Hi there, I was running some queries on cBioPortal and in parallel looking at the data_CNA.txt files and there is a huge discrepancy in the CNA gene lists. On cBioPortal there are over 1600 genes with CNA while on the data_CNA.txt file there are only 900 genes. The sample ID's also don't match up between these two platforms. Both platforms signify using GENIE 9.1, however, I am unsure about which one to use as each gives different results. Why would there be such differences in the data when both are GENIE 9.1 and the platforms are linked? All the best, Hannah

Created by hbergom
Hi @hbergom , Sorry for the delayed reply. Looking at the CNA genes and sample IDs from release 10 (current version available on [http://www.cbioportal.org/genie](http://www.cbioportal.org/genie)), I find the following counts: {| class="border" ->**Source**<- | ->**Number of unique genes**<- |->**Number of rows in file**<-| ->**% of samples IDs in [data_clinical_sample.txt](https://www.synapse.org/#!Synapse:syn25896087)**<- --- | --- | --- | --- | [data_CNA.txt](https://www.synapse.org/#!Synapse:syn25896085)| 935 | 936 | 100 cBioPortal | 915 | 1685 | 100 |} Are you sure you were looking at the number of unique genes in each of the files rather than the number of rows? And can you share an example of a sample ID that was inconsistent between the two files? Thanks, Haley

Inconsistencies between Synapse GENIE 9.1 downloaded data and GENIE 9.1 cBioPortal data page is loading…