Simple question about deleted genes in TCGA CNV level 3 data

Question

[sumitguptabt]

Hi everyone,

I have a simple question about aCGH data: if you have two copies per gene and your log2 ratio is cancer/normal, how can you observe log2 = -4? That means 1/16... 16 original copies? I understand log2 = -1 (1/2).

Thank you!

Answer 1

[German.M.Demidov]

this is cancer, you measure a copy-number of a mixture of cells. if your tumor has a homozygous deletion, but 1/16of the sequenced cells are normal and diploid, you get 1/16 ratio.