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.

项目总结 肿瘤样本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 深入了解癌症的发生、发展和治疗效果。此外，新的分子图谱和 成像技术正在获得牵引力，产生越来越多的数据。确保这些数据集可以轻松地 科学家和临床医生可获得和可解释的是至关重要的。为此，我们寻求 发展和扩展癌症基因组学cBio门户的功能，这是一个独特的平台，能够 大规模癌症基因组数据的交互式探索性分析。CBio门户是使用最广泛的 和癌症基因组学社区中被引用最多的工具。公共网站，有来自325个癌症的数据 研究，每月有34,000名独立用户访问。支持AACR的cBioPortal实例 Genie项目是一个多机构数据共享计划，现在托管着12万个肿瘤的基因组图谱。 由于该软件是在开放源码许可下提供的，因此&gt；65个癌症中心和制药公司 公司有机构安装的cBioPortal来分析他们自己的数据。多个机构正在 为软件做出贡献，包括作为此应用程序一部分的五个部分(纪念斯隆 凯特琳癌症中心，达纳-法伯癌症研究所，哈佛医学院，玛格丽特·癌症公主 中心和费城儿童医院)。以确保这一至关重要的资源继续帮助癌症 并与迅速发展的癌症基因组学和精确学领域保持同步 癌症医学，包括轮廓肿瘤样本数量的持续增加，我们建议 积极维护和发展cBio门户平台。具体地说，我们计划在 整个cBioPortal软件体系结构(目标1)；这包括针对关键性能的重大更改 瓶颈、能够支持联合查询的新API、新的App Store以及对我们的 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cBio门户视图，为精确肿瘤学开发新功能，并提高一般可用性(目标2)。我们 建议继续为五个机构的核心开发人员小组提供资金，扩大代码库 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，为了最大限度地利用科学界，我们计划继续改善社区宣传， 用户支持和培训(目标4)。这些改进将是必要的，以确保cBio门户继续 为癌症研究和开发新的生物标志物和药物提供必要的服务，特别是 随着越来越多的癌症中心使用cBio门户作为其精准医学计划的一部分，以及 制药公司正在将其用于内部研究。我们预计，在未来几年里， 生物门户网站将继续对癌症研究和患者护理的所有领域产生强大的影响。