How to get copy number gain/loss from TCGA gene_level_copy_number

Question

[NB]

I want to get copy number gain/loss for each gene of a patient of a TCGA cohort. I downloaded gene_level_copy_number.tsv file. It contains absolute copy_number for each gene. How can I get gain or loss in copy number ?

I am not able to get normal (blood) sample copy number data too.

Answer 1

[Zhenyu Zhang]

Obviously cnv > 2 is gain, and cnv < 2 is loss for diploid

However, you might also want to consider sample ploidy, or consider local changes or changes in larger ranges. Basically, how to define gain and loss depends on your own definition of what neutral is, and there is no standard in the community. Alternatively, you can run tools like GISTIC.