Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal
Author:
de Bruijn Ino12ORCID, Kundra Ritika1ORCID, Mastrogiacomo Brooke1ORCID, Tran Thinh Ngoc1ORCID, Sikina Luke3ORCID, Mazor Tali3ORCID, Li Xiang1ORCID, Ochoa Angelica1ORCID, Zhao Gaofei1ORCID, Lai Bryan1ORCID, Abeshouse Adam1ORCID, Baiceanu Diana4ORCID, Ciftci Ersin3ORCID, Dogrusoz Ugur5ORCID, Dufilie Andrew3ORCID, Erkoc Ziya3ORCID, Garcia Lara Elena4ORCID, Fu Zhaoyuan3ORCID, Gross Benjamin1ORCID, Haynes Charles6ORCID, Heath Allison6ORCID, Higgins David6ORCID, Jagannathan Prasanna7ORCID, Kalletla Karthik6ORCID, Kumari Priti38ORCID, Lindsay James3ORCID, Lisman Aaron1ORCID, Leenknegt Bas4ORCID, Lukasse Pieter4ORCID, Madela Divya1ORCID, Madupuri Ramyasree1ORCID, van Nierop Pim4ORCID, Plantalech Oleguer4ORCID, Quach Joyce3ORCID, Resnick Adam C.6ORCID, Rodenburg Sander Y.A.4ORCID, Satravada Baby A.1ORCID, Schaeffer Fedde4ORCID, Sheridan Robert1ORCID, Singh Jessica4ORCID, Sirohi Rajat3ORCID, Sumer Selcuk Onur1ORCID, van Hagen Sjoerd4ORCID, Wang Avery1ORCID, Wilson Manda1ORCID, Zhang Hongxin1ORCID, Zhu Kelsey7ORCID, Rusk Nicole1ORCID, Brown Samantha1ORCID, Lavery Jessica A.1ORCID, Panageas Katherine S.1ORCID, Rudolph Julia E.1ORCID, LeNoue-Newton Michele L.9ORCID, Warner Jeremy L.10ORCID, Guo Xindi11ORCID, Hunter-Zinck Haley11ORCID, Yu Thomas V.11ORCID, Pilai Shirin1ORCID, Nichols Chelsea1ORCID, Gardos Stuart M.1ORCID, Philip John1ORCID, Kehl Kenneth L.3ORCID, Riely Gregory J.1ORCID, Schrag Deborah1ORCID, Lee Jocelyn12ORCID, Fiandalo Michael V.12ORCID, Sweeney Shawn M.12ORCID, Pugh Trevor J.7ORCID, Sander Chris13ORCID, Cerami Ethan3ORCID, Gao Jianjiong18ORCID, Schultz Nikolaus1ORCID,
Affiliation:
1. 1Memorial Sloan Kettering Cancer Center, New York, New York. 2. 2Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands. 3. 3Dana-Farber Cancer Institute, Boston, Massachusetts. 4. 4The Hyve, Utrecht, the Netherlands. 5. 5Bilkent University, Ankara, Turkey. 6. 6Children's Hospital of Philadelphia, Philadelphia, Pennsylvania. 7. 7Princess Margaret Cancer Centre, University Health Network, Toronto, Canada. 8. 8Caris Life Sciences, Irving, Texas. 9. 9Vanderbilt University Medical Center, Nashville, Tennessee. 10. 10Brown University, Providence, Rhode Island. 11. 11Sage Bionetworks, Seattle, Washington. 12. 12American Association for Cancer Research: Project GENIE, Philadelphia, Pennsylvania. 13. 13Harvard Medical School, Boston, Massachusetts.
Abstract
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.
Funder
American Association for Cancer Research National Cancer Institute Prostate Cancer Foundation Stand Up To Cancer Ben and Catherine Ivy Foundation National Center for Research Resources Adenoid Cystic Carcinoma Research Foundation Breast Cancer Research Foundation Cholangiocarcinoma Foundation Robertson Foundation Parker Institute for Cancer Immunotherapy
Publisher
American Association for Cancer Research (AACR)
Subject
Cancer Research,Oncology
Cited by
152 articles.
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