PO.MD01.02 · 分子诊断与数据

cBioPortal：癌症基因组学平台

cBioPortal for cancer genomics

编号 4097 展板 2 时间 4/21 09:00–12:00 区域 Section 1 主讲 Ino de Bruijn, MS

分会场 AACR Project GENIE: Genomic Characterization

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作者与单位 Authors & Affiliations

Ino de Bruijn¹, Tali Mazor², Gaofei Zhao¹, Manda Wilson¹, Avery Wang¹, Floris Vleugels³, Pim van Nierop³, Henk-Jan van den Ham³, S. Onur Sumer¹, Jessica Singh³, Baby A. Satravada¹, Oleguer Plantalech³, Angelica Ochoa¹, Zain-ul-Abideen Nasir¹, Ramyasree Madupuri¹, Pieter Lukasse⁴, Aaron Lisman¹, James Lindsay², Xiang Li¹, Bryan Lai¹, Ritika Kundra¹, Priti Kumari⁵, Sowmiyaa Kumar³, Tim Kuijpers³, James Ko¹, Zeynep Karagöz³, Karthik Kalletla⁵, Prasanna K Jagannathan⁶, Jason Hwee¹, Guizela Huelsz Prince⁴, Charles Haynes⁷, Benjamin Gross¹, Zhaoyuan Fu², Ruslan Forostianov⁴, Calla Chennault¹, Rima AlHamad¹, Ugur Dogrusoz⁸, Allison Heath⁷, Adam C. Resnick⁷, Trevor J. Pugh⁶, Chris Sander⁹, Jianjiong Gao¹, Nikolaus Schultz¹, Ethan Cerami²

¹Memorial Sloan Kettering Cancer Center, New York City, NY,²Dana-Farber Cancer Institute, Boston, MA,³The Hyve, Utrecht, Netherlands,⁴SE4BIO, Houten, Netherlands,⁵Caris Life Sciences, Irving, TX,⁶University Health Network, Toronto, ON, Canada,⁷Children's Hospital of Philadelphia, Philadelphia, PA,⁸Bilkent University, Ankara, Turkey,⁹Harvard Medical School, Boston, MA

摘要 Abstract

中文摘要

cBioPortal 是一个被广泛使用的平台，用于对大规模多模态癌症数据集进行交互式可视化与分析。它提供队列探索工具，例如 OncoPrint、突变“棒棒糖”图、生存分析与富集分析、详尽的患者层面视图，以及整合的变异注释，以支持结果解读。 cBioPortal 的公共实例（https://www.cbioportal.org）每月为全球逾 40,000 名独立访客提供服务。它托管了来自逾 500 项研究的数据，所有数据也可通过 cBioPortal Datahub 获取。2025 年，我们新增了 38 项研究（约 35,000 例样本）。我们还在 PCAWG、CCLE 以及全部 32 项 TCGA Pan-Cancer Atlas 研究中新增了 Tumor Break Load（TBL）评分。全球各机构和公司部署的 cBioPortal 实例已超过 99 个。 cBioPortal 与 AACR Project GENIE 合作，通过一个专用实例（https://genie.cbioportal.org）提供对 GENIE 队列的访问。用户可以探索来自 20 家机构的逾 268,000 例经临床测序的样本，以及带有详细临床注释的 GENIE Biopharma Collaborative（BPC）队列，包括 NSCLC（约 2,000 例样本）、结直肠癌（约 1,500 例）和乳腺癌（约 1,200 例），未来还将有更多。在过去一年中，cBioPortal 沿两个互补方向取得了进展。首先，我们引入了一个基于对话的界面，用于自然语言数据探索，反映了我们持续利用 AI（特别是大语言模型）来增强 cBioPortal 中传统查询与可视化工作流程的努力。其次，我们发布了若干核心平台增强功能：1）通过将后端数据库从 MySQL 切换到 ClickHouse（一种 OLAP，即联机分析处理数据库），我们提升了大型队列的性能；2）Plots 标签页现在可以可视化变异等位基因频率、连接同一患者的多个样本，并具备更灵活的分类排序功能；3）通过整合 AlphaMissense 预测，变异解读得到了强化；4）我们发布了重新设计的 About 页面，突出展示本年度的成果与未来路线图。值得注意的是，其中许多功能是使用 AI 辅助技术开发的，而这些技术在软件工程中正日益成为标准实践。 cBioPortal 是开源的（https://github.com/cBioPortal），由 Memorial Sloan Kettering Cancer Center、Dana-Farber Cancer Institute、Children's Hospital of Philadelphia、Princess Margaret Cancer Centre、Bilkent University、SE4BIO 和 The Hyve 的团队协作开发。我们欢迎癌症研究界的贡献。

