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de Bruijn I, Mazor T, Abeshouse A, Baiceanu D, Carrero S, Garcia Lara E, Gross B, Higgins DM, Jagannathan PK, Kumari P, Kundra R, Lai B, Li X, Lindsay J, Lisman A, Madala D, Madupuri R, Ochoa A, Özgül YZ, Plantalech O, Rodenburg S, Satravada BA, Sheridan R, Sikina L, Singh J, Sumer SO, Sun Y, van Nierop P, Wang A, Wilson M, Zhang H, Zhao G, van Hagen S, Dogrusoz U, Heath A, Resnick A, Pugh TJ, Sander C, Cerami E, Gao J, Schultz N. Abstract 4256: cBioPortal for Cancer Genomics. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
cBioPortal for Cancer Genomics is an open-source platform for interactive, exploratory analysis of large-scale clinico-genomic data sets. cBioPortal provides a suite of user-friendly visualizations and analyses, including OncoPrints, mutation “lollipop” plots, variant interpretation, group comparison, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization.
The public site (https://www.cbioportal.org) is accessed by >35,000 unique visitors each month and hosts data from >350 studies spanning individual labs and large consortia. In addition, at least 74 instances of cBioPortal are installed at academic institutions and companies worldwide. To better support all users, we unified our documentation (https://docs.cbioportal.org) and added a user guide and an ongoing series of ‘how-to’ videos to address common questions.
In 2022 we added 32 studies (>38,000 samples) to the public site. In addition, we added a nonsynonymous tumor mutation burden (TMB) value for all samples and enhanced the TCGA PanCancer Atlas studies with DNA methylation and treatment data. All data is available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub.
We also host a dedicated instance for AACR Project GENIE, enabling access to the GENIE cohort of >165,000 clinically sequenced samples from 19 institutions (https://genie.cbioportal.org). The GENIE Biopharma Collaborative (BPC) enables the collection of comprehensive clinical annotations, including response, outcome, and treatment history. The first BPC cohorts are now available: ~2,000 non-small cell lung cancer samples and ~1,500 colorectal cancer samples.
Support for multimodal data analysis has been a major focus, including several new integrations with external tools. Single cell data is now available in the CPTAC GBM study and can be visualized throughout cBioPortal, and via integration with cellxgene. On the patient page, H&E and mIF images can be visualized via integration with Minerva, and the genomic overview now integrates IGV.
We continue to enhance existing features. In the study view, users can now add charts comparing categorical vs continuous data, and the plots tab includes a heatmap option. We replaced the existing fusion data type with a generalized structural variant data type that supports detailed information including breakpoints and orientation, to enable new visualizations and analyses. Pathway level analysis has been extended with a new integration with NDEx.
cBioPortal is fully open source (https://github.com/cBioPortal/). Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, Caris Life Sciences, Bilkent University and The Hyve. We welcome open source contributions from others in the cancer research community.
Citation Format: Ino de Bruijn, Tali Mazor, Adam Abeshouse, Diana Baiceanu, Stephanie Carrero, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Bryan Lai, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Yusuf Ziya Özgül, Oleguer Plantalech, Sander Rodenburg, Baby Anusha Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz. cBioPortal for Cancer Genomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4256.
