cBioPortal for Cancer Genomics is a widely used platform for exploratory, interactive visualization and analysis of large-scale clinico-genomic datasets. cBioPortal provides a range of visualizations and analyses including interactive cohort exploration, OncoPrints, mutation “lollipop” plots, survival analysis, alteration enrichment analysis, and detailed patient-level visualizations. cBioPortal also integrates variant annotations from a variety of sources to facilitate interpretation. The public cBioPortal (https://www.cbioportal.org) is accessed by >40,000 unique visitors each month and hosts data from >460 studies. All data is also available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub. In 2024 we added 76 new studies (∼30,000 samples), including data from the NCI Genomic Data Commons. In addition, >94 instances of cBioPortal are installed at academic institutions and companies worldwide. cBioPortal partners with AACR Project GENIE to provide access to the GENIE cohort in a dedicated instance (https://genie.cbioportal.org). Users can explore the full GENIE cohort of >229,000 clinically sequenced samples from 19 institutions, as well as cohorts with comprehensive clinical annotations including response, outcome, and treatment history, from the GENIE Biopharma Collaborative (BPC). BPC cohorts for NSCLC (∼2,000 samples) and colorectal cancer (∼1,500 samples) are available, with more to come. The past year has brought a variety of enhancements to cBioPortal. A new data type selector on the home page enables users to find studies with specific types of data. The interactive cohort exploration has new ways to explore data with the addition of gene-specific charts to summarize the types of mutations in a gene and the integration of the Plots tab for customizable graphs of any two data attributes. The OncoPrint can now display per group alteration frequency based on any categorical attribute. Variant interpretation is enhanced with the integration of AlphaMissense as a novel annotation source and an update to the latest MutationAssessor data. The patient page also has new visualizations, including mutational signatures and the integration of Chromoscope to visualize structural variations. We also made significant changes to the backend code to improve both the developer and user experience. The backend code was repackaged and upgraded to simplify and improve the development process. In addition, we are working on switching to an Online Analytical Processing (OLAP) database which will bring significant performance improvements. cBioPortal is open source: https://github.com/cBioPortal. 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, Caris Life Sciences, Bilkent University, SE4BIO and The Hyve. We welcome open source contributions from others in the cancer research community. Ino de Bruijn,Tali Mazor,Rima AlHamad,Calla Chennault,Corey Dubin,Jeremy Easton-Marks,Zhaoyuan Fu,Benjamin Gross,Charles Haynes,David M. Higgins,Jason Hwee,Prasanna K. Jagannathan,Mirella Kalafati,Karthik Kalletla,Zeynep Karagöz,James Ko,Tim Kuijpers,Sowmiyaa Kumar,Priti Kumari,Ritika Kundra,Bryan Lai,Xiang Li,James Lindsay,Aaron Lisman,Qi-Xuan Lu,Ramyasree Madupuri,Zain-ul-Abideen Nasir,Angelica Ochoa,Yusuf Ziya Özgül,Oleguer Plantalech,Matthijs N. Pon,Baby A. Satravada,Jessica Singh,Selcuk Onur Sumer,Pim van Nierop,Floris Vleugels,Avery Wang,Manda Wilson,Hongxin Zhang,Gaofei Zhao,Ugur Dogrusoz,Allison Heath,Adam Resnick,Trevor J. Pugh,Chris Sander,Ethan Cerami,JianJiong Gao,Nikolaus Schultz. cBioPortal for cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1117.

