Question: How to interpret this CNV results
gravatar for Jackie
4.0 years ago by
United States
Jackie70 wrote:

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:

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.








affymetrix cnv snp 6.0 • 2.6k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Jackie70
gravatar for Irsan
4.0 years ago by
Irsan7.0k wrote:
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.
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Irsan7.0k

Thanks, that helps!!

ADD REPLYlink written 4.0 years ago by Jackie70
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