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Affiliation(s)
- Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tali Mazor
- 2Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bryan Lai
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiang Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Aaron Lisman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Divya Madala
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | | | - S Onur Sumer
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yichao Sun
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Avery Wang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Allison Heath
- 4Children's Hospital of Philadelphia, Philadelphia, PA
| | - Adam Resnick
- 4Children's Hospital of Philadelphia, Philadelphia, PA
| | - Trevor J. Pugh
- 5Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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Gao J, Mazor T, de Bruijn I, Abeshouse A, Baiceanu D, Erkoc Z, Lara EG, Gross B, Higgins DM, Jagannathan PK, Kumari P, Kundra R, Li X, Lindsay J, Lisman A, Madala D, Madupuri R, Ochoa A, Plantalech O, Rodenburg S, Satravada BA, Sheridan R, Sikina L, Singh J, Sumer SO, Sun Y, van Nierop P, Wang A, Wilson M, Zhang H, Zhao G, van Hagen S, van Bochove K, Dogrusoz U, Heath A, Resnick A, Pugh TJ, Sander C, Cerami E, Schultz N. Abstract 1155: cBioPortal for cancer genomics. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
cBioPortal for Cancer Genomics is an open-source platform for interactive, exploratory analysis of large-scale cancer genomics data sets. cBioPortal provides a user-friendly interface that integrates genomic and clinical data, and provides a suite of visualizations and analyses, including OncoPrints, mutation “lollipop” plots, variant interpretation, group comparison, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization. cBioPortal also integrates external tools including CIViC, Cancer Digital Slide Archive, Next-Generation Clustered Heat Map, IGV and Bioconductor to facilitate interpretation.
The public site (https://www.cbioportal.org) is accessed by ~35,000 unique visitors each month and hosts data from >325 studies spanning individual labs and large consortia. In addition, >67 instances of cBioPortal are installed at academic institutions and pharmaceutical/biotechnology companies worldwide. In 2021 we added data from 32 studies, totaling >24,000 samples, to the public site. All data is also available in the cBioPortal Datahub: https://github.com/cBioPortal/datahub/.
We also host a dedicated instance for AACR Project GENIE, enabling access to the GENIE cohort of >135,000 clinically sequenced samples from 19 institutions (https://genie.cbioportal.org). In addition, the GENIE Biopharma Collaborative (BPC) enables the collection of comprehensive clinical annotations, including response, outcome, and treatment histories. The first BPC release contains data from >1,800 non-small cell lung cancer samples and will be released in early 2022.
The growing GENIE cohort and the BPC clinical data have driven a number of recent developments, including performance improvements (the load time for the GENIE cohort was reduced from minutes to seconds). To leverage the BPC clinical data, we enabled sample selection based on treatment status, extended support for outcome analysis, and enhanced the patient timeline representation to incorporate response data.
Additional development work has focused on improvements to variant interpretation, enhancements to the Mutations tab, and support for novel molecular assays via the ‘generic assay’ data type. Documentation on these new features and many others is available at https://www.cbioportal.org/news.
cBioPortal is fully open source (https://github.com/cBioPortal/) under a GNU Affero GPL license. Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, Bilkent University and The Hyve. We welcome open source contributions from others in the cancer research community.
Citation Format: Jianjiong Gao, Tali Mazor, Ino de Bruijn, Adam Abeshouse, Diana Baiceanu, Ziya Erkoc, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Sander Rodenburg, Baby A. Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S. Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Kees van Bochove, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz. cBioPortal for cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1155.
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Affiliation(s)
- Jianjiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tali Mazor
- 2Dana-Farber Cancer Institute, Boston, MA
| | - Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiang Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Aaron Lisman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Divya Madala
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | - S. Onur Sumer
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yichao Sun
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Avery Wang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Allison Heath
- 5Children's Hospital of Philadelphia, Philadelphia, PA
| | - Adam Resnick
- 5Children's Hospital of Philadelphia, Philadelphia, PA
| | - Trevor J. Pugh
- 6Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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de Bruijn I, Li X, Sumer O, Gross B, Sheridan R, Ochoa A, Wilson M, Wang A, Zhang H, Lisman A, Abeshouse A, Rodenburg S, van Hagen S, Fijneman R, Meijer G, Schultz N, Gao J. Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Interpreting genomic variants in tumor samples presents a challenge in research and the clinical setting. A major barrier is that information about variants is fragmented across disparate databases, and aggregating information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one stop shop for variant annotation, equipped with a powerful API for bulk annotation of variants and a user friendly interface for cancer researchers.
Genome Nexus is available at https://www.genomenexus.org. It a) aggregates variant information from a large number of sources that are relevant to cancer research and clinical applications; b) allows high-performance programmatic access to the aggregated data via a unified API; c) provides a search interface and a reference page for individual cancer variants; d) provides user-friendly tools for annotating variants in patients; e) is freely available under an open source license and can be installed in a private cloud or local environment.
