Multi-omics data integration by generative adversarial network

Khandakar Tanvir Ahmed, Jiao Sun, Sze Cheng, Jeongsik Yong, Wei Zhang

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

Motivation: Accurate disease phenotype prediction plays an important role in the treatment of heterogeneous diseases like cancer in the era of precision medicine. With the advent of high throughput technologies, more comprehensive multi-omics data is now available that can effectively link the genotype to phenotype. However, the interactive relation of multi-omics datasets makes it particularly challenging to incorporate different biological layers to discover the coherent biological signatures and predict phenotypic outcomes. In this study, we introduce omicsGAN, a generative adversarial network model to integrate two omics data and their interaction network. The model captures information from the interaction network as well as the two omics datasets and fuse them to generate synthetic data with better predictive signals. Results: Large-scale experiments on The Cancer Genome Atlas breast cancer, lung cancer and ovarian cancer datasets validate that (i) the model can effectively integrate two omics data (e.g. mRNA and microRNA expression data) and their interaction network (e.g. microRNA-mRNA interaction network). The synthetic omics data generated by the proposed model has a better performance on cancer outcome classification and patients survival prediction compared to original omics datasets. (ii) The integrity of the interaction network plays a vital role in the generation of synthetic data with higher predictive quality. Using a random interaction network does not allow the framework to learn meaningful information from the omics datasets; therefore, results in synthetic data with weaker predictive signals.

Original languageEnglish (US)
Pages (from-to)179-186
Number of pages8
JournalBioinformatics
Volume38
Issue number1
DOIs
StatePublished - Jan 1 2022

Bibliographical note

Funding Information:
Acknowledgements The results are based upon data generated by The Cancer Genome Atlas established by the NCI and NHGRI. Information about TCGA and the investigators and institutions who constitute the TCGA research network can be found at http://cancergenome.nih.gov. The dbGaP accession number to the specific version of the TCGA dataset is phs000178.v8.p7. Funding This work was supported by grants from the National Science Foundation (NSF) [NSF-III1755761]; National Institutes of Health (NIH) [2R01GM113952-06, DK097771].

Publisher Copyright:
© 2021 The Author(s). Published by Oxford University Press. All rights reserved.

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