Mining Outcome-relevant Brain Imaging Genetic Associations via Three-way Sparse Canonical Correlation Analysis in Alzheimer’s Disease
Year: 2017
Type: article
Abstract: Neuroimaging genetics is an emerging field that aims to identify the associations between genetic variants (e.g., single nucleotide polymorphisms (SNPs)) and quantitative traits (QTs) such as brain imaging phenotypes. In recent studies, in order to detect complex multi-SNP-multi-QT associations, bi-multivariate techniques such as various structured sparse canonical correlation analysis (SCCA) algorithms have been proposed and used in imaging genetics studies. However, associations between genetic markers and imaging QTs identified by existing bi-multivariate methods may not be all disease specific. To bridge this gap, we propose an analytical framework, based on three-way sparse canonical correlation analysis (T-SCCA), to explore the intrinsic associations among genetic markers, imaging QTs, and clinical scores of interest. We perform an empirical study using the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort to discover the relationships among SNPs from AD risk gene APOE, imaging QTs extracted from structural magnetic resonance imaging scans, and cognitive and diagnostic outcomes. The proposed T-SCCA model not only outperforms the traditional SCCA method in terms of identifying strong associations, but also discovers robust outcome-relevant imaging genetic patterns, demonstrating its promise for improving disease-related mechanistic understanding.
Source: Scientific Reports
DOI: 10.1038/srep44272
Authors: Xiaoke Hao, Chanxiu Li, Lei Du, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher, Andrew J. Saykin, Li Shen, Daoqiang Zhang, Alzheimer’s Disease Neuroimaging Initiative, Michael W. Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, Sara S. Mason, Colleen S. Albers, David Knopman, Kris Johnson, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, Martin R. Farlow, Ann Marie Hake, Brandy R. Matthews, Jared R. Brosch, Scott Herring, Cynthia Hunt, Leslie M. Shaw, Beau Ances, John C. Morris, Maria Carroll, Mary L. Creech, Erin Franklin, Mark A. Mintun, Stacy Schneider, Angela Oliver, Jeffrey Kaye, Joseph Quinn, Lisa Silbert, Betty Lind, Raina Carter, Sara Dolen, Lon S. Schneider, Sonia Pawluczyk, Mauricio Beccera, Liberty Teodoro, Bryan M. Spann, James Brewer, Helen Vanderswag, Adam Fleisher, Pierre Tariot, Anna Burke, Nadira Trncic, Stephanie Reeder, Judith L. Heidebrink, Joanne L. Lord, Rachelle S. Doody, Javier Villanueva-Meyer, Munir Chowdhury, Susan Rountree, Mimi Dang, Yaakov Stern, Lawrence S. Honig, Karen L. Bell, Daniel Marson, Randall Griffith, David Clark, David Geldmacher, John Brockington, Erik Roberson, Marissa Natelson Love, Hillel Grossman, Effie Mitsis, Raj C. Shah, Leyla deToledo-Morrell, Ranjan Duara, Daniel Varon, Maria T. Greig, Peggy Roberts, Marilyn Albert, Chiadi Onyike, Daniel D’Agostino, Stephanie Kielb, James E. Galvin, Brittany Cerbone, Christina A. Michel, Dana M. Pogorelec, Henry Rusinek, Mony J. de Leon, Lidia Glodzik, Susan De Santi, P. Murali Doraiswamy, Jeffrey R. Petrella, Salvador Borges-Neto, Terence Z. Wong, Edward Coleman, Charles D. Smith, Greg Jicha, Peter Hardy, Partha Sinha, Elizabeth Oates, Gary Conrad, Anton P. Porsteinsson, Bonnie S. Goldstein, Kim Martin, Kelly M. Makino, M. Saleem Ismail, Connie Brand, Ruth A. Mulnard, Gaby Thai, Catherine Mc-Adams-Ortiz, Kyle Womack, Dana Mathews, Mary Quiceno, Allan I. Levey, James J. Lah, Janet S. Cellar, Jeffrey