Canhong Wen1, Yuhui Yang1, Quan Xiao1, Meiyan Huang2, Wenliang Pan3. 1. Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230026, China. 2. Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China. 3. Department of Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, China.
Abstract
MOTIVATION: Imaging genetics is mainly used to reveal the pathogenesis of neuropsychiatric risk genes and understand the relationship between human brain structure, functional and individual differences. Increasingly, the brain-wide imaging phenotypes in voxels are available to test the association with genetic markers. A challenge with analyzing such data is their high dimensionality and complex relationships. RESULTS: To tackle this challenge, we introduce a weighed distance correlation (wdCor) that can assess the association between genetic markers and voxel-based imaging data. Importantly, the wdCor test takes the voxel-based data as a whole multivariate phenotype, which preserves the spatial continuity and might enhance the power. Besides, an adaptive permutation procedure is introduced to determine the P-values of the wdCor test and also alleviate the computational burden in GWAS. In extensive simulation studies, wdCor achieves much better performances compared to the original distance correlation. We also successfully apply wdCor to conduct a large-scale analysis on data from the Alzheimer's disease neuroimaging project (ADNI). AVAILABILITY AND IMPLEMENTATION: Our wdCor method provides new research directions and ideas for multivariate analysis of high-dimensional data, it can also be used as a tool for scientific analysis of imaging genetics research in practical applications. The R package wdcor, and the code for reproducing all results in this article is available in Github: https://github.com/yangyuhui0129/wdcor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Imaging genetics is mainly used to reveal the pathogenesis of neuropsychiatric risk genes and understand the relationship between human brain structure, functional and individual differences. Increasingly, the brain-wide imaging phenotypes in voxels are available to test the association with genetic markers. A challenge with analyzing such data is their high dimensionality and complex relationships. RESULTS: To tackle this challenge, we introduce a weighed distance correlation (wdCor) that can assess the association between genetic markers and voxel-based imaging data. Importantly, the wdCor test takes the voxel-based data as a whole multivariate phenotype, which preserves the spatial continuity and might enhance the power. Besides, an adaptive permutation procedure is introduced to determine the P-values of the wdCor test and also alleviate the computational burden in GWAS. In extensive simulation studies, wdCor achieves much better performances compared to the original distance correlation. We also successfully apply wdCor to conduct a large-scale analysis on data from the Alzheimer's disease neuroimaging project (ADNI). AVAILABILITY AND IMPLEMENTATION: Our wdCor method provides new research directions and ideas for multivariate analysis of high-dimensional data, it can also be used as a tool for scientific analysis of imaging genetics research in practical applications. The R package wdcor, and the code for reproducing all results in this article is available in Github: https://github.com/yangyuhui0129/wdcor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jason L Stein; Xue Hua; Suh Lee; April J Ho; Alex D Leow; Arthur W Toga; Andrew J Saykin; Li Shen; Tatiana Foroud; Nathan Pankratz; Matthew J Huentelman; David W Craig; Jill D Gerber; April N Allen; Jason J Corneveaux; Bryan M Dechairo; Steven G Potkin; Michael W Weiner; Paul Thompson Journal: Neuroimage Date: 2010-02-17 Impact factor: 6.556
Authors: Derrek P Hibar; Jason L Stein; Omid Kohannim; Neda Jahanshad; Andrew J Saykin; Li Shen; Sungeun Kim; Nathan Pankratz; Tatiana Foroud; Matthew J Huentelman; Steven G Potkin; Clifford R Jack; Michael W Weiner; Arthur W Toga; Paul M Thompson Journal: Neuroimage Date: 2011-04-08 Impact factor: 6.556
Authors: Lei Du; Yan Jingwen; Sungeun Kim; Shannon L Risacher; Heng Huang; Mark Inlow; Jason H Moore; Andrew J Saykin; Li Shen Journal: Med Image Comput Comput Assist Interv Date: 2014
Authors: R Hashimoto; K Ohi; H Yamamori; Y Yasuda; M Fujimoto; S Umeda-Yano; Y Watanabe; M Fukunaga; M Takeda Journal: Curr Mol Med Date: 2015 Impact factor: 2.222
Authors: Michal Prendecki; Jolanta Florczak-Wyspianska; Marta Kowalska; Jan Ilkowski; Teresa Grzelak; Katarzyna Bialas; Malgorzata Wiszniewska; Wojciech Kozubski; Jolanta Dorszewska Journal: Oncotarget Date: 2018-10-16
Authors: Omid Kohannim; Derrek P Hibar; Jason L Stein; Neda Jahanshad; Xue Hua; Priya Rajagopalan; Arthur W Toga; Clifford R Jack; Michael W Weiner; Greig I de Zubicaray; Katie L McMahon; Narelle K Hansell; Nicholas G Martin; Margaret J Wright; Paul M Thompson Journal: Front Neurosci Date: 2012-08-06 Impact factor: 4.677