Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal
Authors: de Bruijn Ino , Kundra Ritika , Mastrogiacomo Brooke , Tran Thinh Ngoc , Sikina Luke , Mazor Tali , Li Xiang , Ochoa Angelica , Zhao Gaofei , Lai Bryan , Abeshouse Adam , Baiceanu Diana , Ciftci Ersin , Dogrusoz Ugur , Dufilie Andrew , Erkoc Ziya , Garcia Lara Elena , Fu Zhaoyuan , Gross Benjamin , Haynes Charles , Heath Allison , Higgins David , Jagannathan Prasanna , Kalletla Karthik , Kumari Priti , Lindsay James , Lisman Aaron , Leenknegt Bas , Lukasse Pieter , Madela Divya , Madupuri Ramyasree , van Nierop Pim , Plantalech Oleguer , Quach Joyce , Resnick Adam C. , Rodenburg Sander Y.A. , Satravada Baby A. , Schaeffer Fedde , Sheridan Robert , Singh Jessica , Sirohi Rajat , Sumer Selcuk Onur , van Hagen Sjoerd , Wang Avery , Wilson Manda , Zhang Hongxin , Zhu Kelsey , Rusk Nicole , Brown Samantha , Lavery Jessica A. , Panageas Katherine S. , Rudolph Julia E. , LeNoue-Newton Michele L. , Warner Jeremy L. , Guo Xindi , Hunter-Zinck Haley , Yu Thomas V. , Pilai Shirin , Nichols Chelsea , Gardos Stuart M. , Philip John ,   AACR Project GENIE BPC Core Team, AACR Project GENIE Consortium, Kehl Kenneth L. , Riely Gregory J. , Schrag Deborah , Lee Jocelyn , Fiandalo Michael V. , Sweeney Shawn M. , Pugh Trevor J. , Sander Chris , Cerami Ethan , Gao Jianjiong , Schultz Nikolaus 
Published: September 2023

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 &gt;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.