Browsing by Subject "Single-nucleotide polymorphisms (SNPs)"

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    A Novel SCCA Approach via Truncated ℓ1-norm and Truncated Group Lasso for Brain Imaging Genetics
    (Oxford University Press, 2017-09-18) Du, Lei; Liu, Kefei; Zhang, Tuo; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Han, Junwei; Guo, Lei; Saykin, Andrew J.; Shen, Li; Radiology and Imaging Sciences, School of Medicine
    Motivation: Brain imaging genetics, which studies the linkage between genetic variations and structural or functional measures of the human brain, has become increasingly important in recent years. Discovering the bi-multivariate relationship between genetic markers such as single-nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is one major task in imaging genetics. Sparse Canonical Correlation Analysis (SCCA) has been a popular technique in this area for its powerful capability in identifying bi-multivariate relationships coupled with feature selection. The existing SCCA methods impose either the ℓ 1 -norm or its variants to induce sparsity. The ℓ 0 -norm penalty is a perfect sparsity-inducing tool which, however, is an NP-hard problem. Results: In this paper, we propose the truncated ℓ 1 -norm penalized SCCA to improve the performance and effectiveness of the ℓ 1 -norm based SCCA methods. Besides, we propose an efficient optimization algorithms to solve this novel SCCA problem. The proposed method is an adaptive shrinkage method via tuning τ . It can avoid the time intensive parameter tuning if given a reasonable small τ . Furthermore, we extend it to the truncated group-lasso (TGL), and propose TGL-SCCA model to improve the group-lasso-based SCCA methods. The experimental results, compared with four benchmark methods, show that our SCCA methods identify better or similar correlation coefficients, and better canonical loading profiles than the competing methods. This demonstrates the effectiveness and efficiency of our methods in discovering interesting imaging genetic associations. Availability: The Matlab code and sample data are freely available at http://www.iu.edu/∼shenlab/tools/tlpscca/ .
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    Validation of genetic associations with acute GVHD and nonrelapse mortality in DISCOVeRY-BMT
    (American Society of Hematology, 2019-08-13) Tang, Hancong; Hahn, Theresa; Karaesmen, Ezgi; Rizvi, Abbas A.; Wang, Junke; Paczesny, Sophie; Wang, Tao; Preus, Leah; Zhu, Qianqian; Wang, Yiwen; Haiman, Christopher A.; Stram, Daniel; Pooler, Loreall; Sheng, Xin; Van Den Berg, David; Brock, Guy; Webb, Amy; Pasquini, Marcelo C.; McCarthy, Philip L.; Spellman, Stephen R.; Sucheston-Campbell, Lara E.; Pediatrics, School of Medicine