number alteration. The percentage of SNP copy number values (A) and segmental copy number variations (B) was assigned to four groups and is illustrated. Log2-ratio values smaller than -0.6 are colored in dark blue, values ranging from -0.6 to -0.2 in light blue, log2-ratio values between 0.2 and 0.6 in orange and values greater than 0.6 in red. (A) Comparing the bars, one can see an increase in CNA from normal (∼ 4%) to transgenic (∼ 20 - 25%) and to tumor (∼ 40%). The copy number alterations in both SV40T/t cell lines are even higher compared to those in tumor (see Table S3A in Additional file 5 for entire CNA data). (B) In both normal samples about 76% of the calculated segments show no significant copy number alterations compared to the reference. An increase in CNA of 2% to 3% can be observed when comparing the transgenic samples to the normal samples, and by about 20% when comparing the tumor samples to the normal samples. The highest percentages of segCN were found in the Tumor1 and in the tumor sens. cell line. As observed in the number of segments the recurrent tumor samples form two groups with different magnitude of CNA (see Table S3B in Additional file 5 for entire segCNA data). A characteristic increase in segmental CN can be shown when comparing the stages of our model (see Figure 1).

Standfuß et al. BMC Cancer 2012 12:380   doi:10.1186/1471-2407-12-380
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