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Münch MM, van de Wiel MA, Richardson S, Leday GGR. Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data. Biom J 2020; 63:289-304. [PMID: 33155717 PMCID: PMC7891636 DOI: 10.1002/bimj.201900371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/30/2020] [Accepted: 06/03/2020] [Indexed: 11/09/2022]
Abstract
In precision medicine, a common problem is drug sensitivity prediction from cancer tissue cell lines. These types of problems entail modelling multivariate drug responses on high-dimensional molecular feature sets in typically >1000 cell lines. The dimensions of the problem require specialised models and estimation methods. In addition, external information on both the drugs and the features is often available. We propose to model the drug responses through a linear regression with shrinkage enforced through a normal inverse Gaussian prior. We let the prior depend on the external information, and estimate the model and external information dependence in an empirical-variational Bayes framework. We demonstrate the usefulness of this model in both a simulated setting and in the publicly available Genomics of Drug Sensitivity in Cancer data.
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Affiliation(s)
- Magnus M Münch
- Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, The Netherlands.,Mathematical Institute, Leiden University, Leiden, The Netherlands.,MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Mark A van de Wiel
- Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, The Netherlands.,MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sylvia Richardson
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Gwenaël G R Leday
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, United Kingdom
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