Amplification cut off points

[Matthew Simcock (Student)]

Good Morning,

 

I was wondering whether you could help, I am completing my PhD revisions and one thing the examiners want to know is the cut off that cBioportal uses to signify amplification?

 

I am looking at SGK1 in Prostate cancer samples.

 

Any additional information you have would be massively helpful,

 

Kind Regards,

 

Matt

[Sander Rodenburg]

Hi Matthew,

Amplifications are often calculated using the GISTIC algorithm. See the GISTIC documentation. When an alternative method is used from GISTIC, the thresholds may be calculated differently but cBioPortal does not verify this. Discrete CNA data is just loaded as a matrix of integers ranging -2 to +2.

GISTIC imposes a low-level threshold (shallow gains/dels) and high-level threshold (amplifications/deep deletions). The low level threshold is static, typically 0.1 or 0.3 and the high-level thresholds are based on the arm-level copy number values in the sample. According to the documentation, GISTIC produces output files containing the exact high-level thresholds used for each sample.

Best,

Sander Rodenburg

Data Engineer / cBioPortal specialist

E sanderr...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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