Abstract cBioPortal is a widely used platform for interactive visualization and analysis of large-scale multimodal cancer datasets. It provides cohort exploration tools, such as OncoPrint, mutation “lollipop” plots, survival and enrichment analyses, detailed patient-level views, and integrated variant annotations to support interpretation. The public instance of cBioPortal (https://www.cbioportal.org) serves >40,000 unique visitors globally each month. It hosts data from >500 studies, all also available through the cBioPortal Datahub. In 2025, we added 38 new studies (∼35,000 samples). We also added Tumor Break Load (TBL) scores across PCAWG, CCLE, and all 32 TCGA Pan-Cancer Atlas studies. More than 99 cBioPortal instances are deployed at institutions and companies worldwide. cBioPortal partners with AACR Project GENIE to provide access to the GENIE cohort in a dedicated instance (https://genie.cbioportal.org). Users can explore >268,000 clinically sequenced samples from 20 institutions, as well as GENIE Biopharma Collaborative (BPC) cohorts with detailed clinical annotations, including NSCLC (∼2,000 samples), colorectal cancer (∼1,500), and breast cancer (∼1,200), with more to come. Over the past year, cBioPortal progressed along two complementary directions. First, we introduced a chat-based interface for natural-language data exploration, reflecting ongoing efforts to utilize AI, specifically large language models, to augment traditional query and visualization workflows in cBioPortal. Second, we released several core platform enhancements: 1) we improved the performance for large cohorts by switching the backend database from MySQL to ClickHouse, an OLAP (Online Analytical Processing) database; 2) the Plots tab can now visualize variant allele frequencies, connect multiple samples from the same patient, and has more flexible categorical sorting; 3) variant interpretation has been strengthened through integration of AlphaMissense predictions; 4) we released a redesigned About page highlighting the year’s accomplishments and future roadmap. It is worth noting that many of these features were developed using AI-assisted technologies, which are increasingly standard practice in software engineering. cBioPortal is open source (https://github.com/cBioPortal) and developed collaboratively by groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, Bilkent University, SE4BIO, and The Hyve. We welcome contributions from the cancer research community. Citation Format: Ino de Bruijn, Tali Mazor, Gaofei Zhao, Manda Wilson, Avery Wang, Floris Vleugels, Pim van Nierop, Henk-Jan van den Ham, S. Onur Sumer, Jessica Singh, Baby A. Satravada, Oleguer Plantalech, Angelica Ochoa, Zain-ul-Abideen Nasir, Ramyasree Madupuri, Pieter Lukasse, Aaron Lisman, James Lindsay, Xiang Li, Bryan Lai, Ritika Kundra, Priti Kumari, Sowmiyaa Kumar, Tim Kuijpers, James Ko, Zeynep Karagöz, Karthik Kalletla, Prasanna K Jagannathan, Jason Hwee, Guizela Huelsz Prince, Charles Haynes, Benjamin Gross, Zhaoyuan Fu, Ruslan Forostianov, Calla Chennault, Rima AlHamad, Ugur Dogrusoz, Allison Heath, Adam C. Resnick, Trevor J. Pugh, Chris Sander, Jianjiong Gao, Nikolaus Schultz, Ethan Cerami. cBioPortal for cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4097.

Abstract 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 a new integration with NDEx. cBioPortal is fully open source (https://github.com/cBioPortal/). 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, Caris Life Sciences, Bilkent University and The Hyve. We welcome open source contributions from others in the cancer research community. Citation Format: Ino de Bruijn, Tali Mazor, Adam Abeshouse, Diana Baiceanu, Stephanie Carrero, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Bryan Lai, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Yusuf Ziya Özgül, Oleguer Plantalech, Sander Rodenburg, Baby Anusha Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz. cBioPortal for Cancer Genomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4256.

List of AACR Project GENIE BPC Core Team Members

Abstract International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international cancer registry collecting data from 19 cancer centers, makes data from >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional real-world longitudinal clinical data, including treatment and outcome data, are being collected by the AACR Project GENIE Biopharma Collaborative using the PRISSMM data curation model. Several thousand of these cases are now also available in cBioPortal. We have significantly enhanced the functionalities of cBioPortal to support the visualization and analysis of this rich clinico-genomic linked dataset, as well as datasets generated by other centers and consortia. Examples of these enhancements include (i) visualization of the longitudinal clinical and genomic data at the patient level, including timelines for diagnoses, treatments, and outcomes; (ii) the ability to select samples based on treatment status, facilitating a comparison of molecular and clinical attributes between samples before and after a specific treatment; and (iii) survival analysis estimates based on individual treatment regimens received. Together, these features provide cBioPortal users with a toolkit to interactively investigate complex clinico-genomic data to generate hypotheses and make discoveries about the impact of specific genomic variants on prognosis and therapeutic sensitivities in cancer. Significance: Enhanced cBioPortal features allow clinicians and researchers to effectively investigate longitudinal clinico-genomic data from patients with cancer, which will improve exploration of data from the AACR Project GENIE Biopharma Collaborative and similar datasets.