pedcbioportal

July 2, 2019

• Added data consistng of 785 samples from 4 studies:
  • Non-Small Cell Lung Cancer (TRACERx, NEJM 2017) 327 samples
  • Acute myeloid leukemia or myelodysplastic syndromes (WashU, 2016) 136 samples
  • Basal Cell Carcinoma (UNIGE, Nat Genet 2016) 293 samples
  • Colon Adenocarcinoma (CaseCCC, PNAS 2015) 29 samples

June 19, 2019

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

  

June 12, 2019

• Added data of 1350 samples from 3 studies:
  • Pheochromocytoma and Paraganglioma (TCGA, Cell 2017) 178 samples
  • Metastatic Solid Cancers (UMich, Nature 2017) 500 samples
  • Acute Myeloid Leukemia (OHSU, Nature 2018) 672 samples
• Added survival data for TCGA PanCan Atlas Cohorts (>10,000 samples across 33 tumor types).
• Added hypoxia data for Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)

  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

• Added data of 568 samples from 4 studies:
  • Adenoid Cystic Carcinoma (JHU, Cancer Prev Res 2016) 25 samples
  • Histiocytosis Cobimetinib (MSK, Nature 2019) 52 samples
  • Upper Tract Urothelial Carcinoma (Cornell/Baylor/MDACC, Nat Comm 2019) 47 samples
  • Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019) 444 samples

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

• Added data of 338 samples from 4 studies:
  • Adenoid Cystic Carcinoma (MGH, Nat Gen 2016) 10 samples
  • Gallbladder Cancer (MSK, Cancer 2018) 103 samples
  • The Metastatic Prostate Cancer Project (Provisional, December 2018) 19 samples
  • Adult Soft Tissue Sarcomas (TCGA, Cell 2017) 206 samples

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

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

January 24, 2019

• Added data of 2328 samples from 8 studies:
  • Uveal Melanoma (QIMR, Oncotarget 2016) 28 samples
  • Squamous Cell Carcinoma of the Vulva (CUK, Exp Mol Med 2018) 15 samples
  • TMB and Immunotherapy (MSKCC, Nat Genet 2019) 1661 samples
  • Glioma (MSK, 2018) 91 samples
  • Urothelial Carcinoma (Cornell/Trento, Nat Gen 2016) 72 samples
  • Hepatocellular Carcinoma (MSK, Clin Cancer Res 2018) 127 samples
  • MSK Thoracic PDX (MSK, Provisional) 139 samples
  • Cholangiocarcinoma (MSK, Clin Cancer Res 2018) 195 samples
• Updated data for The Metastatic Breast Cancer Project (Provisional, October 2018) 237 samples

  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

October 19, 2018

• Support selection of transcript of interest in the MutationMapper tool via Genome Nexus.

October 17, 2018

• Added data of 3578 samples from 8 studies:
  • Rhabdoid Cancer (BCGSC, Cancer Cell 2016) 40 samples
  • Diffuse Large B-Cell Lymphoma (Duke, Cell 2017) 1001 samples
  • Diffuse Large B cell Lymphoma (DFCI, Nat Med 2018) 135 samples
  • Breast Fibroepithelial Tumors (Duke-NUS, Nat Genet 2015) 22 samples
  • Uterine Clear Cell Carcinoma (NIH, Cancer 2017) 16 samples
  • Endometrial Cancer (MSK, 2018) 197 samples
  • Breast Cancer (MSK, Cancer Cell 2018) 1918 samples
  • MSS Mixed Solid Tumors (Van Allen, 2018) 249 samples
• Updated data for The Angiosarcoma Project (Provisional, September 2018) 48 samples

  Auguest 20, 2018

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

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.

