Question: Copynumber calculation problem
0
15 months ago by
China/Beijing
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:

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.

Best regards,

cnv varscan2 • 388 views
modified 15 months ago by Kevin Blighe42k • written 15 months ago by jinxinhao198860
1
15 months ago by
Kevin Blighe42k
Guy's Hospital, London
Kevin Blighe42k 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`)