ploidy status of tumor samples

[Hindriksen-2, S.]

Hi there,

I have a couple of questions about the ploidy status of the tumor samples in the cbioportal database.

1. Are the tumor classified as being eulpoid or aneuploid? Is karyotyping performed for these samples?
2. What does the CNA_CLUSTER_K4 stand for (under: more about this tumor)?
3. I thought I could perhaps derive ploidy status from the fraction of copy number altered genome. However, in one particular case (http://www.cbioportal.org/public-portal/case.do?cancer_study_id=stad_tcga&case_id=TCGA-BR-8680) this value is only 6%, but under the header 'more about this tumor' absolute extract ploidy is 1.99 which made me think that maybe the tumor is tetraploid. What exactly do these different values mean and where does the difference come from?

Thank you so much in advance.

Bets wishes,

Sanne

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[Nikolaus Schultz]

Dear Sanne,

1 - No, there is no karyotyping performed on TCGA samples (or any other samples in cBioPortal that I know of)

2 - CNA_CLUSTER_K4 refers to cluster membership based on copy-number (full results to be published soon, the TCGA stomach adenocarcinoma paper is in review)

3 - A ploidy of 1.99 (these numbers are from the ABSOLUTE algorithm and not available for all samples) indicates that the tumor is near diploid (2.0). 

I hope these answers are helpful.

Niki.

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