Shallow and deep deletion

[Pawan Chinari]

Hello cBioPortal,

Recently I have been working with copy number alteration data in cBioPortal. 

In the FAQ page I saw that the deep deletion and shallow deletion are possibly homozygous and heterozygous deletion respectively.

Can I please know if there is a way to confirm that the shallow deletion are really heterozygous and deep deletion are homozygous deletion ?

Best Regards,

Pawan

[JJ Gao]

Hi Pawan,

The short answer is that there is no general way to accurately determine whether they are really heterozygous or homozygous. For more explanation, you might find the following two threads be helpful.

https://groups.google.com/g/cbioportal/c/aICrFOso96Q/m/AUfzr_62AQAJ

https://groups.google.com/g/cbioportal/c/LxPy_lVrKPA/m/grCD51JeCgAJ

Please let us know if you have any more questions.

Best,

-JJ

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/b457d092-52fe-4b59-b350-913dffefdf56n%40googlegroups.com.

[Pawan Chinari]

Hello JJ,

Thanks for your response and inputs regarding my query.

The two related posts are also helpful and they point to the CN segments tab for further details. I did explore that tab and for each gene of interest, I see the "Mean CN log2 value" for each sample and I could sort samples based on value in that tab. 

These are the additional queries that I have -

1. Is it possible to share further details on how best to use the CN segments tab to infer further details about the copy number loss ?

2. Is there a way to find which tumor genomes have undergone whole genome doubling ?

3. How do I infer sub-clonal deletion ?

It will be very helpful if you could shed some light on these queries as well, I look forward to hearing from you.

Best Regards,

Pawan

[Nikolaus Schultz]

Hi Pawan,

These are all good questions but very hard to answer using the data available in cBioPortal. 

If you are aware of a reliable source of WGD status for the TCGA PanCancer Cohort, we could incorporate that data.

That would help you a little bit in exploring CN segment data… keep in mind though that the segment values are not purity corrected, so sorting by log2 value does not always work. And unfortunately, we currently do not have reliable data in cBioPortal on clonality of events.

Niki.

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/20f9162b-c644-45f3-843b-92ca8973cd73n%40googlegroups.com.