July 27, 2018

• Added data of 2787 samples from 10 studies:
  • Mixed Tumors (PIP-Seq 2017) 103 samples
  • Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017) 105 samples
  • Pediatric Neuroblastoma (TARGET, 2018) 1089 samples
  • Pediatric Pan-Cancer (DKFZ - German Cancer Consortium, 2017) 961 samples
  • Skin Cutaneous Melanoma (Broad, Cancer Discov 2014) 78 samples
  • Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014) 39 samples
  • Diffuse Large B-cell Lymphoma (BCGSC, Blood 2013) 53 samples
  • Non-Hodgkin Lymphoma (BCGSC, Nature 2011) 14 samples
  • Chronic lymphocytic leukemia (ICGA, Nat 2011) 105 samples
  • Neuroblastoma (Broad Institute 2013) 240 samples

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

May 10, 2018

• Enhanced OncoPrint to show germline mutations – see example

April 17, 2018

• Added data of 3732 samples from 4 TARGET studies:
  • Pediatric Acute Lymphoid Leukemia - Phase II (TARGET, 2018) 1978 samples
  • Pediatric Acute Myeloid Leukemia (TARGET, 2018) 1025 samples
  • Pediatric Rhabdoid Tumor (TARGET, 2018) 72 samples
  • Pediatric Wilms’ Tumor (TARGET, 2018) 657 samples
• Added data of 3416 samples from 10 published studies:
  • Prostate Adenocarcinoma (MSKCC/DFCI, Nature Genetics 2018) 1013 samples
  • Prostate Adenocarcinoma (EurUrol, 2017) 65 samples
  • Non-Small Cell Lung Cancer (MSK, JCO 2018) 240 samples
  • Small-Cell Lung Cancer (Multi-Institute 2017) 20 samples
  • The Angiosarcoma Project (Provisional, February 2018) 14 samples
  • Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2016) 73 samples
  • Updated Segment data and Allele Frequencies for The Metastatic Breast Cancer Project (Provisional, October 2017) 103 samples
  • Colorectal Cancer (MSK, Cancer Cell 2018) 1134 samples
  • Metastatic Esophagogastric Cancer (MSK,Cancer Discovery 2017) 341 samples
  • Bladder Cancer (TCGA, Cell 2017) 413 samples

April 05, 2018

• Added data from the TCGA PanCanAtlas project with >10,000 samples from 33 tumor types:
  • Adrenocortical Carcinoma (TCGA, PanCancer Atlas)
  • Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)
  • Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
  • Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
  • Colon Adenocarcinoma (TCGA, PanCancer Atlas)
  • Cholangiocarcinoma (TCGA, PanCancer Atlas)
  • Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)
  • Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)
  • Glioblastoma Multiforme (TCGA, PanCancer Atlas)
  • Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
  • Kidney Chromophobe (TCGA, PanCancer Atlas)
  • Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)
  • Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)
  • Acute Myeloid Leukemia (TCGA, PanCancer Atlas)
  • Brain Lower Grade Glioma (TCGA, PanCancer Atlas)
  • Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)
  • Lung Adenocarcinoma (TCGA, PanCancer Atlas)
  • Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)
  • Mesothelioma (TCGA, PanCancer Atlas)
  • Ovarian Serous Cystadenocarcinoma (TCGA, PanCancer Atlas)
  • Pancreatic Adenocarcinoma (TCGA, PanCancer Atlas)
  • Pheochromocytoma and Paraganglioma (TCGA, PanCancer Atlas)
  • Prostate Adenocarcinoma (TCGA, PanCancer Atlas)
  • Rectum Adenocarcinoma (TCGA, PanCancer Atlas)
  • Sarcoma (TCGA, PanCancer Atlas)
  • Skin Cutaneous Melanoma (TCGA, PanCancer Atlas)
  • Stomach Adenocarcinoma (TCGA, PanCancer Atlas)
  • Testicular Germ Cell Tumors (TCGA, PanCancer Atlas)
  • Thyroid Carcinoma (TCGA, PanCancer Atlas)
  • Thymoma (TCGA, PanCancer Atlas)
  • Uterine Corpus Endometrial Carcinoma (TCGA, PanCancer Atlas)
  • Uterine Carcinosarcoma (TCGA, PanCancer Atlas)
  • Uveal Melanoma (TCGA, PanCancer Atlas)

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

• You can now combine multiple studies and view them on the study summary page. Example: liver cancer studies
• You can now bookmark or share your selected samples as virtual studies with the share icon on the study summary page. Example: a virtual study of breast tumors
• Cross-study query reimplemented: Now you can view an OncoPrint of multiple studies. Example: querying NSCLC tumors from 5 studies

