Classifying alterations?

[Indianhedgehog]

Hello, Couldn't find much online about the classification of the alterations. But, from what I understood, based on the "*.segments.txt" file.

1) TCN = nMajor + nMinor = to get the total TCN of the segments. 2) then,ploidy = TCN - ascat.output$ploidy 3) Anything greater than ploidy can be classified as Duplication and less as Deletion.

Please correct me if i am wrong!

Thank you

[tlesluyes]

Hi @Indianhedgehog,

1. Yes if TCN stands for total copy number of a given segment

2. and 3. Not sure what you are trying to do here. The standard baseline for humans is 1+1 (except for the nonPAR region of X in males which is 1+0). Anything different from 1+1 is a CNA (in the context of somatic alterations detected by ASCAT, I'm not talking about CNVs here). Also, WGD should be considered to stratify pseudo-triploid tumours, where 2+1 would be a gain in diploid tumours and would be a gain + loss in WGD tumours (1+1 -> 2+2 -> 2+1).

Cheers,

Tom.

[Indianhedgehog]

Hi Tom, Thanks much.

Is this correct? Can you please check?

Sample            chr   start                         end       nmjor  nminor   tcn class
tumor_H021-2RH2K9   21  16176201    16255628    3   2   5   AMP
tumor_H021-2RH2K9   21  16255960    33842077    3   0   3   LOH
tumor_H021-2RH2K9   21  35481423    48108278    3   0   3   LOH
tumor_H021-2RH2K9   22  16964487    22292995    6   2   8   AMP
**tumor_H021-2RH2K9 X   293788              386679  5   0   5   AMP**
tumor_H021-2RH2K9   X   1393435           1480559   5   3   8   AMP

regarding the samples with WGD events i.e ploidy > 4 how should I classify them? For example, like this?

Sample                          chr start                         end       nmjor  nminor   tcn class
tumor_H021-2RH2K9   21  16176201    16255628    2   1   5   AMP;DEL
tumor_H021-2RH2K9   21  16255960    33842077    3   0   3   LOH

Thank you so much Rajesh

[tlesluyes]

Hi @Indianhedgehog,

You may want to stratify gain versus amplification and loss versus deletion as these all have different meanings. Also, 3+0 in a non-WGD case is both a gain and LOH, not only LOH. For WGD, it does not only relates to tumours with ploidy>4, we've seen plenty of nearly diploid tumours where the vast majority of the genome is 2+0 so they go diploid -> haploid -> diploid through WGD. For cases with WGD, 3+0 is still gain + LOH whereas 2+1 is a loss (1+1 -> 2+2 -> 2+1) but this highly depends on how you want to classify CNAs. In cases with WGD, all segments should be labelled as 'WGD' in your 'class' column, then your expected baseline is 2+2 (maybe 4+4 with 2 WGDs, and so on) and you can see how nMajor/nMinor information fit with your baseline.

Cheers,

Tom.

[Indianhedgehog]

Hi @tlesluyes ,

I was thinking of classifying the segments as something like this.

https://www.nature.com/articles/s41586-022-04738-6#Sec9

What do you think? I believe it should be applicable to WES and WGS data. Sorry if I am asking too many questions, I am new to this and still learning.

Thank you Rajesh

[tlesluyes]

Hi @Indianhedgehog,

Looks good. As indicated in my previous comment, such a classification does consider LOH plus a copy-number event, not just LOH. It also stratifies shallow deletions (losses) versus homdels and gains versus amplifications. This can be applicable to both WES and WGS (as well as SNP arays and targeted seq).

Cheers,

Tom.

[Indianhedgehog]

Thank you !! 😃