Genome Nexus contains annotations from more than a dozen resources, including those that provide variant effect information (VEP), protein sequence annotation (Uniprot, Pfam, dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, SIFT), population prevalence (gnomAD, dbSNP, ExAC), cancer population prevalence (Cancer Hotspots, SignalDB) and clinical actionability (OncoKB, CIViC, Clinvar). The annotations can be accessed through the website, the API, and a command line client.
Genome Nexus is unique in providing a user friendly interface specific to cancer that allows high performance annotation of any variant. It is the main annotation service for the popular cancer genomics tool cBioPortal, which serves thousands of users daily. It is also offered as a standalone tool for annotation, allowing researchers and clinicians as well as genomic infrastructure developers to leverage it directly in their own workflows. For example, a local installation of Genome Nexus is used for annotating all variants in AACR Project GENIE.
Citation Format: Ino de Bruijn, Xiang Li, Onur Sumer, Benjamin Gross, Robert Sheridan, Angelica Ochoa, Manda Wilson, Avery Wang, Hongxin Zhang, Aaron Lisman, Adam Abeshouse, Sander Rodenburg, Sjoerd van Hagen, Remond Fijneman, Gerrit Meijer, Nikolaus Schultz, Jianjiong Gao. Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1156.
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Affiliation(s)
- Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiang Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Onur Sumer
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Manda Wilson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avery Wang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron Lisman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Gerrit Meijer
- 3Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Jianjiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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de Bruijn I, Li X, Sumer SO, Gross B, Sheridan R, Ochoa A, Wilson M, Wang A, Zhang H, Lisman A, Abeshouse A, Zhang E, Thum A, Sadagopan A, Heins Z, Kandoth C, Rodenburg S, Tan S, Lukasse P, van Hagen S, Fijneman RJA, Meijer GA, Schultz N, Gao J. Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. JCO Clin Cancer Inform 2022; 6:e2100144. [PMID: 35148171 PMCID: PMC8846305 DOI: 10.1200/cci.21.00144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Interpretation of genomic variants in tumor samples still presents a challenge in research and the clinical setting. A major issue is that information for variant interpretation is fragmented across disparate databases, and aggregation of information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one-stop shop for variant annotation with a user-friendly interface for cancer researchers and clinicians. METHODS Genome Nexus (1) aggregates variant information from sources that are relevant to cancer research and clinical applications, (2) allows high-performance programmatic access to the aggregated data via a unified application programming interface, (3) provides a reference page for individual cancer variants, (4) provides user-friendly tools for annotating variants in patients, and (5) is freely available under an open source license and can be installed in a private cloud or local environment and integrated with local institutional resources. RESULTS Genome Nexus is available at https://www.genomenexus.org. It displays annotations from more than a dozen resources including those that provide variant effect information (variant effect predictor), protein sequence annotation (Uniprot, Pfam, and dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, and SIFT), population prevalences (gnomAD, dbSNP, and ExAC), cancer population prevalences (Cancer hotspots and SignalDB), and clinical actionability (OncoKB, CIViC, and ClinVar). We describe several use cases that demonstrate the utility of Genome Nexus to clinicians, researchers, and bioinformaticians. We cover single-variant annotation, cohort analysis, and programmatic use of the application programming interface. Genome Nexus is unique in providing a user-friendly interface specific to cancer that allows high-performance annotation of any variant including unknown ones. CONCLUSION Interpretation of cancer genomic variants is improved tremendously by having an integrated resource for annotations. Genome Nexus is freely available under an open source license.
