I have some data on Copy Number Variation (SNP chip) for a population of samples.

In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another set (considered as controls) which do not. The cases have not a matched-control. All the controls are taken as a random sample from the population that does not present the disease.

For both cases and controls I have the copy number of some regions. How can I compute the copy number change in cases, such as in GDC?

Should I use (as described in the previously linked page):

performing tangent normalization, which subtracts variation that is found in a set of normal samples

and do you know of any tool to perform this computation?

The data I have is formatted in this way:

Sample_ID   chrom      start           end  CN
Sample11       19   11991477      12133823   1
Sample11        2   52260564      52431658   1
Sample12        7    5721757       5896192   3
Sample13       10    2269963       2473585   3

1 Answer 1


GISTIC does exactly this, and is very possibly the tool used in your link above.

The input files need to be in a different format than what you currently have, but if you're using a SNP6 array, there are guides out there that will tell you how to get the proper files from your .cel files.

  • $\begingroup$ Thanks. Unfortunately the data has been presented to me in this format. I could try to get the original .cel files but I think they'll be unavailable. Do you know of any methodology to get the same result but with the data format I provided in the question? $\endgroup$
    – gc5
    Commented May 24, 2018 at 14:13
  • $\begingroup$ Well, you could hack together something simple in python or R that takes all the controls, creates lists of amplified/deleted regions, then removes the CNVs in the cases that intersect those regions (maybe by a minimum amount, like 30%). It kind of depends on how perfect you want your analysis to be. Removing the regions that are "variable" in the controls is pretty easy. $\endgroup$ Commented May 24, 2018 at 15:40
  • $\begingroup$ I think it may be the only solution in this case. Thanks $\endgroup$
    – gc5
    Commented May 24, 2018 at 15:52

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.