Focal copy number alterations in IGV
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3.2 years ago
neuro3030 ▴ 50

I am visualizing a segmented copy number file (.seg) from the TCGA in IGV.

From the example screenshot below, the gene RAC2 shows loss in a few samples (blue). Assuming all of the samples that are blue for RAC2 are significant using GISTIC, how do you interpret the sample with a portion of the gene in blue (sample is about midway down)?

For instance, assuming the raw score for the blue portion is -0.6552, and the white portion (corresponding to the other half of the gene) is -0.0054, how can you determine which portion of the gene is significantly deleted? Are both the blue and the white? Just the blue portion?

thanks and any help would be great

enter image description here

igv tcga CNA copy number • 1.2k views
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Did you try looking at the raw SCNA data from TCGA?

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