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Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal

2023; American Association for Cancer Research; Volume: 83; Issue: 23 Linguagem: Inglês

10.1158/0008-5472.can-23-0816

1538-7445

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, Uḡur Doḡrusöz, Andrew Dufilie, Ziya Erkoç, Elena Garcia Lara, Zhaoyuan Fu, Benjamin E. Gross, Charles Haynes, Allison P. Heath, David Higgins, Prasanna Jagannathan, Karthik Kalletla, Priti Kumari, James Lindsay, Aaron Lisman, Bas Leenknegt, Pieter Lukasse, Divya Madela, Ramyasree Madupuri, Pim van Nierop, Oleguer Plantalech, Joyce Quach, Adam Resnick, Sander Y.A. Rodenburg, Baby A. Satravada, Fedde Schaeffer, Robert L. Sheridan, Jessica Singh, Rajat Sirohi, S. 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 Yu, Shirin Pilai, Chelsea Nichols, Stuart M. Gardos, John Philip, Kenneth L. Kehl, Gregory J. Riely, Deborah Schrag, Jocelyn Lee, Michael V. Fiandalo, Shawn M. Sweeney, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz,

Epigenetics and DNA Methylation

Abstract 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 (i) visualization of the longitudinal clinical and genomic data at the patient level, including timelines for diagnoses, treatments, and outcomes; (ii) 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 (iii) 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 to generate hypotheses and make discoveries about the impact of specific genomic variants on prognosis and therapeutic sensitivities in cancer. Significance: Enhanced cBioPortal features allow clinicians and researchers to effectively investigate longitudinal clinico-genomic data from patients with cancer, which will improve exploration of data from the AACR Project GENIE Biopharma Collaborative and similar datasets.