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# News

# November 18, 2024

# October 30, 2024

# October 8, 2024

# September 27, 2024

# August 28, 2024

  • New feature (Windows users only): The Group Comparison results can now be visualized in 3D with AVM, an interactive 3D visualization software tool with data shaping functions and integrated pathways. Read more on AVM for cBioPortal.
    • Note for private instances: To enable this feature in private cBioPortal instances, please see this instruction. image image

# July 29, 2024

# July 10, 2024

# May 29, 2024

# May 7, 2024

# Apr 2, 2024

  • Introducing the cBioPortal Newsletter! Stay updated with the latest developments, insights, and community highlights of cBioPortal. Subscribe via LinkedIn or google groups. We'll be sharing valuable updates every few months.

# March 27, 2024

  • New Feature: 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. Example: Mutation count vs subtype in Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)

    image

  • Enhancement: 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.

    image

# Mar 5, 2024

  • Local Installations Feature: Make representation of custom driver annotation configurable: image

# Feb 7, 2024

  • New feature: The Datasets Page now lists what studies have samples profiled for Structural Variants:

    image

  • New Major Release: v6.0.0 includes a major repackaging of the backend software to improve the development experience. The backend has been upgraded to use Java Spring Boot v3.1.4. The CORE and MAF modules have been moved to new repositories. All other modules have been compacted into a single source repository. We have also updated the JVM to 21 and many libraries have been updated to address security and performance issues. See more information in the v6.0.0 release notes.

  • Local Installations Feature: When mutational signature data is loaded, show COSMIC reference signatures on the Patient View:

    image

# Dec 29, 2023

# Dec 5, 2023

# Oct 17, 2023

# Oct 3, 2023

# Sep 5, 2023

  • New feature: Add gene-specific CNA charts to show all levels of copy number alterations (including gain and hetloss) on Study View:

# Aug 30, 2023

  • Enhancement: Exclude a patient from your selection directly from the Patient View:

    image

# Aug 21, 2023

# Aug 1, 2023

  • Enhancement: One-sided Fisher's exact tests were changed to be two-sided. The affected pages are:

    • Results View Page - Mutual Exclusivity Tab
    • Results View Page - Comparison Tab - Genomic Alterations Tab
    • Comparison Page - Genomic Alterations Tab
    • Comparison Page - Mutations Tab

    Please note that the Mutations tab on the Comparison page is a recent feature and was introduced with the two-sided Fisher's exact test already implemented.

    Several users pointed out that using a one-sided test was incorrect for these comparisons. Please see discussions here for more information.

# Jul 18, 2023

# May 2, 2023

# Apr 25, 2023

  • Local Installations Feature: When custom driver annotations for structural variants are loaded, one can now filter by them in both the Oncoprint and the Study View.

# Apr 11, 2023

  • New Feature: Disable autocommit and manually commit filters in study view. Manually commit filters can improve cBioPortal performance when query large dataset.

# Apr 5, 2023

# Apr 4, 2023

  • New Feature: Allow numeric data type for custom data charts.

    This also allows to have numerical custom data after we query based on genes (custom data 2 in the image):

# Jan 10, 2023

# Dec 13, 2022

# Oct 12, 2022

# Sep 6, 2022

  • Enhancement: Oncoprint can now save clinical tracks after login:

# Aug 11, 2022

  • New Major Release: v5.0.0 release drops support for fusions in the mutation data format. Going forward fusions can only be imported in the Structural Variant (SV) format. This is mainly a refactoring effort to simplify the codebase and pave the way for the development of novel structural variant visualizations in the future. For cBioPortal instance maintainer, please reference our Migration Guide for instruction.

# Jul 26, 2022

# Jun 7, 2022

# May 31, 2022

  • New Feature: Added Quartiles, Median split and Generate bins options for bar charts on the study view page, where Generate bins allows user to define bin size and min value

# May 12, 2022

# May 24, 2022

  • New Feature: Add Help buttons on various pages and tabs, including the homepage

# May 10, 2022

# May 5, 2022

# Apr 20, 2022

# Mar 1, 2022

# Feb 8, 2022

  • New Feature: Create X vs Y violin plots in Study View using any categorical and numerical clinical data:

# Jan 19, 2022

  • New Feature: Numerical filters on the Study View are now editable:

  • New Feature: In the annotation column choose between showing a single icon OncoKB icon or multiple (one for therapeutic, diagnostic and prognostic):

# Jan 10, 2022

# 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. image

  • Enhancement: upgraded the Genomic Evolution tab in Patient View with timeline Example image

