Dataset Information

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

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.

SUBMITTER: de Bruijn I

PROVIDER: S-EPMC10690089 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

de Bruijn Ino I Kundra Ritika R Mastrogiacomo Brooke B Tran Thinh Ngoc TN Sikina Luke L Mazor Tali T Li Xiang X Ochoa Angelica A Zhao Gaofei G Lai Bryan B Abeshouse Adam A Baiceanu Diana D Ciftci Ersin E Dogrusoz Ugur U Dufilie Andrew A Erkoc Ziya Z Garcia Lara Elena E Fu Zhaoyuan Z Gross Benjamin B Haynes Charles C Heath Allison A Higgins David D Jagannathan Prasanna P Kalletla Karthik K Kumari Priti P Lindsay James J Lisman Aaron A Leenknegt Bas B Lukasse Pieter P Madela Divya D Madupuri Ramyasree R van Nierop Pim P Plantalech Oleguer O Quach Joyce J Resnick Adam C AC Rodenburg Sander Y A SYA Satravada Baby A BA Schaeffer Fedde F Sheridan Robert R Singh Jessica J Sirohi Rajat R Sumer Selcuk Onur SO van Hagen Sjoerd S Wang Avery A Wilson Manda M Zhang Hongxin H Zhu Kelsey K Rusk Nicole N Brown Samantha S Lavery Jessica A JA Panageas Katherine S KS Rudolph Julia E JE LeNoue-Newton Michele L ML Warner Jeremy L JL Guo Xindi X Hunter-Zinck Haley H Yu Thomas V TV Pilai Shirin S Nichols Chelsea C Gardos Stuart M SM Philip John J Philip John J Kehl Kenneth L KL Riely Gregory J GJ Schrag Deborah D Lee Jocelyn J Fiandalo Michael V MV Sweeney Shawn M SM Pugh Trevor J TJ Sander Chris C Cerami Ethan E Gao Jianjiong J Schultz Nikolaus N

Cancer research 20231201 23

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 ...[more]

PMID: 37668528

Similar Datasets

Project description:Peritoneal metastases (PM) are common in metastatic colorectal cancer (mCRC). We aimed to characterize patients with mCRC and PM from a clinical and molecular perspective using the American Association of Cancer Research Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) registry. Patients' tumor samples underwent targeted next-generation sequencing. Clinical characteristics and treatment outcomes were collected retrospectively. Overall survival (OS) from advanced disease and progression-free survival (PFS) from start of cancer-directed drug regimen were estimated and adjusted for the left truncation bias. A total of 1,281 patients were analyzed, 244 (19%) had PM at time of advanced disease. PM were associated with female sex [OR: 1.67; 95% confidence interval (CI): 1.11-2.54; P = 0.014] and higher histologic grade (OR: 1.72; 95% CI: 1.08-2.71; P = 0.022), while rectal primary tumors were less frequent in patients with PM (OR: 0.51; 95% CI: 0.29-0.88; P < 0.001). APC occurred less frequently in patients with PM (N = 151, 64% vs. N = 788, 79%) while MED12 alterations occurred more frequently in patients with PM (N = 20, 10% vs. N = 32, 4%); differences in MED12 were not significant when restricting to oncogenic and likely oncogenic variants according to OncoKB. Patients with PM had worse OS (HR: 1.45; 95% CI: 1.16-1.81) after adjustment for independently significant clinical and genomic predictors. PFS from initiation of first-line treatment did not differ by presence of PM. In conclusion, PM were more frequent in females and right-sided primary tumors. Differences in frequencies of MED12 and APC alterations were identified between patients with and without PM. PM were associated with shorter OS but not with PFS from first-line treatment.SignificanceUtilizing the GENIE BPC registry, this study found that PM in patients with colorectal cancer occur more frequently in females and right-sided primary tumors and are associated with worse OS. In addition, we found a lower frequency of APC alterations and a higher frequency in MED12 alterations in patients with PM.

Dataset Information

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

Significance

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets