Relationship between ploidy and CN values

[Ryan Morin]

Hi

I have a sample that gets a ploidy estimate of 4.8 for its best fit and yet the copy number values are mainly between 1 and 3 (mostly 2). I am not sure how to interpret the meaning of this. Should this be considered as 2x the reported copy number for cancer cells? For example, when CN2 is reported, this means that the tumour cells have 4 copies of that region, CN3 6 copies, CN4 8 copies, etc?

"cellularity" "ploidy.estimate" "ploidy.mean.cn"

0.55 4.1 2.41370999024359

0.89 4.8 2.41370999024359

0.96 6.2 2.41370999024359

Thanks

Ryan

[Francesco Favero]

Hi Ryan,

yes, it can happen then the ploidy estimated parameter and the average of the copy number diverge quite a lot. I didn’t investigated thoroughly the causes, it might change if you use the median normalisation instead of the default mean method. However if the profile looks OK in a visually  inspection I wouldn’t re-run the analysis.

The mean of the copy number is always the preferred ploidy value, so in your case 2.4.

The estimated ploidy value inidicate wich copy number correspond to the normalised average depth ratio (1). So I assume your depth-ratio profiles are skewed at values lower then 1, right?

Best

Francesco

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[Ryan Morin]

That makes sense. The normalized depth ratio is definitely low. If ploidy is in fact 2.4 rather than the higher value, does this otherwise imply a low purity tumour? Is there a way to obtain the cellularity if I opt for a lower ploidy value?

Best,

Ryan

[Ryan Morin]

I think I have answered my own question:

cp_table$cellularity[cp_table$ploidy==2.4] 

This gives the cellularity estimate for the ploidy that is in agreement with the CN profile predicted.

[pin wu]

Hi Ryan,

I encountered the same problem as you, for example the sample's polidy.estimate value  is 4 but the polidy.mean.cn value is 2. In addition, I also found that in the file genome_view.pdf, the B-allele  copy number is almost zero. Do you have the same problem? Do you have any explanation for this?

Best regards,

wupin

在 2016年8月25日星期四 UTC+8上午9:02:26，Ryan Morin写道：