The cBioPortal for Cancer Genomics

癌症基因组学的 cBioPortal

• 批准号: 9980313
• 负责人: Ethan Cerami
• 金额: $ 128.15万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9980313
• 关键词: Adoption; Antineoplastic Agents; Architecture; Area; Basic Cancer Research; Big Data; Biological Markers; Cancer Center; Cancer Patient; Clinic; Clinical; Clinical Trials Design; Code; Collaborations; Collection; Communities; Community Developments; Community Outreach; Computer software; Consultations; Dana-Farber Cancer Institute; Data; Data Analyses; Data Set; Development; Documentation; Drug Targeting; Ecosystem; Education; Education and Outreach; Ensure; Feedback; Funding; Future; Genomic medicine; Genomics; Goals; Growth; Immunogenomics; Immunotherapy; Institution; Investments; Licensing; Malignant Neoplasms; Memorial Sloan-Kettering Cancer Center; Molecular; Molecular Profiling; Mutation; Pathway Analysis; Patient Care; Patients; Pediatric Hospitals; Performance; Pharmaceutical Preparations; Philadelphia; Privatization; Research; Research Personnel; Resources; Sampling; Scientist; Secure; Site; Survival Analysis; System; Technology; The Cancer Genome Atlas; TimeLine; Training; Visualization; anticancer research; base; cBioPortal; cancer genomics; cancer initiation; clinically actionable; cohort; community planning; complex data; genetic variant; genomic data; human genome sequencing; improved; informatics infrastructure; insight; interoperability; migration; new technology; novel; online resource; open source; outreach; personalized medicine; precision medicine; precision oncology; programs; recruit; research and development; social media; software development; software systems; symposium; tool; treatment effect; tumor; usability; user-friendly; virtual; web services; webinar

PROJECT SUMMARY Genomic sequencing and molecular profiling of tumor samples is becoming routine at many cancer centers, and the scientific community is poised to sequence hundreds of thousands of tumor samples over the next five years, providing unprecedented insight into cancer initiation, progression, and treatment effects. Ensuring that these data sets are easily accessible and interpretable to scientists and clinicians is of vital importance. Towards this end, we seek to continually evolve and expand the capabilities of the cBioPortal for Cancer Genomics, a unique and vital platform that enables interactive exploratory data analysis of large-scale cancer genomic data sets. The cBioPortal has become the most widely used tool within the cancer genomics community and is the most highly cited. The public site (cbioportal.org) contains data from more than 20,000 tumor samples, including all data from The Cancer Genome Atlas, and is accessed by more than 25,000 unique users each month. Since the software is available under an open source license, there are >40 local installations of the software system at cancer centers and drug companies, and multiple institutions are making contributions to the software, including the four that are part of this application (Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, 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, and the imminent steep increase in the number of profiled tumor samples, we propose to actively sustain and evolve the cBioPortal platform. Specifically, we will implement major architectural changes to the cBioPortal software to ensure future scalability and performance, and accelerate new feature development (Aim 1). We will also develop novel analysis tools for drug target discovery in large cancer genomics cohorts, as well as new features for precision cancer medicine, including for clinical trial design and the budding field of immunogenomics (Aim 2). We also plan to build and leverage a vibrant open source software development community to maintain and adapt the software and develop essential new features (Aim 3). Finally, to maximize use in the scientific community, we plan to expand community outreach and education, and create mechanisms for community engagement and feedback (Aim 4). With these improvements, the cBioPortal has the potential to significantly accelerate cancer research and development of new biomarkers and drugs. Several cancer centers are already using the cBioPortal as part of their precision medicine programs to guide interpretation of genomic variants. We expect that, over the next few years, the cBioPortal will have a tremendous impact on all areas of basic cancer research and patient care.

项目摘要 在许多癌症中心，肿瘤样品的基因组测序和分子分析已成为常规的 在接下来的五个 几年，提供了对癌症启动，进展和治疗效果的前所未有的见解。确保这一点 这些数据集很容易访问和解释为科学家，临床医生至关重要。 为此，我们寻求不断发展和扩大癌症的癌症的能力 基因组学是一个独特而重要的平台，可实现大规模取消的交互式探索性数据分析 基因组数据集。 CBIOPORTAL已成为癌症基因组中使用最广泛的工具 社区，被引用最多。公共网站（cbioportal.org）包含来自20,000多个的数据 肿瘤样品，包括来自癌症基因组地图集的所有数据，可访问超过25,000 每个月的唯一用户。由于该软件在开源许可下可用，因此本地有> 40个 癌症中心和制药公司的软件系统的安装以及多个机构正在制造 对该软件的贡献，包括本申请中的四个（纪念Sloan Kettering） 癌症中心，达纳 - 法伯癌症研究所，玛格丽特公主癌症中心和儿童医院 费城）。确保这种重要资源继续帮助癌症研究界并保持 随着癌症基因组学和精确癌症医学的迅速发展的速度，即将 我们提议积极维持和进化的肿瘤样品的数量大幅增加 CBIOPORTAL平台。具体而言，我们将对CBIOPORTAL软件实施重大的体系结构更改 确保将来的可扩展性和性能，并加速新功能开发（AIM 1）。我们也会 开发用于大型癌症基因组学队列中药物目标发现的新型分析工具以及新的 精密癌症医学的功能，包括用于临床试验设计和萌芽场 免疫基因组学（AIM 2）。我们还计划建立和利用充满活力的开源软件开发 社区维护和适应软件并开发基本的新功能（AIM 3）。最后，到 在科学界最大化使用，我们计划扩大社区的外展和教育，并创建 社区参与和反馈的机制（AIM 4）。通过这些改进，cbioportal具有 显着加速新生物标志物和药物的癌症研究和开发的潜力。 几个癌症中心已经在使用CBIOPORTAL作为其精确医学计划的一部分来指导 基因组变体的解释。我们希望在接下来的几年中，CBIOPORTAL将有一个 对基本癌症研究和患者护理的所有领域的巨大影响。