# October 20, 2020

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

# October 16, 2020

image
image

# October 13, 2020

  • Enhancement: Study View now allows comparing samples with mutations or copy number alterations in different genes image

  • 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 image

# September 30, 2020

# September 22, 2020

  • Enhancement: The timeline feature in Patient View has been refactored with an improved UI. Example image

  • 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 image

  • Enhancement: The Plots tab is now supported in multi-study queries. example image

  • 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 image

  • New Feature: you can now send the OncoPrint data to the OncoPrinter tool for customization. image

  • Enhancement: Mutational spectrum data can be downloaded from OncoPrint image

# June 2, 2020

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

# 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:

    Screen Shot 2020-04-24 at 9 18 25 AM

# 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:

    mutation_mapper_tool_grch38

# 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.

image
image

# 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

image
image

# 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.

    pathwaymapper_screenshot

# 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:

    group_results640px

  • 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:

    hgvsg genome nexus

  • Enhancement: Add a pencil button near gene list in results page which opens interface for quickly modifying the oql of the query:

    edit query pencil

  • 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

    image

  • Enhancement: Add Count Bubbles to Oncoprint Toolbar

    Screenshot from 2019-12-06 11-36-21

  • 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

image
image

# November 15, 2019

  • Enhancement: heatmap tracks in OncoPrint now has separate headers and sub-menus. example

image
image

  • 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

image
image

# 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:

    homepage download tab removed

    Results page:

    results page download tab

    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:

    gnomad feature news

# June 12, 2019

# June 7, 2019

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

group-comparison
group-comparison

# May 8, 2019

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

    ptm feature_news

# 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:

    quick_search_news

# 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

image
image

# 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

image
image

# 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! 🎉🎉🎉

image
image

# 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

image
image

# October 19, 2018

mutation_mapper_dropdown
mutation_mapper_dropdown

# 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.

image
image

# 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.

image
image

# 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

image
image

# May 10, 2018

  • Enhanced OncoPrint to show germline mutations -- see example

image
image

# April 17, 2018

# April 5, 2018

# March 20, 2018

  • The sixth phase of the cBioPortal architectural upgrade is now complete: The Download tab has been moved to the new architecture.
  • Data can now be downloaded in tabular format from OncoPrint.
  • Added an option to download an SVG file on the Cancer Type Summary tab.

# January 15, 2018

  • The fifth phase of the cBioPortal architectural upgrade is now complete: The OncoPrint and Survival tabs have been moved to the new architecture.

# November 20, 2017

image
image

# October 17, 2017

  • The fourth phase of the cBioPortal architectural upgrade is now complete: The Mutual Exclusivity and Cancer Type Summary tabs have been moved to the new architecture.
  • Updated protein structure alignment data in Mutations tab are now retrieved from Genome Nexus via the G2S web service.

# October 2, 2017

# August 3, 2017

  • The third phase of the cBioPortal architectural upgrade is now complete: The Mutations tab now has a fresh look and faster performance -- see example

image
image

  • Variant interpretations from the CIViC database are now integrated into the annotation columns on the Mutations tab and in the patient view pages
  • New summary graph for all cancer studies and samples on the front page

# June 26, 2017

  • The second phase of the cBioPortal architectural upgrade is now complete: The query interface now has a fresh look and faster performance.

image
image

# May 12, 2017

# May 5, 2017

  • First phase of cBioPortal architectural upgrade complete: Patient view now has fresh look and faster performance. example

# March 28, 2017

  • New features:

    • Per-sample mutation spectra are now available in OncoPrints -- see example

    image

    • mRNA heat map clustering is now supported in OncoPrints
    • MDACC Next-Generation Clustered Heat Maps are now available in the patient view
    • cBioPortal web site style change

# Feburary 2, 2017

  • New features:
    • 3D hotspot mutation annotations are now available from 3dhotspots.org
  • New data:
    • CPTAC proteomics data have been integrated for TCGA breast, ovarian, and colorectal provisional studies

# December 23, 2016

  • New features:

    • Heat map visualization of gene expression data in the OncoPrint

    OncoPrint Heatmap

    • Heat map visualization of gene expression data in the Study View page connecting to MDACC's TCGA Next-Generation Clustered Heat Map Compendium

# October 7, 2016

  • New features:

    • All data sets can now be downloaded as flat files from the new Data Hub
    • Annotation of putative driver missense mutations in OncoPrints, based on OncoKB, mutation hotspots, and recurrence in cBioPortal and COSMIC

    OncoPrint-OncoKB

    • Copy number segments visualization directly in the browser in a new CN Segments tab via IGV.js

    image

  • Improvements:

