Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis
Year: 2017
Type: article
Abstract: MOTIVATION: Neuroimaging genetics identifies the relationships between genetic variants (i.e., the single nucleotide polymorphisms) and brain imaging data to reveal the associations from genotypes to phenotypes. So far, most existing machine-learning approaches are widely used to detect the effective associations between genetic variants and brain imaging data at one time-point. However, those associations are based on static phenotypes and ignore the temporal dynamics of the phenotypical changes. The phenotypes across multiple time-points may exhibit temporal patterns that can be used to facilitate the understanding of the degenerative process. In this article, we propose a novel temporally constrained group sparse canonical correlation analysis (TGSCCA) framework to identify genetic associations with longitudinal phenotypic markers. RESULTS: The proposed TGSCCA method is able to capture the temporal changes in brain from longitudinal phenotypes by incorporating the fused penalty, which requires that the differences between two consecutive canonical weight vectors from adjacent time-points should be small. A new efficient optimization algorithm is designed to solve the objective function. Furthermore, we demonstrate the effectiveness of our algorithm on both synthetic and real data (i.e., the Alzheimer's Disease Neuroimaging Initiative cohort, including progressive mild cognitive impairment, stable MCI and Normal Control participants). In comparison with conventional SCCA, our proposed method can achieve strong associations and discover phenotypic biomarkers across multiple time-points to guide disease-progressive interpretation. AVAILABILITY AND IMPLEMENTATION: The Matlab code is available at https://sourceforge.net/projects/ibrain-cn/files/ . CONTACT: [email protected] or [email protected].
Source: Bioinformatics
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,989
Funders: U.S. Department of Defense, Foundation for the National Institutes of Health, Alzheimer's Association, Bristol-Myers Squibb, Eli Lilly and Company, Pfizer, Biogen, University of Southern California, F. Hoffmann-La Roche, Meso Scale Diagnostics, Alzheimer's Disease Neuroimaging Initiative, BioClinica, Novartis Pharmaceuticals Corporation, Northern California Institute for Research and Education, National Natural Science Foundation of China, Eisai, Nanjing University of Aeronautics and Astronautics, Servier, H. Lundbeck A/S, IXICO, Scheme for Promotion of Academic and Research Collaboration, National Institutes of Health, Genentech, University of California, San Diego, Canadian Institutes of Health Research, National Institute on Aging, National Institute of Biomedical Imaging and Bioengineering, U.S. National Library of Medicine, National Center for Advancing Translational Sciences
Awards: G1012222616, G104586243, G1298807586, G1308337445, Indiana Alzheimer Disease Center, Bioinformatics Strategies for Multidimensional Brain Imaging Genetics, Genetic architecture of memory and executive functioning in Alzheimer's disease, G1554142629, G156407016, G1593117279, G1650819308, G1654311910, G1823308732, G1880935189, Alzheimer's Disease Neuroimaging Initiative, G2022000225, G206425981, G2100670906, G2105457377, G2152643862, G2189010064, G2340207221, G2423387114, G2471646051, G2522063444, G2536464517, G2554420656, Indiana Clinical and Translational Sciences Institute, G2835601961, G29951154, G3130427885, G3131374986, G3146424788, G3216574877, G3553156159, G3582805754, G3705772492, G3710456697, G3752451908, G3870774570, G3908963977, EFFECTS OF TRAUMATIC BRAIN INJURY AND POSTTRAUMATIC STRESS DISORDER ON ALZHEIMERS DISEASE, G3966393351, G4119534169, G4172682916, G43180419, G4401988282, G4475667458, G4501223628, Integrative Bioinformatics Approaches to Human Brain Genomics and Connectomics, THE NCAA-DOD GRAND ALLIANCE: CONCUSSION ASSESSMENT, RESEARCH, AND EDUCATION (CARE) CONSORTIUM, G470063782, G4800177743, G4860885537, G5207404921, G5209990037, G528601746, G5365730499, EFFECTS OF TRAUMATIC BRAIN INJURY (TBI) AND POST TRAUMATIC STRESS DISORDER (PTSD) ON ALZHEIMER'S DISEASE (AD) IN VETERANS USING IMAGING AND BIOMARKERS IN THE AD NEUROIMAGING INITIATIVE (ADNI)", G5389965057, G5484442508, G5654639750, G5740349702, G5850682332, G5898594745, G613619302, G6173816828, G6177725095, G6210868510, G6213069043, G6371410416, G6412110892, G6447063303, G6719828067, G6792506723, G6899163935, G6948409098, G72415811, G7298697282, G7414321945, Memory Circuitry in MCI and Early Alzheimerâs Disease Prodrome: Molecular Drivers, G7644015481, G764699806, Amyloid Imaging, VMCI, and Analysis for ADNI, G7799614282, G781725486, Metabolic Networks and Pathways in Alzheimer's Disease, G8151151163, G8228018387, G8281378126, G839208290, G8632625050, G8852128998, G8895907669, G8897063270, G8957659042, G9000039018, G9000074849, G9000122335, G920654007
OpenAlex ID: W2735438349