cBioPortal Newsletter December 2024

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Ritika Kundra

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Dec 20, 2024, 1:11:03 PM (yesterday) Dec 20

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December, 2024

Welcome to the December 2024 edition of the cBioPortal Newsletter!

As the year comes to a close, we’re thrilled to highlight the latest advancements and improvements in cBioPortal. From new features to enriched datasets, there’s plenty to explore. Join us as we take a closer look at what’s new and exciting!

Introducing the cBioPortal Foundation

The cBioPortal Foundation is dedicated to supporting the development and adoption of cBioPortal, an open-source software for the interactive exploration of multidimensional cancer data sets. To support this mission, visit our new donation page.

New data:

5,567 samples from 6 TARGET studies from the Genomic Data Commons (GDC) as part of the Cancer Research Data Commons (NCI-CRDC) initiative.
34,904 samples from 9 studies including MSK-CHORD (MSK, Nature 2024), longitudinal and clinical data for 24,950 patients.

For the full list, visit our News page.

New Features:

Performance enhancement for the Study View on the AACR GENIE Portal:

Querying on the AACR GENIE Study View is 10x faster with the adoption of a new analytical processing database (ClickHouse). Watch a video demonstrating the difference in speed here. The main public portal (cbioportal.org) will transition in 2025.

New feature and enhancement in the Mutation Table and Mutation Mapper Tool:

The Functional Impact column now includes annotations from AlphaMissense. See screenshot.
The Mutation Assessor annotation under the Functional Impact column has been updated to v4. See screenshot.

New portal for canine cancer researchers: Canine Cancer Genome Atlas

In dogs over the age of ten, cancer is the leading cause of death, affecting 50% of older canines. One in four dogs will eventually succumb to the disease. The similarities between canine and human cancers make dogs a valuable model in comparative oncology. cBioPortal hosts comprehensive collections of mutational data from human cancer samples, offering a crucial resource for addressing clinical challenges and discovering new insights in research. Until recently, similar genomic resources did not exist in veterinary medicine.

The Canine Comparative Oncology Laboratory at the University of Turin, in collaboration with The Hyve, launched the Canine Cancer Genome Atlas. This project aims to compile a genomic database of canine tumors across various histotypes.

The Canine Cancer Genome Atlas now holds:

Mutation data

Structural variant data
Clinical data

From 23 canine cancer studies, with a total of 723 samples.

Publicly accessible via caninecancergenomeatlas.org

Feature Highlight: Chromoscope

The Structural Variants (SVs) for the Pan-cancer analysis of whole genomes (ICGC/TCGA, Nature 2020) study can now be viewed in Chromoscope on the Patient View. Chromoscope is an interactive visualization tool that supports multiscale and multiform visualizations for analyzing structural variants. It is developed by the Park and HiDive labs at Harvard Medical School, and funded in part through the Fund for Innovation in Cancer Informatics (ICI). Check it out here.

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. Wishing the cBioPortal community happy holidays!