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

• Added data of 1646 samples from 7 published studies:
  • NGS in Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas tumors (MSK, Neuro Oncol 2017) 22 samples
  • MSK-IMPACT Clinical Sequencing Cohort for Non-Small Cell Cancer (MSK, Cancer Discovery 2017) 915 samples
  • Paired-exome sequencing of acral melanoma (TGEN, Genome Res 2017) 38 samples
  • MSK-IMPACT Clinical Sequencing Cohort in Prostate Cancer (MSK, JCO Precision Oncology 2017) 504 samples
  • Whole-exome sequences (WES) of pretreatment melanoma tumors (UCLA, Cell 2016) 39 samples
  • Next generation sequencing (NGS) of pre-treatment metastatic melanoma samples (MSK, JCO Precision Oncology 2017) 66 samples
  • Targeted gene sequencing in 62 high-grade primary Unclassified Renal Cell Carcinoma (MSK, Nature 2016) 62 samples
• Updated data for MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017) with overall survival data.

  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

• 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.

May 12, 2017

• Added data of 12,211 samples from 11 published studies:
  • MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017) 10,945 samples
  • Whole-genome sequencing of pilocytic astrocytomasatic (DKFZ, Nat Genetics, 2013) 96 samples
  • Hepatocellular Carcinomas (INSERM, Nat Genet 2015) 243 samples
  • Cystic Tumor of the Pancreas (Johns Hopkins, PNAS 2011) 32 samples
  • Whole-Genome Sequencing of Pancreatic Neuroendocrine Tumors (ARC- Net, Nature, 2017) 98 samples
  • Medulloblastoma (Sickkids, Nature 2016) 46 samples
  • Genetic Characterization of NSCLC young adult patients (University of Turin, Lung Cancer 2016) 41 samples
  • Genomic Profile of Patients with Advanced Germ Cell Tumors (MSK, JCO 2016). 180 samples
  • Ampullary Carcinoma (Baylor, Cell Reports 2016) 160 samples
  • Mutational profiles of metastatic breast cancer (INSERM, 2016) 216 samples
  • Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016) 154 samples

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

  

  • 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

  

  • 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

  

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

  

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

July 24, 2016

• Added data of 4,375 samples from 21 published studies:
  • Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015) 102 samples
  • Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014) 28 samples
  • Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013) 24 samples
  • Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015) 12 samples
  • Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016) 34 samples
  • Breast Cancer (METABRIC, Nat Commun 2016) 1980 samples
  • Chronic Lymphocytic Leukemia (Broad, Cell 2013) 160 samples
  • Chronic Lymphocytic Leukemia (IUOPA, Nature 2015) 506 samples
  • Colorectal Adenocarcinoma (DFCI, Cell Reports 2016) 619 samples
  • Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015) 42 samples
  • Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012) 58 samples
  • Hepatocellular Adenoma (Inserm, Cancer Cell 2014) 46 samples
  • Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013) 44 samples
  • Insulinoma (Shanghai, Nat Commun 2013) 10 samples
  • Malignant Pleural Mesothelioma (NYU, Cancer Res 2015) 22 samples
  • Mantle Cell Lymphoma (IDIBIPS, PNAS 2013) 29 samples
  • Myelodysplasia (Tokyo, Nature 2011) 29 samples
  • Neuroblastoma (Broad, Nat Genet 2013) 56 samples
  • Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013) 40 samples
  • Pancreatic Adenocarcinoma (QCMG, Nature 2016) 383 samples
  • Recurrent and Metastatic Head & Neck Cancer (JAMA Oncology, 2016) 151 samples
• New TCGA study:
  • Pan-Lung Cancer (TCGA, Nat Genet 2016) 1144 samples
• Updated TCGA provisional studies
  • updated to the Firehose run of January 28, 2016
  • RPPA data updated with the latest data from MD Anderson
  • OncoTree codes assigned per sample

June 6, 2016

• New features:
  • Annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages (via OncoKB)
    
• 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

• New features:
  • Visualization of “Enrichments Analysis” results via volcano plots
  • Improved performance of the cross cancer expression view by switching to Plot.ly graphs
  • Improvements to the “Clinical Data” tab on the study view page
  • More customization options for the cross-cancer histograms
  • Performance improvements in the study view and query result tabs
• Added data of 1235 samples from 3 published studies:
  • Merged Cohort of LGG and GBM (TCGA, 2016)
  • Lung Adenocarcinoma (MSKCC, 2015)
  • Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)

