Gene–gene interaction detection with deep learning
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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en
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12
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Communications Biology, Volume 5, issue 1, pp. 1-12
Abstract
The extent to which genetic interactions affect observed phenotypes is generally unknown because current interaction detection approaches only consider simple interactions between top SNPs of genes. We introduce an open-source framework for increasing the power of interaction detection by considering all SNPs within a selected set of genes and complex interactions between them, beyond only the currently considered multiplicative relationships. In brief, the relation between SNPs and a phenotype is captured by a neural network, and the interactions are quantified by Shapley scores between hidden nodes, which are gene representations that optimally combine information from the corresponding SNPs. Additionally, we design a permutation procedure tailored for neural networks to assess the significance of interactions, which outperformed existing alternatives on simulated datasets with complex interactions, and in a cholesterol study on the UK Biobank it detected nine interactions which replicated on an independent FINRISK dataset.Description
Funding Information: The work used computer resources of the Aalto University School of Science Science-IT project. This work was supported by the Academy of Finland (Flagship programme: Finnish Center for Artificial Intelligence, FCAI, and grants 319264, 292334, 286607, 294015, 336033, 321356), the EU Horizon 2020 (grant no. 101016775), and UKRI Turing AI World-Leading Researcher Fellowship, EP/W002973/1. This research has been conducted using the UK Biobank Resource under application number 46791. | openaire: EC/H2020/101016775/EU//INTERVENE
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Cui, T, El Mekkaoui, K, Reinvall, J, Havulinna, A S, Marttinen, P & Kaski, S 2022, 'Gene–gene interaction detection with deep learning', Communications Biology, vol. 5, no. 1, 1238, pp. 1-12. https://doi.org/10.1038/s42003-022-04186-y