How to interpret the gene level copy number file generated by ASCAT2 on GDC?

Question

[little10214]

Dear all,

I download some copy number files on GDC, but I don't know how to interpret them.

For example, in project TCGA-COAD, case ID TCGA-AA-3562 has a file (TCGA-COAD.d6976aba-7f10-4991-a4b1-755b06af66bf.gene_level_copy_number.tsv), and this file shows that copy number 3 has the highest frequency.

In my experience, copy number 2 should has the highest frequency. And for copy number <2, I say it is copy number loss, for copy number >2, I say it is copy number gain.

So, my question is how to interpret the gene level copy number file generated by ASCAT2 on GDC?

Thank you very much.

[loughrae]

Hi, did you ever find an answer to this? I downloaded two LUSC files and also saw that most genes were in 3 copies. It's possible these are actually triploid, as I looked at a sample from a cancer that's known to be generally diploid and it was mainly in 2 copies, but I don't want to assume. I can't seem to find documentation on how these files were prepared and what the columns mean.

[Kevin Blighe]

I have made an attempted answer, here: A: Understanding TCGA's ASCAT copy number data