How to interpret this CNV results

Question

[Jackie]

I have downloaded a CNV file from a public database, and the platform on which the CNVs are called is Affymetrix SNP 6.0. Please take a look at the data at this link: https://docs.google.com/spreadsheets/d/10oIX-fD_kyANkbdjEf0piJxq3Nx9x5OBji1HVHrGrOo/edit#gid=0.

This is the result for a tumor-normal paired sample. don't know what tool was used to call CNVs and generate this file.

I don't have experiences handling any CNV data before, my questions are:

1. What does seg.mean mean? Is this an indicator of whether it's an amplification or deletion? How to tell?
2. What's listed above are all the entries in that file, so I assume these are all the CNVs identified across the genome. It seems that, for some chromosomes, i.e., chr1, the segment(s) identified are huge (chr1:61723-249224376), does that mean, basically the whole chr1 is amplified or deleted? Can someone with much CNV experience tell me, if this kind of entry looks a valid result.

Thanks,
-J

Answer 1

[Irsan]

Each entry/row/record is a contiguous piece of the genome with equal copy number. This is called a segment. The seg.mean is the log2(tumor / control) signal also called the log-ratio. A log ratio of 0 means tumor and normal have equal copy number, bigger than 0 means tumor has more copies and vice versa. Indeed in cancer genomes it often happens that complete chromosomes are altered. Often People use thresholds for calling a segment to be altered from 0. If you save this file as a .seg file (delete the first column) you can open it in a program called IGV and browser though the results.

[Jackie]

Thanks, that helps!!