Abstract 910: The cBioPortal for cancer genomics
Authors: Jianjiong Gao, Tali Mazor, Adam Abeshouse, Ersin Ciftci, Ino de Bruijn, Benjamin Gross, Karthik Kalletla, Priti Kumari, Ritika Kundra, James Lindsay, Aaron Lisman, Pieter Lukasse, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Pichai Raman, Fedde Schaeffer, Robert Sheridan, Jing Su, S. Onur Sumer, Yichao Sun, Sander Tan, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Kelsey Zhu, Kees van Bochove, Ugur Dogrusoz, Trevor J. Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz
Journal: Cancer Research (2019)

Abstract The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a biologist-friendly interface. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including OncoPrint, mutation diagram, variant interpretation, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization, among others. The public site (http://www.cbioportal.org) hosts data from more than 200 studies from individual labs and large consortia, including the newly added TCGA Pan-Cancer Atlas data and the Count Me In project. These studies can be explored and queried individually or combined together into “virtual studies”. Users are now allowed to login and save virtual studies for query and analysis. The site is currently accessed by approximately 30,000 unique visitors per month. The software is also installed locally at dozens of academic institutions and pharmaceutical/biotechnology companies. A notable instance is the cBioPortal for AACR GENIE (http://www.cbioportal.org/genie/) hosting 60,000 clinically sequenced samples from multiple institutions. Over the past year, the code base has been fully refactored, resulting in a more responsive and interactive website. A new web API is in beta facilitating easier programmatic access to data. In addition, all public studies are available for download from the new datahub (https://github.com/cBioPortal/datahub/). The cBioPortal remains under active development. The portal is fully open source (https://github.com/cBioPortal/) under a GNU Affero GPL license. Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, and The Hyve. Ongoing and future development is focused on: (1) building the open source community; (2) continued performance improvements; (3) expanding user support, documentation and training resources; (4) developing novel features to support immunogenomics and immunotherapy; (5) enhancing individual variants and overall patient interpretation; (6) creating a simplified query interface; and (7) enabling comparative analysis of user-defined patient cohorts. Citation Format: Jianjiong Gao, Tali Mazor, Adam Abeshouse, Ersin Ciftci, Ino de Bruijn, Benjamin Gross, Karthik Kalletla, Priti Kumari, Ritika Kundra, James Lindsay, Aaron Lisman, Pieter Lukasse, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Pichai Raman, Fedde Schaeffer, Robert Sheridan, Jing Su, S. Onur Sumer, Yichao Sun, Sander Tan, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Kelsey Zhu, Kees van Bochove, Ugur Dogrusoz, Trevor J. Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 910.