I have questions regarding the CNV calls calculated from TCGA.
What I understand, they used a CBS algorithm to find segments which are changed compared to a reference and the segment mean value is a measure of this change. In general, a mean log2 Ratio of the probe intensities.
Actually, the segments can be defined as deletions or duplications beyond a threshold (defined from you. Severel papers used +/-0.2).
Sample Chromosome Start End Number_of_probes Segment_Mean TCGA-CC-A8HV-01 chr1 51598 5999008 100 -0.0325 TCGA-CC-A8HV-01 chr1 6001979 6002289 153 -2.1264 TCGA-CC-A8HV-01 chr1 6002874 14443436 2 -0.0923
Afterwards, TCGA "re"calculated (to enhance?) the CNV detection results in cancer samples using the segmentation data with GISTIC2. Is this right?
I compared some of the segment mean data and the results from GISTIC2 (estimates) for cancer samples and found differences on gene and sample level.
If the GISTIC2 method provides better results do I have to use then a similar algorithm for non-cancer healthy samples and germline CNVs? And which are these tools? Can I use GISTIC, as well?