The cBioPortal for Cancer Genomics

癌症基因组学的 cBioPortal

• 批准号: 10697321
• 负责人: Ethan Cerami
• 金额: $ 149.3万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-05 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10697321
• 关键词: Acceleration; Address; American Association of Cancer Research; Architecture; Area; Big Data; Biological Assay; Biological Markers; Biotechnology; Cancer Center; Cancer Patient; Clinical; Cloud Computing; Code; Collaborations; Communities; Community Outreach; Computer software; Consultations; Dana-Farber Cancer Institute; Data; Data Analyses; Data Set; Development; Ecosystem; Education and Outreach; Ensure; Funding; Future; GENIE; Genes; Genomics; Growth; Imaging Techniques; Institution; Internet; Licensing; Malignant Neoplasms; Memorial Sloan-Kettering Cancer Center; Molecular; Molecular Profiling; Patient Care; Pediatric Hospitals; Performance; Pharmaceutical Preparations; Pharmacologic Substance; Philadelphia; Publishing; Research; Research Personnel; Resources; Sampling; Scientist; Series; Services; Site; Technology; Traction; Training; Variant; Visualization; anticancer research; base; cBioPortal; cancer care; cancer genomics; cancer initiation; complex data; data mining; data pipeline; data sharing; data visualization; genomic data; genomic profiles; hackathon; human genome sequencing; improved; insight; interoperability; large datasets; medical schools; molecular imaging; novel; online resource; open source; outreach; personalized medicine; precision medicine; precision oncology; programs; research and development; social media; software development; technology platform; tool; treatment effect; tumor; usability; user-friendly; web portal; webinar

PROJECT SUMMARY Genomic sequencing of tumor samples is now a routine component of cancer care, providing unprecedented insight into cancer initiation, progression, and treatment effects. Additionally, novel molecular profiling and imaging techniques are gaining traction, generating ever more data. Ensuring that these data sets are easily accessible and interpretable to scientists and clinicians is of vital importance. Towards this end, we seek to evolve and expand the capabilities of the cBioPortal for Cancer Genomics, a unique platform that enables interactive exploratory analysis of large-scale cancer genomic data. The cBioPortal is the most widely used and most highly cited tool within the cancer genomics community. The public site, with data from 325 cancer studies, is accessed by >34,000 unique users each month. The cBioPortal instance that supports AACR Project GENIE, a multi-institutional data sharing initiative, now hosts genomic profiles from >120,000 tumors. Since the software is available under an open source license, >65 cancer centers and pharmaceutical companies have institutional installations of cBioPortal to analyze their own data. Multiple institutions are making contributions to the software, including the five that are part of this application (Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Harvard Medical School, Princess Margaret Cancer Centre, and Children’s Hospital of Philadelphia). To ensure that this vital resource continues to aid the cancer research community and to keep pace with the rapidly advancing fields of cancer genomics and precision cancer medicine, including the continuing increase in the number of profiled tumor samples, we propose to actively sustain and evolve the cBioPortal platform. Specifically, we plan to make improvements across the entire cBioPortal software architecture (Aim 1); this includes significant changes to address key performance bottlenecks, a new API capable of supporting federated queries, a new App Store, and improvements to our cloud infrastructure and data pipelines. We will also support several new molecular data types, add two entirely new cBioPortal views, develop new features for precision oncology, and improve general usability (Aim 2). We propose to continue funding a group of core developers across five institutions, expand the base of code contributors, and continue to collaborate with The Hyve to support biotech and pharmaceutical companies (Aim 3). Finally, to maximize use in the scientific community, we plan to continue to improve community outreach, user support, and training (Aim 4). These improvements will be necessary to ensure that cBioPortal continues to provide an essential service for cancer research and development of new biomarkers and drugs, especially as more cancer centers are using the cBioPortal as part of their precision medicine programs, and as pharmaceutical companies are using it for internal research. We expect that, over the next few years, the cBioPortal will continue to have a strong impact on all areas of cancer research and patient care.

项目摘要 肿瘤样品的基因组测序现在是癌症护理的常规组成部分，提供了前所未有的 深入了解癌症的启动，进展和治疗效果。另外，新颖的分子分析和 成像技术正在获得吸引力，产生更多的数据。确保这些数据集很容易 可访问和解释的科学家和临床医生至关重要。为此，我们试图 进化并扩展了CBIOPORTAL的癌症基因组学的能力，这是一个独特的平台，可实现 大规模癌症基因组数据的互动探索性分析。 cbioportal是最广泛使用的 以及癌症基因组学社区中最引人注目的工具。公共场所，有来自325个癌症的数据 研究，每月> 34,000个唯一用户访问。支持AACR的CBIOPORTAL实例 Project Genie是一项多机构数据共享计划，现在拥有> 120,000个肿瘤的基因组概况。 由于该软件可在开源许可下获得，因此> 65个癌症中心和药品 公司拥有机构安装CBIOPORTAL来分析自己的数据。多个机构是 为软件做出贡献，包括属于此应用程序的五个（纪念Sloan） 玛格丽特公主哈佛医学院达纳 - 法伯癌研究所Kettering Cancer Center 中心和费城儿童医院）。确保这种重要资源继续帮助癌症 研究社区并与癌症基因组学和精度的快速发展领域保持同步 癌症医学，包括缺型肿瘤样本的持续增加，我们建议 积极维持和发展CBIOPORTAL平台。具体来说，我们计划在 整个CBIOPORTAL软件体系结构（AIM 1）；这包括解决关键绩效的重大更改 瓶颈是一种新的API，能够支持联合查询，一个新的应用商店，并改进了我们 云基础架构和数据管道。我们还将支持几种新的分子数据类型，完全添加两种 新的CBIOPORTAL视图，为精确肿瘤学开发新功能，并提高一般可用性（AIM 2）。我们 提议继续为五个机构的一组核心开发人员提供资金，扩大代码的基础 贡献者，并继续与Hyve合作以支持生物技术和制药公司（AIM 3）。最后，为了最大程度地利用科学界的使用，我们计划继续改善社区外展活动， 用户支持和培训（AIM 4）。这些改进将是必要的，以确保CBIOPORTAL继续 为新生物标志物和药物的癌症研究和开发提供必不可少的服务，尤其是 随着越来越多的癌症中心作为其精确医学计划的一部分， 制药公司将其用于内部研究。我们希望在接下来的几年中 CBIOPORTAL将继续对癌症研究和患者护理的所有领域产生强烈的影响。