    • Improved cancer study view page (bug fixes and increased performance)

# July 24, 2016

# June 6, 2016

  • New features:
    • Annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages (via OncoKB)
      oncokb-screenshot
  • Improvements:
    • Improved OncoPrint visualization using WebGL: faster, more zooming flexibility, visualization of recurrent variants
    • Improved Network tab with SBGN view for a single interaction
    • Performance improvement of tables in the study view page
    • Mutation type summary on the Mutations tab

# March 31, 2016

# January 12, 2016

# December 23, 2015

  • New features:
    • Visualization of RNA-seq expression levels across TCGA studies (cross-cancer queries)
      cross cancer expression
    • Selection of genes in the study view to initiate queries
      query gene in study view
  • Improvement:
    • 3-D structures in the "Mutations" tab are now rendered by 3Dmol.js (previously JSmol)
    • Improved performance by code optimization and compressing large data by gzip

# December 1, 2015

  • New feature: Annotated statistically recurrent hotspots, via new algorithm by Chang et al. 2015
    Annotate recurrent hotspots

# November 9, 2015

  • New features:
    • Links to MyCancerGenome.org for mutations
      Link to MyCancerGenome.org
    • Improved display of selection samples on the study view page
  • Improvements:
    • "Enrichments" analysis is now run across all genes
    • The "Network" tab is now using Cytoscape.js (Adobe Flash is no longer required)

# October 6, 2015

# August 21, 2015

  • All TCGA data updated to the Firehose run of April 16, 2015.
  • New feature: Enrichments Analysis finds alterations that are enriched in either altered or unaltered samples.
  • Improvement: improved OncoPrint with better performance.

# June 3, 2015

  • Improvements:
    • Allowed downloading data in each chart/table in study summary page.
    • Added log-rank test p-values to the survival plots in study summary page.
    • Improved visualization of patient clinical data in patient-centric view.
    • Added option to merge multiple samples for the same patient in OncoPrint.

# April 28, 2015

  • New features:
    • Redesigned query interface to allow selecting multiple cancer studies
    • Redesigned Plots tab

# January 20, 2015

  • All TCGA data updated to the Firehose run of October 17, 2014
  • COSMIC data updated to V71
  • New features:
    • Query page: better search functions to find cancer studies
    • OncoPrints now support color coding of different mutation types
    • OncoPrints now support multiple clinical annotation tracks
    • OncoPrinter tool now supports mRNA expression changes
      Oncoprint with multiple clinical tracks

# January 6, 2015

  • New feature: You can now view frequencies of mutations and copy-number alterations in the study view. These tables are updated dynamically when selecting subsets of samples.
    Alterations in heavily copy-number altered endometrial cancer cases

# December 9, 2014

# October 24, 2014

# August 8, 2014

  • Released two new tools
    • Oncoprinter lets you create Oncoprints from your own, custom data
    • MutationMapper draws mutation diagrams (lollipop plots) from your custom data

# May 21, 2014

  • All TCGA data updated to the Firehose run of April 16, 2014

# May 12, 2014

# March 27, 2014

  • New features:
    • Visualizing of mutations mapped on 3D structures (individual or multiple mutations, directly in the browser)
    • Gene expression correlation analysis (find all genes with expression correlation to your query genes)
    • The Patient-Centric View now displays mutation frequencies across all cohorts in cBioPortal for each mutation
    • The Mutation Details Tab and the Patient-Centric View now display the copy-number status of each mutation
      3D viewer & Co-expression

# March 18, 2014

  • All TCGA data updated to the Firehose run of January 15, 2014
  • Updated to the latest COSMIC data (v68)
  • Added two new provisional TCGA studies:
    • Adrenocortical Carcinoma
    • Uterine Carcinosarcoma
  • Added mutation data of 898 samples from 11 published studies:
    • Hepatocellular Carcinoma (RIKEN, Nature Genetics 2012)
    • Hepatocellular Carcinoma (AMC, Hepatology in press)
    • Medulloblastoma (Broad, Nature 2012)
    • Medulloblastoma (ICGC, Nature 2012)
    • Medulloblastoma (PCGP, Nature 2012)
    • Multiple Myeloma (Broad, Cancer Cell 2014)
    • Pancreatic Adenocarcinoma (ICGC, Nature 2012)
    • Small Cell Carcinoma of the Ovary (MSKCC, Nature Genetics in press)
    • Small Cell Lung Cancer (CLCGP, Nature Genetics 2012)
    • Small Cell Lung Cancer (Johns Hopkins, Nature Genetics 2012)
    • NCI-60 Cell Lines (NCI, Cancer Res. 2012)

