cBioPortal Newsletter June 2024

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Tali Mazor

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Jun 6, 2024, 10:12:07 AMJun 6

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June, 2024

Welcome to the second edition of the cBioPortal Newsletter!

In this issue, we'll delve into the recent progress and enhancements made to cBioPortal. From feature updates to expanded datasets, we're excited to share our progress with you. So, let's dive in and explore what's new!

Hackathon!

In April, ~40 core contributors came together for a hackathon in New York City. Contributors from Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Princess Margaret Cancer Center, Children’s Hospital of Philadelphia, Caris Life Sciences, The Hyve, SE4BIO and City University of New York joined together in person & virtually for two days of code hacking and product spec’ing. We made substantial progress across a broad range of projects, including performance enhancements, data harmonization, data loading and documentation.

Google Summer of Code

We’re pleased to announce 9 contributors will be joining us this summer as part of the Google Summer of Code 2024. These contributors will be working on some of the projects listed here.

Here is a list of new features in the past few months. For the full list, visit our News page.

Added data from 9,632 samples across 10 studies including:

Pre-cancer Colorectal Polyps (HTAN Vanderbilt, Cell 2021): 61 pre-malignant colorectal polyps analyzed with whole-exome sequencing and single-cell transcriptomics, each paired with matched normal colon tissues.
Ovarian Cancer - MSK SPECTRUM (MSK, Nature 2022): Multi-region, multi-modal profiling of 42 untreated high-grade serous ovarian cancer using single-cell RNA sequencing, whole-genome sequencing, targeted sequencing, digital histopathology and multiplexed immunofluorescence.
Genetic ancestry data has been added to all 32 TCGA PanCancer studies and can be visualized in the portal as a generic assay. See example.

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

Gene-specific charts in Study View now support mutation data. Two chart types are available: sample mutational status and mutation types. See the ‘Feature Highlight’ below for more information.
The Plots tab is now available in the Study View. After exploring a cohort and applying any filters of interest in the Study View Summary page, you can now click over to the new Plots tab to explore the cohort by plotting any two attributes against each other. See example.

The custom selection feature in Study View, which filters to a user-defined list of samples/patients, no longer requires the inclusion of the study ID with each sample ID. If viewing multiple studies in Study View and filtering to a sample ID which exists in more than one study, all samples will be displayed by default or the study ID can be included for additional specificity. See screenshot.

New features in the Group Comparison view:

Categorical data loaded into the generic assay format is now available in group comparison. See example.

New features in the Results View (after submitting a query):

It is now possible to remove a gene track in the OncoPrint. See screenshot.

Feature Highlight: Gene-specific charts in Study View

The cBioPortal study view allows you to explore all the data that’s available for a study. Summary charts show the most frequently mutated and copy number altered genes, but sometimes you want to explore alterations in a specific gene in more detail, or examine mRNA expression or other molecular data that are not summarized.

This is all possible via the ‘Gene Specific’ tab In the Charts menu. Enter your gene(s) of interest, and then select the molecular profile of interest.

Chart options are displayed below and include:

Sample mutation status: mutated, not mutated, not profiled
Sample mutation type frequencies: missense, in frame deletion, etc
Sample copy number status: amplification, gain, diploid, shallow deletion, deep deletion, not profiled
mRNA or protein expression, as z-scores or counts

These charts work just like any other chart in study view: use them to filter to a subset of samples or watch them update when other charts are used to filter. They can also be used as the basis of a group comparison – watch one of our how-to videos to see an example of comparing outcomes based on expression of a gene.

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.