Abstract 4256: cBioPortal for Cancer Genomics

• Published in: Cancer research (Chicago, Ill.) Ill.), 2023-04, Vol.83 (7_Supplement), p.4256-4256
• Main Authors: de Bruijn, Ino, Mazor, Tali, Abeshouse, Adam, Baiceanu, Diana, Carrero, Stephanie, Garcia Lara, Elena, Gross, Benjamin, Higgins, David M., Jagannathan, Prasanna K., Kumari, Priti, Kundra, Ritika, Lai, Bryan, Li, Xiang, Lindsay, James, Lisman, Aaron, Madala, Divya, Madupuri, Ramyasree, Ochoa, Angelica, Özgül, Yusuf Ziya, Plantalech, Oleguer, Rodenburg, Sander, Satravada, Baby Anusha, Sheridan, Robert, Sikina, Lucas, Singh, Jessica, Sumer, S Onur, Sun, Yichao, van Nierop, Pim, Wang, Avery, Wilson, Manda, Zhang, Hongxin, Zhao, Gaofei, van Hagen, Sjoerd, Dogrusoz, Ugur, Heath, Allison, Resnick, Adam, Pugh, Trevor J., Sander, Chris, Cerami, Ethan, Gao, Jianjiong, Schultz, Nikolaus
• Format: Article
• Language: English
• ISSN: 1538-7445; 1538-7445
• DOI: 10.1158/1538-7445.AM2023-4256

cBioPortal for Cancer Genomics is an open-source platform for interactive, exploratory analysis of large-scale clinico-genomic data sets. cBioPortal provides a suite of user-friendly visualizations and analyses, including OncoPrints, mutation “lollipop” plots, variant interpretation, group comparison, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization. The public site (https://www.cbioportal.org) is accessed by >35,000 unique visitors each month and hosts data from >350 studies spanning individual labs and large consortia. In addition, at least 74 instances of cBioPortal are installed at academic institutions and companies worldwide. To better support all users, we unified our documentation (https://docs.cbioportal.org) and added a user guide and an ongoing series of ‘how-to’ videos to address common questions. In 2022 we added 32 studies (>38,000 samples) to the public site. In addition, we added a nonsynonymous tumor mutation burden (TMB) value for all samples and enhanced the TCGA PanCancer Atlas studies with DNA methylation and treatment data. All data is available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub. We also host a dedicated instance for AACR Project GENIE, enabling access to the GENIE cohort of >165,000 clinically sequenced samples from 19 institutions (https://genie.cbioportal.org). The GENIE Biopharma Collaborative (BPC) enables the collection of comprehensive clinical annotations, including response, outcome, and treatment history. The first BPC cohorts are now available: ~2,000 non-small cell lung cancer samples and ~1,500 colorectal cancer samples. Support for multimodal data analysis has been a major focus, including several new integrations with external tools. Single cell data is now available in the CPTAC GBM study and can be visualized throughout cBioPortal, and via integration with cellxgene. On the patient page, H&E and mIF images can be visualized via integration with Minerva, and the genomic overview now integrates IGV. We continue to enhance existing features. In the study view, users can now add charts comparing categorical vs continuous data, and the plots tab includes a heatmap option. We replaced the existing fusion data type with a generalized structural variant data type that supports detailed information including breakpoints and orientation, to enable new visualizations and analyses. Pathway level analysis has been extended with