Hey Kevin, thanks for your comments
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nazaninhoseinkhan
several copy number alterations in the same position in an individual
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
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Ram
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nazaninhoseinkhan
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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
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Kevin Blighe
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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.