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Associating brain imaging phenotypes and genetic in Alzheimer’s disease via JSCCA approach with autocorrelation constraints

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Abstract

Imaging genetics research can explore the potential correlation between imaging and genomics. Most association analysis methods cannot effectively use the prior knowledge of the original data. In this respect, we add the prior knowledge of each original data to mine more effective biomarkers. The study of imaging genetics based on the sparse canonical correlation analysis (SCCA) is helpful to mine the potential biomarkers of neurological diseases. To improve the performance and interpretability of SCCA, we proposed a penalty method based on the autocorrelation matrix for discovering the possible biological mechanism between single nucleotide polymorphisms (SNP) variations and brain regions changes of Alzheimer’s disease (AD). The addition of the penalty allows the proposed algorithm to analyze the correlation between different modal features. The proposed algorithm obtains more biologically interpretable ROIs and SNPs that are significantly related to AD, which has better anti-noise performance. Compared with other SCCA-based algorithms (JCB-SCCA, JSNMNMF), the proposed algorithm can still maintain a stronger correlation with ground truth even when the noise is larger. Then, we put the regions of interest (ROI) selected by the three algorithms into the SVM classifier. The proposed algorithm has higher classification accuracy. Also, we use ridge regression with SNPs selected by three algorithms and four AD risk ROIs. The proposed algorithm has a smaller root mean square error (RMSE). It shows that proposed algorithm has a good ability in association recognition and feature selection. Furthermore, it selects important features more stably, improving the clinical diagnosis of new potential biomarkers.

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Funding

This work was supported by the Natural Science Foundation of Shanghai (No. 18ZR1417200) and National Natural Science Foundation of China (No. 61803257).

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  1. Kai Wei and Wei Kong are Joint First Authors.

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  1. Shanghai Maritime University, Shanghai, 201306, China

    Kai Wei, Wei Kong & Shuaiqun Wang

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  1. Kai Wei
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  2. Wei Kong
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Correspondence to Wei Kong.

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Wei, K., Kong, W. & Wang, S. Associating brain imaging phenotypes and genetic in Alzheimer’s disease via JSCCA approach with autocorrelation constraints. Med Biol Eng Comput 60, 95–108 (2022). https://doi.org/10.1007/s11517-021-02439-2

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