several copy number alterations in the same position in an individual

Question

[nazaninhoseinkhan]

Dear all, I have a question. After performing somatic copy number alteration analysis using GISTIC, there are several SCNA identified for the same patient in the same position and the same chromosome (patients ID, Chr name, Start, End):

TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  104510915
TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  107612922
TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  108595568
TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  109150479
TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  109720212
TCGA-BJ-A2N9-01A-11D-A18E-01    7   705284  144276996

Can you explain how I can interpret these cases?

Does it mean that there is a heterogeneity in the samples?Different cells has different alterations?

I will appreciate any help

Nazanin

[Ram]

FYI I have removed the "same patient" "same position' etc. tags. Tags on biostars are useful to pick posts by topic - they are not to be used like hashtags on Twitter/Instagram.

Answer 1

[Kevin Blighe]

Hey Nazanin, I cannot be sure about the answer without fully understanding the internal coding of the GISTIC algorithm. However, obviously, some tumour cells exhibit aneuploidy, whereby chromosomes can be duplicated even up to >90x; so, perhaps this is one reason?

The other reason, of course, is just as you mentioned, i.e., the typical heterogeneity that is observed in any bulk tumour tissue. The heterogeneity explanation is the more likely one, in my opinion.

Kevin

[nazaninhoseinkhan]

Hey Kevin, thanks for your comments