cBioPortal Newsletter November 2025

6 views

Skip to first unread message

Ritika Kundra

unread,

Nov 4, 2025, 12:28:23 PMNov 4

to cbiopor...@googlegroups.com

November 2025

Welcome to the November 2025 edition of the cBioPortal Newsletter!

We’re excited to share the latest updates from the cBioPortal for Cancer Genomics — including newly added datasets, new feature enhancements for data exploration, and upcoming opportunities to connect with us in person.

Symposium: cBioPortal — Making Cancer Data Accessible for All
November 11, 2025, Amsterdam UMC / AVL

We will be participating in a full-day cBioPortal symposium hosted at the Netherlands Cancer Institute (NKI/AVL) in Amsterdam. The event will showcase cBioPortal's role in open cancer genomics data access through a full-day agenda. Registration is open to researchers, clinicians, and the broader scientific community. Find more information about the symposium and registration here: https://www.avl.nl/agenda/2025/cbioportal/

cBioPortal was at AACR-NCI-EORTC in Boston, October 22–26th, 2025

cBioPortal was featured at the AACR Project GENIE booth during the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics. We appreciate everyone who visited our booth! If you couldn't make it or still have questions, feel free to contact us through our user support Google group at cbiop...@googlegroups.com.

For more on the collaboration between cBioPortal and AACR Project GENIE, see the Data Highlight below.

Data Highlight: AACR Project GENIE Available in cBioPortal!

AACR Project GENIE is a multi-institutional registry that aggregates harmonized real-world clinical and genomic data from next-generation sequencing (NGS) assays performed at participating cancer centers. The dataset includes tumor profiling results linked to structured clinical annotations and is versioned and updated on a regular release schedule. As of this newsletter, the main AACR Project GENIE registry, currently in its 18th public release, includes data from over 250,000 tumor samples from over 211,000 patients.

In addition to the main registry, GENIE also includes the AACR GENIE BioPharma Collaborative (BPC), which is focused on detailed clinical annotations of a subset of patients within the GENIE Registry. In addition to the demographic and genomic data from the main registry, the GENIE-BPC cohorts include detailed clinical information such as treatment history, outcomes, and metastatic events.

This data is available in cBioPortal through the dedicated GENIE portal.

AACR GENIE 18.0 Public Study View

Longitudinal timeline view of a patient in AACR GENIE-BPC NSCLC v2.0 Public

Added data from 9,749 samples across 13 studies, including:

Melanoma (MSK, Cell 2017) - iAtlas Harmonized: We now host the first CRI iAtlas immuno-oncology dataset in cBioPortal with additional cohorts actively being onboarded, enabling exploration of immune response features alongside genomics and clinical outcomes.
New cell line datasets, including the whole genome and whole exome data from the Broad Institute’s DepMap Portal (25Q2).

Google Summer of Code 2025 Wrap-up

This year’s GSoC projects delivered impactful enhancements to cBioPortal, improving data harmonization, analysis, and visualization capabilities for the community. We now have one of the projects live in cBioPortal! See the feature highlight for more information.

New Feature Release: Variant Allele Frequency Visualization

A Google Summer of Code 2025 project is now live - Show Variant Allele Frequency (VAF) on the Plots Tab

Contributor: Rishi Prasad Sulakhe

This project enhanced cBioPortal’s analytical capabilities by enabling visualization of Variant Allele Frequency (VAF) across studies. It introduced VAF-based plotting in the Plots Tab, allowing researchers to better assess mutation clonality and prevalence across cancer types.

To learn more about the other cBioPortal GSoC projects, visit the project summaries from our contributors.

New features in the Study View (exploring a study):

We have introduced a Custom Variant Annotation Filter within Study View to give users more granular control when exploring genomic data. Custom variant annotations can be added to mutation, copy number, and structural variant data via the custom namespace columns. The new Custom Variant Annotation Filter in the Study View enables users to apply annotation-based filters, combine them using AND/OR logic for tailored analyses, and customize and retain settings to streamline future data exploration.

You can try this new feature in Melanoma (MSK, Cell 2017) - iAtlas Harmonized Study using the four available custom variant annotations:

Learn More

To learn more about cBioPortal, review our documentation, which includes FAQs, webinars, and tutorials. If you have questions, please don't hesitate to reach out to us at cbiop...@googlegroups.com. Stay tuned for more updates, and thank you for your continued support in advancing cancer genomics research with cBioPortal.