在cBioPortal中分析和可视化AACR Project GENIE Biopharma合作中的纵向基因组和临床数据。
Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal.
发表日期：2023 Sep 05
作者：
Ino de Bruijn, Ritika Kundra, Brooke Mastrogiacomo, Thinh Ngoc Tran, Luke Sikina, Tali Mazor, Xiang Li, Angelica Ochoa, Gaofei Zhao, Bryan Lai, Adam Abeshouse, Diana Baiceanu, Ersin Ciftci, Ugur Dogrusoz, Andrew Dufilie, Ziya Erkoc, Elena Garcia Lara, Zhaoyuan Fu, Benjamin E Gross, Charles D Haynes, Allison Heath, David M Higgins, Prasanna Jagannathan, Karthik Kalletla, Priti Kumari, James R Lindsay, Aaron Lisman, Bas Leenknegt, Pieter Lukasse, Divya Madala, Ramyasree Madupuri, Pim van Nierop, Oleguer Plantalech, Joyce Quach, Adam Resnick, Sander Y A Rodenburg, Baby A Satravada, Fedde Schaeffer, Robert Sheridan, Jessica Singh, Rajat Sirohi, Selcuk Onur Sumer, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Kelsey Zhu, Nicole Rusk, Samantha Brown, Jessica A Lavery, Katherine S Panageas, Julia E Rudolph, Michele L LeNoue-Newton, Jeremy L Warner, Xindi Guo, Haley Hunter-Zinck, Thomas V Yu, Shirin Pillai, Chelsea Nichols, Stuart M Gardos, John Philip, Genie Bpc Core Team, Aacr Project Genie Consortium, Kenneth L Kehl, Gregory J Riely, Deb Schrag, Jocelyn Lee, Michael V Fiandalo, Shawn M Sweeney, Trevor J Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz
来源：
CANCER RESEARCH
摘要：
国际癌症登记处提供了真实世界的基因组和临床数据，但其共同分析仍然具有挑战性。AACR GENIE项目是一个国际性的癌症登记处，收集来自19个癌症中心的数据，并通过cBioPortal for Cancer Genomics（https://genie.cbioportal.org）向公众提供逾13万名患者的数据。对于2.5万名患者，AACR GENIE生物制药合作专案团队还使用PRISSMM数据整理模型收集了额外的真实世界纵向临床数据，包括治疗和结果数据。这些案例中的数千个现在也可在cBioPortal中获取。我们显著增强了cBioPortal的功能，以支持对这一丰富的临床与基因组相关数据的可视化和分析，以及其他中心和合作专案生成的数据集。这些增强功能的例子包括：1）在患者层面可视化纵向临床和基因组数据，包括诊断、治疗和结果的时间轴，2）能够根据治疗状态选择样本，便于对特定治疗前后的分子和临床特征进行比较，以及3）基于个体治疗方案的生存分析估计。综合起来，这些功能为cBioPortal用户提供了一个交互式工具包，可研究复杂的临床与基因组数据，以生成关于特定基因组变异对癌症预后和治疗敏感性的影响的假设并进行发现。
International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international cancer registry collecting data from 19 cancer centers, makes data from >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional real-world longitudinal clinical data, including treatment and outcome data, are being collected by the AACR Project GENIE Biopharma Collaborative using the PRISSMM data curation model. Several thousand of these cases are now also available in cBioPortal. We have significantly enhanced the functionalities of cBioPortal to support the visualization and analysis of this rich clinico-genomic linked dataset, as well as datasets generated by other centers and consortia. Examples of these enhancements include 1) visualization of the longitudinal clinical and genomic data at the patient level, including timelines for diagnoses, treatments, and outcomes, 2) the ability to select samples based on treatment status, facilitating a comparison of molecular and clinical attributes between samples before and after a specific treatment, and 3) survival analysis estimates based on individual treatment regimens received. Together, these features provide cBioPortal users with a toolkit to interactively investigate complex clinico-genomic data in order to generate hypotheses and make discoveries about the impact of specific genomic variants on prognosis and therapeutic sensitivities in cancer.