Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

Bin Zhu, Nan Song, Ronglai Shen, Arshi Arora, Mitchell J. Machiela, Lei Song, Maria Teresa Landi, Debashis Ghosh, Nilanjan Chatterjee, Veera Baladandayuthapani, Hongyu Zhao

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Abstract

Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types. mRNA and miRNA expression profile frequently performed the best, followed by DNA methylation profile. Germline susceptibility variants displayed low prognostic performance consistently across cancer types. The integration of omic profiles with clinical variables can lead to substantially improved prognostic performance over the use of clinical variables alone in half of cancer types examined. Moreover, we showed that the kernel machine learning method consistently outperformed existing prognostic signatures, suggesting that including a large number of omic biomarkers may provide substantial improvement in prognostic assessment. Our study provides a comprehensive portrait of omic architecture for tumor prognosis across cancers, and highlights the prognostic value of genome-wide omic biomarker aggregation, which may facilitate refined prognostic assessment in the era of precision oncology.

Original languageEnglish (US)
Article number16954
JournalScientific Reports
Volume7
Issue number1
DOIs
Publication statusPublished - Dec 1 2017

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Zhu, B., Song, N., Shen, R., Arora, A., Machiela, M. J., Song, L., ... Zhao, H. (2017). Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers. Scientific Reports, 7(1), [16954]. https://doi.org/10.1038/s41598-017-17031-8