cBioPortal
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Jan 4, 2022

Nov 12, 2021

Nov 3,2021

Oct 1, 2021

  • New Feature: Arm level Copy Number events are now loaded into cBioPortal using the Categorial Generic Assay Data Type. They can be found in a tab under the Add Charts Button of the Study View Example: Arm Level Data in TCGA PanCancer Atlas

Sep 22, 2021

Sep 21, 2021

  • Enhancement: Dowloading the Lollipop plot on the Mutations Tab of the Results View will now also include the annotation tracks:

Aug 17, 2021

Aug 10, 2021

Jul 27, 2021

  • New Feature: Add a custom filter to any column of the Mutations Tab in the Results View Example: CTNNB1 in MSK-IMPACT (2017) cohort
  • New Feature: Show detailed descriptions for each annotation source in the header of the the Mutations Table in both the Results View and the Patient View Example link

Jul 6, 2021

June 23, 2021

June 1, 2021

May 10, 2021

May 4, 2021

April 21, 2021

April 20, 2021

March 30, 2021

March 11, 2021

February 16, 2021

January 28, 2021

January 12, 2021

December 31, 2020

November 3, 2020

  • New Feature: The map of local installations of cBioPortal is available now. Please consider registering your instance here.
  • Enhancement: upgraded the Genomic Evolution tab in Patient View with timeline Example

October 20, 2020

  • Enhancement: Expression tab has now been merged into the Plots tab

October 16, 2020

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October 13, 2020

  • Enhancement: Study View now allows comparing samples with mutations or copy number alterations in different genes
  • New Feature: When treatment timeline is available (e.g. in this study), Study View now allows the selection and comparison of patients treated with specific drugs, or samples sequenced pre or post specific drug treatments

September 30, 2020

September 22, 2020

  • Enhancement: The timeline feature in Patient View has been refactored with an improved UI. Example
  • Enhancement: Logrank p-values are now provided for all survival analysis (previously only availalbe when comparing two groups). Example

August 11, 2020

July 21, 2020

  • New Feature: The Mutations tab now has the option to show mutation effects for different transcripts / isoforms. Note that some annotation features are only available for the canonical isoform. example
  • Enhancement: The Plots tab is now supported in multi-study queries. example
  • New Feature: You can now share custom groups in the Study View example

June 11, 2020

June 9, 2020

  • Enhancement: using OQL to query for mutations based on a protein position range. example
  • New Feature: you can now send the OncoPrint data to the OncoPrinter tool for customization.
  • Enhancement: Mutational spectrum data can be downloaded from OncoPrint

June 2, 2020

  • Enhancement: Pediatric cancer studies are now grouped and highlighted in the query page

May 6, 2020

April 24, 2020

  • New Feature: Add a new chart on the Study View for selecting samples based on pre-defined case lists:

April 10, 2020

  • New Feature: Make cohorts on the Study View using continuous molecular profiles of one or more gene(s), such as mRNA expression, methylation, RPPA and continuous CNA. example
    Combine this with the group comparison feature to compare e.g. all quartiles of expression:
  • New Feature: Annotate mutations using the Mutation Mapper Tool on the GRCh38 reference genome:

April 3, 2020

  • New Feature: Extended the Comparison tab to support the comparison of altered samples per gene or alteration. This example query compares NSCLC patients with 1) both mutated and amplified EGFR, 2) mutated EGFR only, and 3) amplified EGFR only.
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March 27, 2020

  • Enhancement: User selections in the Plots tab are now saved in the URL. example
  • New Feature: Added table of data availability per profile in the Study View. example

March 20, 2020

  • Enhancement: Extended Survival Analysis to support more outcome measures. example
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March 18, 2020

March 3, 2020

  • New Feature: Added Pathways tab to the Results View page, which visualizes the alteration frequencies of genes in pathways of interest. The pathways are pulled from https://www.pathwaymapper.org and shown in a read only view. One can edit these pathways in the PathwayMapper editor. For more information see the tutorial.

February 12, 2020

February 6, 2020

  • New Feature: Extend the recent group comparison feature by allowing comparisons inside the Results View page. The new tab allows for quick comparison of altered vs unaltered cases by survival, clinical information, mutation, copy number events and mRNA expression:
  • Performance enhancement: the Study View's mutation table now loads faster for studies with multiple gene panels. For the genie portal, which has a study with many different gene panels this resulted in a speed-up from ~90-120 seconds to 5 seconds.
  • Read more about the v3.2.2 release here

January 30, 2020

  • Enhancement: Show HGVSg in mutations table and linkout to Genome Nexus:
  • Enhancement: Add a pencil button near gene list in results page which opens interface for quickly modifying the oql of the query:
  • See more updates here

January 29, 2020

December 19, 2019

  • Enhancement: We restored support for submitting large queries from external applications using HTTP POST requests. Accepted parameters are the same as appear in the url of a query submitted from the homepage.
  • See more updates here

December 12, 2019

  • Enhancement: Several enhancements to the display of gene panels on the Patient View page, by The Hyve, described in more detail here
  • Enhancement: Add Count Bubbles to Oncoprint Toolbar
  • See more updates here