# December 9, 2013

  • Added mutation data of 99 bladder cancer samples (BGI, Nature Genetics 2013)

# December 6, 2013

  • Data sets matching four recently submitted or published TCGA studies are now available
    • Glioblastoma (Cell 2013)
    • Bladder carcinoma (Nature, in press)
    • Head & neck squamous cell carcinoma (submitted)
    • Lung adenocarcinoma (submitted)

# November 8, 2013

  • All TCGA data updated to the Firehose run of September 23, 2013.
  • Updated to the latest COSMIC data (v67).
  • Added mutation data of 792 samples from 9 published cancer studies:
    • Esophageal Adenocarcinoma (Broad, Nature Genetics 2013)
    • Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
    • Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
    • Kidney Renal Clear Cell Carcinoma (BGI, Nature Genetics 2012)
    • Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)
    • Prostate Adenocarcinoma (Broad/Cornell, Nature Genetics 2012)
    • Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
    • Skin Cutaneous Melanoma (Yale, Nature Genetics 2012)
    • Skin Cutaneous Melanoma (Broad, Cell 2012)

# October 21, 2013

  • Improved interface for survival plots, including information on individual samples via mouse-over
  • New fusion glyph in OncoPrints FGFR3 fusions in head and neck carcinoma
  • Improved cross-cancer query: new alteration frequency histogram (example below - query gene: CDKN2A) and mutation diagram Cross Cancer Query

# September 9, 2013

  • Updated COSMIC data (v66 Release)
  • Improved / interactive visualization on the "Protein changes" tab
  • Enhanced mutation diagrams: color-coding by mutation time and syncing with table filters
  • Addition of DNA cytoband information in the patient view of copy-number changes
  • OncoPrints now allow the display of an optional track with clinical annotation (Endometrial cancer example below) Oncoprint with clinical track

# July 25, 2013

  • Multi-gene correlation plots.
  • Variant allele frequency distribution plots for individual tumor samples.
  • Tissue images for TCGA samples in the patient view, via Digital Slide Archive. Example.

# July 16, 2013

  • All TCGA data updated to the May Firehose run (May 23, 2013).
    • TCGA Pancreatic Cancer study (provisional) added.

# July 4, 2013

  • Improved rendering of mutation diagrams, including ability to download in PDF format.
  • Improved home page: Searchable cancer study & gene set selectors, data sets selector.

# June 17, 2013

  • Improved interface for correlation plots, including information on individual samples via mouse-over.
  • Gene Details from Biogene are now available in the Network view.
  • Added mutation and copy number data from a new adenoid cystic carcinoma study: Ho et al., Nature Genetics 2013.
  • Added mutation data from 6 cancer studies.
    • Breast Invasive Carcinoma (Shah et al., Nature 2012)
    • Breast Invasive Carcinoma (Banerji et al., Nature 2012)
    • Breast Invasive Carcinoma (Stephens et al., Nature 2012)
    • Lung Adenocarcinoma (Imielinksi et al., Cell 2012)
    • Lung Adenocarcinoma (Ding et al., Nature 2008)
    • Colorectal Cancer (Seshagiri et al., Nature 2012)

# June 4, 2013

  • All TCGA data updated to the April Firehose run (April 21, 2012).

# May 14, 2013

  • Added a published TCGA study: Acute Myeloid Leukemia (TCGA, NEJM 2013).

# April 28, 2013

  • All TCGA data updated to the March Firehose run (March 26, 2012).
  • mRNA percentiles for altered genes shown in patient view.

# April 2, 2013

  • All TCGA data updated to the February Firehose run (February 22, 2012).

# March 28, 2013

  • All TCGA data updated to the January Firehose run (January 16, 2012).
  • Data from a new bladder cancer study from MSKCC has been added (97 samples, Iyer et al., JCO in press).

# February 16, 2013

  • The cBio Portal now contains mutation data from all provisional TCGA projects. Please adhere to the TCGA publication guidelines when using these and any TCGA data in your publications.
  • All data updated to the October Firehose run (October 24, 2012).
  • Sequencing read counts and frequencies are now shown in the Mutation Details table when available.
  • Improved OncoPrints, resulting in performance improvements.

