Question

[Greer, Yoshimi (NIH/NCI) [E]]

cBioPortal, 

To whom it may concern, 

 

Thank you for hosting wonderful webinars. It’s been very helpful.

 

I would like to ask you a question. 

When you say “deep deletion”, that means homologous deletion?

So why there is some detectable mRNA expression? 

 

As an example, please see attached – this is MDA-MB231 cell line data from NCI-60.

CD274 shows DeepDel in CNA, but there is detectable mRNA expression? Also mRNA Expt panel showing 93%. What does 93% mean?

 

Thank you for your response in advance, 

 

Yoshimi

 

 

-- 

Yoshimi Endo Greer, MD, PhD

Staff Scientist

Women's Malignancies Branch

CCR/NCI/NIH

Bldg.10, Room 4B50

9000 Rockville Pike

Bethesda, MD 20892, USA

240-858-3275 (Tel)

301-451-2745 (Fax)

Email: gre...@mail.nih.gov

URL: https://ccr.cancer.gov/yoshimi-endo-greer

 

[Nikolaus Schultz]

Hi Yoshimi,

Part of your answer is provided here in the FAQs:

https://www.cbioportal.org/faq#what-do-amplification-gain-deep-deletion-shallow-deletion-and--2--1-0-1-and-2-mean-in-the-copy-number-data

And right below, here:

https://www.cbioportal.org/faq#what-is-gistic-what-is-rae

These calls are automated and are therefore subject to errors. The issue is further complicated by the fact that many tumor genomes have undergone whole genome doubling and now have four copies to lose in total. We therefore call these events “deep deletions” instead of homozygous losses. 

Another complication is the possibility of a partial homozygous loss - in these cases a part of the gene may be fully lost, but if the start site and some of the early exon are still present, that part may still be expressed and measurable on the mRNA level.

In your case, however, it looks like an overcall and this is just a heterozygous loss of CD274. You can inspect the copy-number pattern here in the CN Segments tab. There is clearly a deletion at the CD274 locus (-0.55), but other parts on the same choromsome have even deeper deletions (-1.18, visible when you zoom out).

https://bit.ly/3fJEgV0

And to answer your last question: 93% expression means that the expression of the gene is higher than in 93% of all other samples in the study (93rd percentile). In this case, this is another indicator that the gene is not deleted.

I hope this was helpful.

Niki.

-- 
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/MN2PR09MB335817F08A7560B639969E14ECA10%40MN2PR09MB3358.namprd09.prod.outlook.com.
<20200508 YEG question cBioPortal .jpg>