Numeric focal-level Copy Number Variation (CNV) values were generated with “Masked Copy Number Segment” files from tumor aliquots using GISTIC2, on a project level.
Only protein-coding genes were kept, and their numeric CNV values were further thresholded by a noise cutoff of 0.3:
- Genes with focal CNV values smaller than -0.3 are categorized as a “loss” (-1)
- Genes with focal CNV values larger than 0.3 are categorized as a “gain” (+1)
- Genes with focal CNV values between and including -0.3 and 0.3 are categorized as “neutral” (0).
In a diploid genome, a single-copy gain in a perfectly pure, homogeneous sample has a copy ratio of 3/2. In log2 scale, this is log2(3/2) = 0.585, and a single-copy loss is log2(1/2) = -1.0.