# November 21, 2012

  • Major new feature: Users can now visualize genomic alterations and clinical data of individual tumors, including:
    • Summary of mutations and copy-number alterations of interest
    • Clinical trial information
    • TCGA Pathology Reports
  • New cancer summary view (Example Endometrial Cancer)
  • Updated drug data from KEGG DRUG and NCI Cancer Drugs (aggregated by PiHelper)

# October 22, 2012

  • All data updated to the Broad Firehose run from July 25, 2012.
  • COSMIC data added to Mutation Details (via Oncotator).
  • All predicted functional impact scores are updated to Mutation Assessor 2.0.
  • Users can now base queries on genes in recurrent regions of copy-number alteration (from GISTIC via Firehose).
  • The Onco Query Language (OQL) now supports queries for specific mutations or mutation types.
  • Data sets added that match the data of all TCGA publications (GBM, ovarian, colorectal, and lung squamous).

# July 18, 2012

  • Mutation data for the TCGA lung squamous cell carcinoma and breast cancer projects (manuscripts in press at Nature).
  • All data updated to the latest Broad Firehose run (May 25, 2012).
  • Drug information added to the network view (via Drugbank).
  • Improved cross-cancer queries: Option to select data types, export of summary graphs.
  • Users can now base queries on frequently mutated genes (from MutSig via Firehose).

# May 16, 2012

  • All data updated to the latest Broad Firehose run (March 21, 2012).
  • Extended cross-cancer functionality, enabling users to query across all cancer studies in our database.
  • New "build a case" functionality, enabling users to generate custom case sets, based on one or more clinical attributes.
  • New OncoPrint features, including more compact OncoPrints, and support for RPPA visualization.

# February 27, 2012

  • All data updated to the latest Broad Firehose run (January 24, 2012).
  • Validated mutation data for colorectal cancer.
  • New feature: Mutation Diagrams that show mutations in the context of protein domains. TP53 Mutations in Ovarian Cancer

# January 30, 2012

  • Updated data for several TCGA cancer studies.
  • Some small bug-fixes.

# December 22, 2011

  • Fourteen new TCGA cancer studies: This includes complete data for TCGA Colorectal Carcinoma and provisional data for thirteen other cancer types in the TCGA production pipeline. Please note that data from these thirteen new cancer types are provisional, not final and do not yet include mutation data. As per NCI guidelines, preliminary mutation data cannot be redistributed until they have been validated. TCGA

  • Four new data types:

    • Reverse-phase protein array (RPPA) data.
    • microRNA expression and copy-number (including support for multiple loci)
    • RNA-Seq based expression data.
    • log2 copy-number data.

  • Updated TCGA GBM copy-number, expression, and methylation data.

  • New gene symbol validation service. You can now use gene aliases and/or Entrez Gene IDs within your gene sets.

  • Links to IGV for visualization of DNA copy-number changes.

  • Background information from the Sanger Cancer Gene Census.

  • Two new Tutorials to get you quickly started in using the portal.

# November 14, 2011

  • New and improved mutation details, with sorting and filtering capabilities.
  • In collaboration with Bilkent University, we have added a new Network tab to our results pages. The network tab enables users to visualize, analyze and filter cancer genomic data in the context of pathways and interaction networks derived from Pathway Commons. GBM Network

# September 3, 2011

  • You can now query across different cancer studies (feature available directly from the home page).
  • Our MATLAB CGDS Cancer Genomics Toolbox is now available. The toolbox enables you to download data from the cBio Portal, and import it directly into MATLAB.
  • The code for the cBio Portal has now been fully open sourced, and made available at Google Code. If you would like to join our open source efforts and make the portal even better, drop us an email.

# March 2, 2011

New plotting features and other improvements:

  • Correlation plots that show the relationship between different data types for individual genes.
  • Survival analysis - assess survival differences between altered and non-altered patient sets.
  • Updated R Package with support for correlation plots and general improvements for retrieving and accessing data in R data frames.
  • The Web Interface now supports basic clinical data, e.g. survival data.
  • Networks for pathway analysis are now available for download. Survival Analysis

# December 15, 2010

Several new features, including:

  • Redesigned and streamlined user interface, based on user feedback and usability testing.
  • Advanced support for gene-specific alterations. For example, users can now view mutations within TP53, and ignore copy number alterations, or only view amplifications of EGFR, and ignore deletions.
  • Improved performance.
  • Frequently Asked Questions document released.
  • Updated Video Tutorial (update: old link no longer functional. Now see: YouTube

# November 4, 2010

  • Enhanced Oncoprints, enabling users to quickly visualize genomic alterations across many cases. Oncoprints now also work in all major browsers, including Firefox, Chrome, Safari, and Internet Explorer.
  • Official release of our Web Interface, enabling programmatic access to all data.
  • Official release of our R Package, enabling programmatic access to all data from the R platform for statistical computing. OncoPrints

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