查看英文原文 English abstract

cBioPortal is a widely used platform for interactive visualization and analysis of large-scale multimodal cancer datasets. It provides cohort exploration tools, such as OncoPrint, mutation “lollipop” plots, survival and enrichment analyses, detailed patient-level views, and integrated variant annotations to support interpretation. The public instance of cBioPortal ( https://www.cbioportal.org ) serves >40,000 unique visitors globally each month. It hosts data from >500 studies, all also available through the cBioPortal Datahub. In 2025, we added 38 new studies (~35,000 samples). We also added Tumor Break Load (TBL) scores across PCAWG, CCLE, and all 32 TCGA Pan-Cancer Atlas studies. More than 99 cBioPortal instances are deployed at institutions and companies worldwide. cBioPortal partners with AACR Project GENIE to provide access to the GENIE cohort in a dedicated instance ( https://genie.cbioportal.org ). Users can explore >268,000 clinically sequenced samples from 20 institutions, as well as GENIE Biopharma Collaborative (BPC) cohorts with detailed clinical annotations, including NSCLC (~2,000 samples), colorectal cancer (~1,500), and breast cancer (~1,200), with more to come. Over the past year, cBioPortal progressed along two complementary directions. First, we introduced a chat-based interface for natural-language data exploration, reflecting ongoing efforts to utilize AI, specifically large language models, to augment traditional query and visualization workflows in cBioPortal. Second, we released several core platform enhancements: 1) we improved the performance for large cohorts by switching the backend database from MySQL to ClickHouse, an OLAP (Online Analytical Processing) database; 2) the Plots tab can now visualize variant allele frequencies, connect multiple samples from the same patient, and has more flexible categorical sorting; 3) variant interpretation has been strengthened through integration of AlphaMissense predictions; 4) we released a redesigned About page highlighting the year's accomplishments and future roadmap. It is worth noting that many of these features were developed using AI-assisted technologies, which are increasingly standard practice in software engineering. cBioPortal is open source ( https://github.com/cBioPortal ) and developed collaboratively by groups at Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children's Hospital of Philadelphia, Princess Margaret Cancer Centre, Bilkent University, SE4BIO, and The Hyve. We welcome contributions from the cancer research community.

利益披露 Disclosure

I. de Bruijn, None.. T. Mazor, None.. G. Zhao, None.. M. Wilson, None.. A. Wang, None.. F. Vleugels, None.. P. van Nierop, None.. H. van den Ham, None.. S. Sumer, None.. J. Singh, None.. B. A. Satravada, None.. O. Plantalech, None.. A. Ochoa, None.. Z. Nasir, None.. R. Madupuri, None.. P. Lukasse, None.. A. Lisman, None.. J. Lindsay, None.. X. Li, None.. B. Lai, None.. R. Kundra, None.. P. Kumari, None.. S. Kumar, None.. T. Kuijpers, None.. J. Ko, None.. Z. Karagöz, None.. K. Kalletla, None.. P. Jagannathan, None.. J. Hwee, None.. G. Huelsz Prince, None.. C. Haynes, None.. B. Gross, None.. Z. Fu, None.. R. Forostianov, None.. C. Chennault, None.. R. AlHamad, None.. U. Dogrusoz, None.. A. Heath, None.. A. C. Resnick, None.. T. J. Pugh, None.. C. Sander, None.. J. Gao, None.. N. Schultz, None.. E. Cerami, None.

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