CNA calling using Affymetrix SNP Array 6.0

Question

[LC]

Hi Everyone,

I have a question regarding the use of Affymetrix SNP Array 6.0 to detect CNAs. This process was carried out with the data that I am working with and after processing with DNAcopy the data looks like this:

As you can see the start locations for a number of CNAs on chromosome 17 is 527 while there end location varies. Shown here is only a fraction of the cases where this occurs. I was just wondering why this would be the case, is it not unusual for a CNA to start predominantly in one place? Or is this just an artifact of the array/methods used?

Thank you so much for any help you can provide.

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

Answer 1

[Kevin Blighe]

What is the source of the DNA, and how did you execute DNAcopy? I have previously used the Affymetrix SNP 6.0 on breast cancer samples...

[LC]

Hi, the data that I'm working with is the Metabric breast cancer data, so it's already been processed by other people. I myself didn't run DNAcopy.

[Kevin Blighe]

Oh right, from Curtis, Caldas, and co... Yes, they used DNAcopy - I met their bioinformatician in Cambridge, UK. His office was extremely small, almost like a dark closet.

The finding is probably related to the fact that different METABRIC tumours have different copy number at that interval - I'm not 100% certain. Loss at the chromosomal ends is quite common and, evidently, in some tumours, the loss extends up to 18 megabase along the chromosomal arm.

[LC]

Yeah that's the one!

That makes sense but is there a reason they all start at the same location? Is it to do with probe positions on the affymetrix array? Is there a probe at position 527 on chr 17?

Sorry if these are obvious questions I'm trying to get my head around CNA calling using arrays.

[Kevin Blighe]

Could be related to tumour heterogeneity and also the probe positioning on the array - indeed.