The cBioPortal for Cancer Genomics

项目摘要 肿瘤样本的基因组测序和分子分析在许多癌症中心正变得常规， 科学界准备在未来五年内对数十万个肿瘤样本进行测序 多年来，提供了前所未有的洞察癌症的开始，进展和治疗效果。确保 科学家和临床医生很容易获得和解释这些数据集是至关重要的。 为此，我们寻求不断发展和扩大cBioPortal for Cancer的功能 Genomics是一个独特而重要的平台，可以对大规模癌症进行交互式探索性数据分析 基因组数据集。cBioPortal已成为癌症基因组学中使用最广泛的工具 社区，是被引用次数最多的。公共网站（cbioportal.org）包含来自20，000多个 肿瘤样本，包括来自癌症基因组图谱的所有数据， 每个月都有用户。由于该软件是在开源许可证下提供的， 在癌症中心和制药公司安装软件系统，多个机构正在 对软件的贡献，包括此应用程序的四个部分（纪念斯隆凯特琳 癌症中心，丹娜-法伯癌症研究所，玛格丽特公主癌症中心和儿童医院 Philadelphia）。为了确保这一重要资源继续帮助癌症研究界， 随着癌症基因组学和精确癌症医学领域的迅速发展， 在分析肿瘤样本数量的急剧增加，我们建议积极维持和发展 cBioPortal平台。具体而言，我们将对cBioPortal软件实施重大架构变更， 确保未来的可扩展性和性能，并加快新功能的开发（目标1）。我们还将 开发新的分析工具，用于在大型癌症基因组学队列中发现药物靶点， 精确癌症医学的功能，包括临床试验设计和新兴领域， 免疫基因组学（Aim 2）。我们还计划建立和利用一个充满活力的开源软件开发 社区维护和调整软件并开发重要的新功能（目标3）。最后为 最大限度地利用科学界，我们计划扩大社区外展和教育，并创造 社区参与和反馈机制（目标4）。通过这些改进，cBioPortal 有可能大大加快癌症研究和新生物标志物和药物的开发。 一些癌症中心已经将cBioPortal作为其精准医学计划的一部分， 基因组变异的解释。我们预计，在未来几年内，cBioPortal将有一个 对基础癌症研究和患者护理的所有领域产生巨大影响。

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.