January 12, 2016

• New features:
  • Visualization of multiple samples in a patient
  • Visualization of timeline data of a patient (example)
    
• All TCGA data updated to the latest Firehose run of August 21, 2015
• New TCGA studies:
  • Cholangiocarcinoma (TCGA, Provisional)
  • Mesothelioma (TCGA, Provisional)
  • Testicular Germ Cell Cancer (TCGA, Provisional)
  • Thymoma (TCGA, Provisional)
• Added data of 650 samples from 10 published studies:
  • Neuroblastoma (AMC Amsterdam, Nature 2012)
  • Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
  • Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014)
  • Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discovery 2014)
  • Low-Grade Gliomas (UCSF, Science 2014)
  • Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
  • Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
  • Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
  • Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
  • Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
• All mutation data mapped to UniProt canonical isoforms

December 29, 2015

• New features:
  • Tumor vs Normals visalization in the cancer study(only studies mapped to normal dataset)
  • Tumor vs Normals visalization in cross-cancer study view

December 23, 2015

• New features:
  • Visualization of RNA-seq expression levels across TCGA studies (cross-cancer queries)
    
  • Selection of genes in the study view to initiate queries
    
• 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</br>

November 9, 2015

• New features:
  • Links to MyCancerGenome.org for mutations
    
  • 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

• New TCGA data:
  • Breast Invasive Carcinoma (TCGA, Cell 2015)
  • Prostate Adenocarcinoma (TCGA, in press)
  • Uveal Melanoma (TCGA, Provisional)
• Added data of 763 samples from 12 published studies:
  • Small Cell Lung Cancer (U Cologne, Nature 2015)
  • Uterine Carcinosarcoma (JHU, Nat Commun 2014)
  • Microdissected Pancreatic Cancer Whole Exome Sequencing (UTSW, Nat Commun 2015)
  • Pancreatic Neuroendocrine Tumors (JHU, Science 2011)
  • Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
  • Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
  • Rhabdomyosarcoma (NIH, Cancer Discov 2014)
  • Thymic epithelial tumors (NCI, Nat Genet 2014)
  • Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
  • Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
  • Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
  • Gallbladder Carcinoma (Shanghai, Nat Genet 2014)

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
    

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.
  

December 9, 2014

• New TCGA data:
  • Added complete and up-to-date clinical data for all TCGA provisional studies
  • All TCGA data updated to the Firehose run of July 15, 2014
  • New TCGA provisional studies: Esophageal cancer, Pheochromocytoma and Paraganglioma (PCPG)
  • New published TCGA studies: Thyroid Cancer and Kidney Chromophobe
• Added data of 172 samples from 4 published studies:
  • Cholangiocarcinoma (National University of Singapore, Nature Genetics 2012)
  • Cholangiocarcinoma (National Cancer Centre of Singapore, Nature Genetics 2013)
  • Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nature Genetics 2013)
  • Bladder Cancer (MSKCC, Eur Urol 2014)
• New features:
  • Redesigned Mutual Exclusivity tab
  • Added correlation scores for scatter plots on the Plots tab
  • Download links to GenomeSpace

October 24, 2014

• Added data of 885 samples from 11 published studies:
  • Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biology 2014)
  • Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
  • Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nature Genetics 2014)
  • Melanoma (Broad/Dana Farber, Nature 2012)
  • Nasopharyngeal Carcinoma (National University Singapore, Nature Genetics 2014)
  • Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
  • Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
  • Stomach Adenocarcinoma (TCGA, Nature 2014)
  • Stomach Adenocarcinoma (Pfizer and University of Hong Kong, Nature Genetics 2014)
  • Stomach Adenocarcinoma (University of Hong Kong, Nature Genetics 2011)
  • Stomach Adenocarcinoma (University of Tokyo, Nature Genetics 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

• Improved study summary page including survival analysis based on clinical attributes
  e.g. TCGA Endometrial Cancer cohort
  

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
    

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
• Improved cross-cancer query: new alteration frequency histogram (example below - query gene: CDKN2A) and mutation diagram

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)

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.

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.

• 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.

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.

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.