cBioPortal is an interactive, web-based application for cohort analysis or molecular and clinical data review that users can run from their own computers by going here or through the HCI Bioinformatic Analysis Shared Resource website.
Access to public data is available to anyone behind the HCI firewall using their UNID and email password. Please note the HCI instance of cBioPortal is branded with our logo, which is on contrast to the public instance of cBioPortal hosted by MSKCC, ORIEN, or others. Please contact Aaron Atkinson or the Bioinformatics Core with any problems with credentials.
MSKCC offers an extensive series of cBioPortal online tutorials here. We will also be scheduling training seminars in the near term through HCI’s cBioPortal vendor “The Hyve”, or users can request assistance by contacting the Bioinformatics Core or Aaron Atkinson.
TCC and ORIEN Avatar Data
As part of the Translational Genomics initiative, HCI is part of the Oncology Research Information Exchange Network (ORIEN) Avatar ResearchTM program. Access to Avatar and TCC data is governed by the TCC IRB - 89989. To be added to that protocol please contact the Program Manager, Cristina Christenson, to be added to the IRB and complete your CITI and GCP training. With confirmation users are on the protocol together with completed training please send Cristina Christenson and Aaron Atkinson for access to those studies.
For the initial version we have uploaded both tumor and normal mutational data that includes single and complex nucleotide variants and MSI together with extensive clinical data extracted from REDCap and other sources. Subsequent versions will include additional data and refinements.
Future cBioPortal Versions/Data
Pending uploads will include both clinical and research grade results from Foundation and Tempus. In addition, value-added pipelines for copy number variation, loss of heterozygosity, off-target oncogenic viruses, and expansion of clinical data will follow shortly. There is also a potential to host mouse data. Please direct any recommendations or requests for future data availability as well to the Bioinformatics Core.
Private Group Data
As upload procedures and pipeline versions stabilize we can assist with additional private studies. Please contact the Bioinformatics Core to address those needs or similar data requests.