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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.

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 user-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 almost 300 studies spanning individual labs and large consortia. Data is also available in the cBioPortal Datahub (https://github.com/cBioPortal/datahub/). In 2020 we added data from 21 studies, totaling almost 30,000 samples. In addition, we added data to existing TCGA PanCancer Atlas studies, including MSI status, mRNA-seq z-scores relative to normal tissue, microbiome data, and RPPA-based protein expression. The cBioPortal also supports AACR Project GENIE with a dedicated instance hosting the GENIE cohort of 112,000 clinically sequenced samples from 19 institutions worldwide (https://genie.cbioportal.org). The site is accessed by over 30,000 unique visitors per month. To support these users, we hosted a five-part instructional webinar series. Recordings of these webinars are available on our website and have already been viewed thousands of times. In addition, more than 50 instances are installed at academic institutions and pharmaceutical/biotechnology companies. In support of these local instances, we continue to simplify the installation process: we now provide a docker compose solution which includes all microservices to run the web app as well as data validation, import and migration. We continue to enhance and expand the functionality of cBioPortal. This year we significantly enhanced the group comparison feature; it is now integrated into gene-specific queries and supports comparison of more data types including DNA methylation, microbiome, and any outcome measure. We also expanded support of longitudinal data: the existing patient timeline has been refactored and now supports a wider range of data and visualizations; a new “Genomic Evolution” tab highlights changes in mutation allele frequencies across multiple samples from a patient; and samples can now be selected based on pre- or post-treatment status. Other features released this year include: allowing users to add gene-level plots for continuous molecular profiles in study view, enabling users to select the desired transcript on the Mutations tab, and integration of PathwayMapper. The 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. Citation Format: Jianjiong Gao, Tali Mazor, Ino de Bruijn, Adam Abeshouse, Diana Baiceanu, Ziya Erkoc, Benjamin Gross, David Higgins, Prasanna K. Jagannathan, Karthik Kalletla, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Pieter Lukasse, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Joyce Quach, Sander Rodenburg, Anusha Satravada, Fedde Schaeffer, Robert Sheridan, Lucas Sikina, S. Onur Sumer, Yichao Sun, Paul van Dijk, 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. The cBioPortal for Cancer Genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 207.

Conference Name: Proceedings of the 10th International Conference, NUMGRID 2020 Date of Conference: November 2020 Tetrahedralization algorithms are used for many applications such as Ray Tracing and Finite Element Methods. For most of the applications, constrained tetrahedralization algorithms are chosen because they can preserve input triangles. The constrained tetrahedralization algorithms developed so far might suffer from a lack of memory. We propose an out-of-core near Delaunay constrained tetrahedralization algorithm using the divide-and-conquer paradigm to decrease memory usage. If the expected memory usage is below the user-defined memory limit, we tetrahedralize using TetGen. Otherwise, we subdivide the set of input points into two halves and recursively apply the same idea to the two halves. When compared with the TetGen, our algorithm tetrahedralizes the point clouds using less amount of memory but takes more time and generates tetrahedralizations that do not satisfy the Delaunay criterion at the boundaries of the merged regions. We quantify the error using the aspect-ratio metric. The difference between the tetrahedralizations that our approach produce and the Delaunay tetrahedralization are small and the results are acceptable for most applications.

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.