The cBioPortal for Cancer Genomics

癌症基因组学的 cBioPortal

• 批准号: 10528935
• 负责人: Ethan Cerami
• 金额: $ 145.62万
• 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/10528935
• 关键词: 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; 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; anticancer research; base; cBioPortal; cancer care; cancer genomics; cancer initiation; community planning; complex data; data mining; data pipeline; data sharing; data visualization; genetic variant; 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; 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.

项目概要 肿瘤样本的基因组测序现已成为癌症护理的常规组成部分，提供了前所未有的 深入了解癌症的发生、进展和治疗效果。此外，新颖的分子分析和 成像技术越来越受到关注，产生越来越多的数据。确保这些数据集很容易 科学家和临床医生的可理解性和可解释性至关重要。为此，我们寻求 发展和扩展癌症基因组学 cBioPortal 的功能，这是一个独特的平台，使 大规模癌症基因组数据的交互式探索性分析。 cBioPortal 是使用最广泛的 也是癌症基因组学界引用次数最多的工具。公共网站，包含 325 种癌症的数据 研究，每月有超过 34,000 名独立用户访问。支持AACR的cBioPortal实例 Project GENIE 是一项多机构数据共享计划，目前拥有超过 120,000 个肿瘤的基因组图谱。 由于该软件是在开源许可证下提供的，超过 65 个癌症中心和制药公司 公司拥有 cBioPortal 的机构安装来分析自己的数据。多个机构正在 对软件做出贡献，包括本应用程序中的五个贡献（纪念斯隆 凯特林癌症中心、达纳法伯癌症研究所、哈佛医学院、玛格丽特公主癌症 中心和费城儿童医院）。确保这一重要资源继续帮助癌症 研究界并跟上快速发展的癌症基因组学和精准领域的步伐 癌症医学，包括分析肿瘤样本数量的持续增加，我们建议 积极维护和发展 cBioPortal 平台。具体来说，我们计划在各个方面进行改进 整个 cBioPortal 软件架构（目标 1）；这包括解决关键性能问题的重大改变 瓶颈、能够支持联合查询的新 API、新的 App Store 以及我们的改进 云基础设施和数据管道。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，开发精准肿瘤学的新功能，并提高一般可用性（目标 2）。我们 建议继续资助五个机构的一组核心开发人员，扩大代码基础 贡献者，并继续与 Hyve 合作支持生物技术和制药公司（Aim 3）。最后，为了最大限度地在科学界使用，我们计划继续改善社区外展， 用户支持和培训（目标 4）。这些改进对于确保 cBioPortal 继续发展是必要的 为癌症研究和新生物标志物和药物的开发提供基本服务，特别是 随着越来越多的癌症中心使用 cBioPortal 作为其精准医疗计划的一部分，并且 制药公司正在将其用于内部研究。我们预计，在未来几年内， cBioPortal 将继续对癌症研究和患者护理的所有领域产生重大影响。