Question: Copynumber calculation problem
gravatar for jinxinhao1988
21 months ago by
jinxinhao198860 wrote:

Hi all,

I've got a question about copynumber calculation. I used Varscan2 and DNAcopy to call CNV. and got the results as follows:

This is the outcome of chr20.

As we can see that the mean of three logratio valuesis 1.2212. Since the logratio is LOG[(tumor copynumber)/(normal copynumber),2] and we assume that the normal copynumber is 2 copies. If tumor has gained 4 copies than normal sample, the logratio should be LOG[(2+4)/2,2]=LOG(3,2)=1.321928 The result we got(1.2212) is around 1.3219, and if this means that we can predict the tumor sample has gained 4 copies than normal sample.

I wonder if my calculation process is correct. Any suggestion is appreciated.

Thank you for your time.

Best regards,

cnv varscan2 • 499 views
ADD COMMENTlink modified 21 months ago by Kevin Blighe51k • written 21 months ago by jinxinhao198860
gravatar for Kevin Blighe
21 months ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

That's the output of the circular binary segmentation (CBS) algorithm from DNAcopy, after you had already ran VarScan, right? The ratios are therefore log (base 2).

1.2212 would therefore just be equivalent to an original ratio (tumour / normal) of just 2.331406:

2^1.2212 = 2.331406

So, the tumour is duplicated (x2).

Be careful, though, because you have deletions in between your segments (2^0.425 = 1.342573 and 2^0.4161=1.334316)

ADD COMMENTlink written 21 months ago by Kevin Blighe51k
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