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Affiliation(s)
- Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert Sheridan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avery Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aaron Lisman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Adam Abeshouse
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Cornell University, Ithaca, NY
| | - Alice Thum
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,MongoDB, New York, NY
| | | | - Zachary Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Boston University, Boston, MA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Pathology and Lab Medicine, University of California, Los Angeles, CA
| | | | - Sander Tan
- The Hyve, Utrecht, the Netherlands,Directie Informatie Technologie, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY,Jianjiong Gao, PhD, Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065; e-mail:
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Gao J, Mazor T, Abeshouse A, de Bruijn I, Gross B, Kalletla K, Kumari P, Kundra R, Li X, Lindsay J, Lisman A, Lukasse P, Madupuri R, Ochoa A, Plantalech O, Rodenburg S, Schaeffer F, Sheridan R, Sikina L, Su J, Sumer SO, Sun Y, van Dijk P, van Hagen S, van Nierop P, Wang A, Wilson M, Zhang H, Zhao G, Zhu K, van Bochove K, Dogrusoz U, Heath A, Resnick A, Pugh TJ, Sander C, Cerami E, Schultz N. Abstract 3209: The cBioPortal for Cancer Genomics. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a biologist-friendly interface. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including OncoPrint, mutation diagram, variant interpretation, survival analysis, expression correlation analysis, alteration enrichment analysis, cohort and patient-level visualization, among others.
The public site (https://www.cbioportal.org) hosts data from more than 280 studies from diverse sources including individual labs and large consortia. All data is also available in the cBioPortal Datahub (https://github.com/cBioPortal/datahub/). Data from 40 studies, totaling more than 10,000 samples, was added in 2019, including the latest release from the Cancer Cell Line Encyclopedia and the Pediatric Preclinical Testing Consortium. The site is accessed by over 30,000 unique visitors per month. cBioPortal also supports AACR Project GENIE with a dedicated instance hosting the GENIE cohort of 80,000 clinically sequenced samples from 19 institutions worldwide (http://genie.cbioportal.org).
In addition, more than 40 instances are installed locally at academic institutions and pharmaceutical/biotechnology companies. In support of these local installations, cBioPortal now has improved documentation and simplified installation via container technologies such as Docker and Kubernetes.
Building on our successful refactoring of the code base, we have released a variety of new features and enhancements to cBioPortal over the past year. Most notably, we released a group comparison feature, enabling users to define groups of interest based on any clinical or genomic features. User-defined groups can be compared simultaneously across genomic and clinical data, including survival analysis and genomic alteration enrichment analysis. Additional new features include: integration of mutation annotations from dbSNP, ClinVar and gnomAD; support for waterfall plots to enable treatment response analysis; saving user preferences for chart layout on study view.
The cBioPortal remains under active development. The portal is fully open source (https://github.com/cBioPortal/) under a GNU Affero GPL license. Development is a collaborative effort among groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children's Hospital of Philadelphia, Princess Margaret Cancer Centre, and The Hyve. Ongoing and future development is focused on: (1) building the open source community; (2) continued performance improvements; (3) expanding user support, documentation and training resources; (4) supporting longitudinal data analysis and visualization; (5) developing novel features to support immunogenomics and immunotherapy; (6) enhancing individual variants and overall patient interpretation; (7) supporting single cell data visualizations and analysis.
Citation Format: Jianjiong Gao, Tali Mazor, Adam Abeshouse, Ino de Bruijn, Benjamin Gross, Karthik Kalletla, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Pieter Lukasse, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Sander Rodenburg, Fedde Schaeffer, Robert Sheridan, Lucas Sikina, Jing Su, S. Onur Sumer, Yichao Sun, Paul van Dijk, Sjoerd van Hagen, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Kelsey Zhu, Kees van Bochove, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for Cancer Genomics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3209.
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Affiliation(s)
- Jianjiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Tali Mazor
- 2Dana-Farber Cancer Institute, Boston, MA
| | - Adam Abeshouse
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Benjamin Gross
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Xiang Li
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | - Aaron Lisman
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | - Angelica Ochoa
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | | | | | | | - Jing Su
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - S. Onur Sumer
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Yichao Sun
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | | | - Avery Wang
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Manda Wilson
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Kelsey Zhu
- 5Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Allison Heath
- 3Children's Hospital of Philadelphia, Philadelphia, PA
| | - Adam Resnick
- 3Children's Hospital of Philadelphia, Philadelphia, PA
| | - Trevor J. Pugh
- 5Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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