Discrete Copy Number Alteration

[Herty Liany]

Dear All,

I would like to seek an advice on how to convert copy number alteration results from GISTIC 2.0 onto discrete copy number alteration in the scale of -2,-1,0,1, and 2 as given in cBioportal?

I understand that GISTIC 2.0 produces GISTIC Scores file whereby the scores file lists the q-values [presented as -log10(q)], G-scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions.

May i know how to convert GISTIC 2.0 output onto discrete copy number alteration as found in cBioportal?

Thanks very much.

Regards,

Herty

[Benjamin Gross]

Hi Herty,

Perhaps others on the team or community can comment, but I believe our discrete GISTIC data comes via running GISTIC (upstream) on a platform like GenePattern (genepattern.org) which provides discrete data in the following manner:

...by applying both low- and high-level thresholds to the gene copy levels of all the samples. The entries with value +/- 2 exceed the high-level thresholds for amps/dels, and those with +/- 1 exceed the low-level thresholds but not the high-level thresholds. The low-level thresholds are just the 'amplifications_threshold' and 'deletions_threshold' noise threshold input values (typically 0.1 or 0.3) and are the same for every threshold.
By contrast, the high-level amplification (or deletion) thresholds are calculated on a sample-by-sample basis and are based on the maximum (or minimum) median arm-level amplification (or deletion) copy number found in the sample. The idea, for deletions anyway, is that this level is a good approximation for hemizygous given the purity and ploidy of the sample. 

Regards,

Benjamin

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[Herty Liany]

thanks very much Benjamin:)

Best,

Herty