CNA Coding Documentation

From cBioPortal Docs:

profile_description: A description of the copy number data, e.g., "Putative copy-number from GISTIC 2.0.

Values:

• "-2" = homozygous deletion;
• "-1" = hemizygous deletion;
• "0" = neutral / no change;
• "1" = gain;
• "2" = high level amplification."

From CMO (2022-11-05) The mapping follows the same nomenclature as GENIE (which follows cBioPortal vocab), this is the mapping:

• "-2" is a deep loss, possibly a homozygous deletion
• "-1" is a single-copy loss (heterozygous deletion)
• "0" is diploid
• "1" indicates a low-level gain
• "2" is a high-level amplification.

For -1.5 entries, we actually convert them to -2 instead of -1.

In the package, any CNA event (1, 2, -1, -1.5, -2) will be counted as an event in the binary matrix unless high_level_cna_only is changed to TRUE

Sources 2022-11-05 Email with Ritika https://docs.cbioportal.org/file-formats/#discrete-copy-number-data