November 29, 2019

  • Enhancement: Support group comparison for custom charts in Study View page
  • Enhancement: Performance improvement of Co-Expression analysis.
  • Enhancement: Kaplan-Meier plots now supports custom time range.
  • See more updates here

November 22, 2019

  • New Feature: Support for Treatment response data in the Oncoprint and Plots tab, including new Waterfall plot type. Read more in The Hyve's blog post
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November 15, 2019

  • Enhancement: heatmap tracks in OncoPrint now has separate headers and sub-menus. example
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  • Enhancement: global settings for query session

November 7, 2019

October 30, 2019

October 23, 2019

  • Enhancement: Quick example links in Plots tab. example

October 14, 2019

  • New Feature: Fusion Genes table in Study View. example
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October 11, 2019

  • Enhancement: The Download interface on the homepage has been removed. Enhanced download functionality is now available after querying on the results page.
    Home page:
    Results page:
    Note that as before one can always download the full raw data on the Data Sets page or from Datahub.

October 9, 2019

September 18, 2019

  • New Feature: The list and order of charts of a study will be automatically saved now as a user preference on the study view page.

September 6, 2019

August 13, 2019

July 26, 2019

July 24, 2019

July 13, 2019

  • Public Release 6.1 of AACR Project GENIE:
    • The sixth data set, GENIE 6.0-public, was released in early July 2019. A patch to GENIE 6.0-public, GENIE 6.1-pubic, was subsequently released on July 13, 2019. The combined data set now includes nearly 70,000 de-identified genomic records collected from patients who were treated at each of the consortium's participating institutions, making it among the largest fully public cancer genomic data sets released to date. The combined data set now includes data for nearly 80 major cancer types, including data from nearly 11,000 patients with lung cancer, greater than 9,700 patients with breast cancer, and nearly 7,000 patients with colorectal cancer.
  • More detailed information can be found in the AACR GENIE Data Guide. In addition to accessing the data via the cBioPortal, users can download the data directly from Sage Bionetworks. Users will need to create an account for either site and agree to the terms of access.
  • For frequently asked questions, visit the AACR FAQ page.

July 2, 2019

June 19, 2019

  • New Feature: Show Genome Aggregation Database (gnomAD) population frequencies in the mutations table - see example:

June 12, 2019

June 7, 2019

  • New Group Comparison Feature: Compare clinical and genomic features of user-defined groups of samples/patients. View Tutorial

May 8, 2019

  • New Feature: Show Post Translational Modification (PTM) information from dbPTM on the Mutation Mapper - see example:

April 26, 2019

March 29, 2019

  • New Feature: Use the new quick search tab on the homepage to more easily navigate to a study, gene or patient:

March 15, 2019

February 22, 2019

  • Enhancement: Exon number and HGVSc annotations are available in optional columns in the Mutations tab on the Results page and in the Patient View.
  • New feature: option to a show regression line in the scatter plot in the Plots tab on the Results page
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February 19, 2019

  • New feature: Copy-Number Segments tab on the Study View page using igv.js v2 - see example
  • Improved Copy-Number Segments tab on the Results page
  • New feature: OncoKB and Cancer Hotspots tracks in the Mutations tab on the Results page
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January 24, 2019

January 10, 2019

  • cBioPortal now supports queries for driver mutations, fusions and copy number alterations as well as germline/somatic mutations using Onco Query Language (OQL) -- see example
  • A new tutorial explores OQL and provides examples of how OQL can be a powerful tool to refine queries.

December 17, 2018

  • The 10th phase of cBioPortal architectural upgrade is now complete: the Study View has been moved to the new architecture with numerous improvements. This marks the completion of the cBioPortal architectural refactoring! 🎉🎉🎉

October 29, 2018

  • The ninth phase of the cBioPortal architectural upgrade is now complete: the results page is now a single-page application with better performance.
  • Supported plotting mutations by type in Plots tab
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October 19, 2018

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October 17, 2018

August 20, 2018

  • Now you can log in on the public cBioPortal with your Google account and save your virtual studies for quick analysis.
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August 7, 2018

  • The eighth phase of the cBioPortal architectural upgrade is now complete: The Plots, Expression, Network, and Bookmarks tabs, and therefore all analysis tabs in the results page, have been moved to the new architecture.
  • Updated the MutationMapper tool, now connecting to Genome Nexus for annotating mutations on the fly.
  • Total Mutations and Fraction Genome Altered are now available in Plots tab for visualization and analysis.
  • Enhanced clinical attribute selector for OncoPrint, now showing sample counts per attribute.
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July 27, 2018

June 20, 2018

  • The seventh phase of the cBioPortal architectural upgrade is now complete: The Enrichments and Co-Expression tabs have been moved to the new architecture.
  • Supported merged gene tracks in OncoPrint and Onco Query Language -- see example
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May 10, 2018

  • Enhanced OncoPrint to show germline mutations -- see example
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April 17, 2018

April 5, 2018