Analysis and visualization of longitudinal genomic and clinical data from the AACR Project GENIE Biopharma Collaborative in cBioPortal Journal Article
| Authors: | de Bruijn, I.; Kundra, R.; Mastrogiacomo, B.; Tran, T. N.; Sikina, L.; Mazor, T.; Li, X.; Ochoa, A.; Zhao, G.; Lai, B.; Abeshouse, A.; Baiceanu, D.; Ciftci, E.; Dogrusoz, U.; Dufilie, A.; Erkoc, Z.; Lara, E. G.; Fu, Z.; Gross, B.; Haynes, C.; Heath, A.; Higgins, D.; Jagannathan, P.; Kalletla, K.; Kumari, P.; Lindsay, J.; Lisman, A.; Leenknegt, B.; Lukasse, P.; Madela, D.; Madupuri, R.; van Nierop, P.; Plantalech, O.; Quach, J.; Resnick, A. C.; Rodenburg, S. Y. A.; Satravada, B. A.; Schaeffer, F.; Sheridan, R.; Singh, J.; Sirohi, R.; Sumer, S. O.; van Hagen, S.; Wang, A.; Wilson, M.; Zhang, H.; Zhu, K.; Rusk, N.; Brown, S.; Lavery, J. A.; Panageas, K. S.; Rudolph, J. E.; LeNoue-Newton, M. L.; Warner, J. L.; Guo, X.; Hunter-Zinck, H.; Yu, T.; Pilai, S.; Nichols, C.; Gardos, S. M.; Philip, J.; AACR Project GENIE BPC Core Team, AACR Project GENIE Consortium; Kehl, K. L.; Riely, G. J.; Schrag, D.; Lee, J.; Fiandalo, M. V.; Sweeney, S. M.; Pugh, T. J.; Sander, C.; Cerami, E.; Gao, J.; Schultz, N. |
| Article Title: | 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. |
| Keywords: | classification; cancer |
| Journal Title: | Cancer Research |
| Volume: | 83 |
| Issue: | 23 |
| ISSN: | 0008-5472 |
| Publisher: | American Association for Cancer Research |
| Date Published: | 2023-12-01 |
| Start Page: | 3861 |
| End Page: | 3867 |
| Language: | English |
| ACCESSION: | WOS:001154743000004 |
| DOI: | 10.1158/0008-5472.Can-23-0816 |
| PROVIDER: | wos |
| PMCID: | PMC10690089 |
| PUBMED: | 37668528 |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledged in the PubMed record and PDF. Corresponding MSK author is Ino de Bruijn -- Source: Wos |
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