cBioPortal Newsletter May 2025

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Tali Mazor

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May 22, 2025, 12:26:25 PMMay 22

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May 2025

Welcome to the May 2025 edition of the cBioPortal Newsletter!

We’re excited to describe the latest updates to cBioPortal, share our roadmap for future development, and provide updates on the AACR Annual Meeting and Google Summer of Code.

cBioPortal Roadmap

We’re excited to share an updated About page. This page provides a deeper overview of the goals behind the cBioPortal project and includes a roadmap so you can see what features and improvements are coming in the future, such as improved performance and longitudinal clinical data analysis

If you’d like to support any of our future work, please consider donating to the cBioPortal Foundation. The cBioPortal Foundation is committed to advancing the development and adoption of cBioPortal. Support our mission by visiting our donation page.

AACR Annual Meeting

Thanks to everyone who stopped by our booth at the AACR Annual Meeting! We enjoyed hearing your questions, requests, and kind words of support. If you weren’t in attendance or still have questions, you can always reach us via our user support Google group: cbiop...@googlegroups.com.

We were thrilled to see the impact of cBioPortal throughout the AACR Annual Meeting, as evidenced by the 33 abstracts that mentioned cBioPortal. We were also proud to see MSK-IMPACT, the clinical sequencing program at Memorial Sloan Kettering Cancer Center, honored with the AACR Team Science Award. From the beginning, the MSK-IMPACT program placed an emphasis on enabling research and cBioPortal is proud to have played a pivotal role in making data from the MSK-IMPACT program accessible.

New Datasets Added!

We’ve added data from 4,571 samples across 10 new studies. Highlights include:

Ovarian Cancer (Gray Foundation, Cancer Discov 2024): 567 ovarian cancer cases with spatial data generated using GeoMx, a digital platform for RNA/protein profiling in tissue regions using barcoded probes and CyCIF, an antibody-based platform for single-cell resolution imaging of protein expression.
Normal Melanocytes (UCSF, Nature 2020), Normal Keratinocytes (UCSF, BioRxiv 2024), Normal Fibroblasts (UCSF, BioRxiv 2024): Added whole-exome and targeted sequencing data from normal human skin tissues, profiling fibroblasts, melanocytes, and keratinocytes to uncover cell-type-specific mutational patterns under chronic UV exposure.

Check out the full list on our News page.

New Feature in cBioPortal

The Plots tab now has an option to draw a line connecting multiple samples from the same patient. This option is available when data is visualized as a box plot and when there is data from multiple samples from the same patient. Example: Mutation count in a cohort of primary grade II glioma vs patient-matched recurrences of all grades

Google Summer of Code

We are excited to share that we will have 4 contributors working on cBioPortal this summer through the Google Summer of Code. The projects they will be working on are:

Feature Highlight: Customize your queries with Onco Query Language (OQL)

Did you know you can run a customized query in cBioPortal? Perhaps you want to look at one specific mutation or only query for amplifications in your gene of interest.

Onco Query Language (OQL) is used to define which specific types of alterations are included in a query. By default, querying for a gene includes mutations, structural variants, amplifications and deep deletions. OQL can be used to specify specific mutations (e.g. BRAF V600E) or types of mutations (e.g. BRCA1 truncating mutations), lower level copy number alterations (e.g. CDKN2A shallow deletions), changes in mRNA or protein expression, and more.

OQL follows a simple format: after entering a query gene, add a colon, and then follow the colon with the appropriate keyword(s). All available keywords are described in the OQL documentation page.

For example, to query for BRAF V600E mutations, putative driver events in EGFR, and mutations, deep deletions and shallow deletions in CDKN2A, run this query:

BRAF: MUT=V600E

EGFR: DRIVER

CDKN2A: MUT HOMDEL HETLOSS

Here are the results of that query in the Lung Adenocarcinoma TCGA PanCancer Atlas cohort:

For comparison, this is a query for the same genes without OQL:

Try out OQL with your next query and see how powerful it can be. Additional information about OQL is available in our user guide.

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.