Hi,
I am trying to access gene-level copy number amplification/deletion data across centers - the data release guide indicates that this data is available for the UCSF panels/pipelines ('gene_level_cna' column in table 4, unless this is referring to something else), but I am not finding it anywhere within the data_CNA.txt file, and none are listed on cbioportal. This table also lists that WAKE gene-level CNA data should not be available, but it is listed within the data_CNA file and on cbio. Please let me know which centers have gene-level CNA data available on genie/cbio and how to access.
Thanks in advance!
-Madison
Created by Madison Darmofal maddarm Hi @maddarm ,
Thanks for pointing out these data discrepancies. We will need to investigate more, but if it is not within the data_CNA.txt file, this is most likely an annotation error OR the panel does technically cover CNA, but it is not uploaded for the GENIE consortium.
Edit: UCSF data is located within the `data_cna_hg19.seg` file, but they do not have the discrete copy number fields. we are looking to correct the WAKE assay information - thanks!