M. Burns, Russell H. Swerdlow, William M. Brooks, Liana Apostolova, Kathleen Tingus, Ellen Woo, Daniel H. S. Silverman, Po H. Lu, George Bartzokis, Neill R. Graff-Radford, Francine Parfitt, Tracy Kendall, Heather Johnson, Christopher H. van Dyck, Richard E. Carson, Martha G. MacAvoy, Pradeep Varma, Howard Chertkow, Howard Bergman, Chris Hosein, Sandra Black, Bojana Stefanovic, Curtis Caldwell, Ging-Yuek Robin Hsiung, Howard Feldman, Benita Mudge, Michele Assaly, Elizabeth Finger, Stephen Pasternack, Irina Rachisky, Dick Trost, Andrew Kertesz, Charles Bernick, Donna Munic, Marek-Marsel Mesulam, Kristine Lipowski, Sandra Weintraub, Borna Bonakdarpour, Diana Kerwin, Chuang-Kuo Wu, Nancy Johnson, Carl Sadowsky, Teresa Villena, Raymond Scott Turner, Kathleen Johnson, Brigid Reynolds, Reisa A. Sperling, Keith A. Johnson, Gad Marshall, Jerome Yesavage, Joy L. Taylor, Barton Lane, Allyson Rosen, Jared Tinklenberg, Marwan N. Sabbagh, Christine M. Belden, Sandra A. Jacobson, Sherye A. Sirrel, Neil Kowall, Ronald Killiany, Andrew E. Budson, Alexander Norbash, Patricia Lynn Johnson, Thomas O. Obisesan, Saba Wolday, Joanne Allard, Alan Lerner, Paula Ogrocki, Curtis Tatsuoka, Parianne Fatica, Evan Fletcher, Pauline Maillard, John Olichney, Charles DeCarli, Owen Carmichael, Smita Kittur, Michael Borrie, T.-Y. Lee, Rob Bartha, Sterling Johnson, Sanjay Asthana, Cynthia M. Carlsson, Steven G. Potkin, Adrian Preda, Dana Nguyen, Vernice Bates, Horacio Capote, Michelle Rainka, Douglas W. Scharre, Maria Kataki, Anahita Adeli, Earl A. Zimmerman, Dzintra Celmins, Alice D. Brown, Godfrey D. Pearlson, Karen Blank, Karen Anderson, Laura A. Flashman, Marc Seltzer, Mary L. Hynes, Robert B. Santulli, Kaycee M. Sink, Leslie Gordineer, Jeff D. Williamson, Pradeep Garg, Franklin Watkins, Brian R. Ott, Henry Querfurth, Geoffrey Tremont, Stephen Salloway, Paul Malloy, Stephen Correia, Howard J. Rosen, Bruce L. Miller, David Perry, Jacobo Mintzer, Kenneth Spicer, David Bachman, Nunzio Pomara, Raymundo Hernando, Antero Sarrael, Norman Relkin, Gloria Chaing, Michael Lin, Lisa Ravdin, Amanda Smith, Balebail Ashok Raj, Kristin Fargher
Institutions: Nanjing University of Aeronautics and Astronautics, Northwestern Polytechnical University, Indiana University Indianapolis, Indiana University School of Medicine, University of California, San Francisco, University of California San Diego, Mayo Clinic, Brigham and Women's Hospital, Georgetown University Medical Center, University of California, Berkeley, University of Pennsylvania, University of Southern California, University of California, Davis, Harvard University, Washington University in St. Louis, Oregon Health & Science University, Banner Alzheimer’s Institute, University of Michigan, Baylor College of Medicine, Columbia University Irving Medical Center, University of Alabama at Birmingham, Icahn School of Medicine at Mount Sinai, Rush University Medical Center, Johns Hopkins University, New York University, Duke Medical Center, University of Kentucky, University of Rochester Medicine, University of California, Irvine, The University of Texas Southwestern Medical Center, Emory University, University of Kansas Medical Center, University of California, Los Angeles, Mayo Clinic in Florida, Yale University, Jewish General Hospital, McGill University, Sunnybrook Health Science Centre, Cleveland Clinic, Lou Ruvo Brain Institute, Northwestern University, Palm Beach Neurology, Premiere Research Institute, Stanford University, Banner Sun Health Research Institute, Boston University, Howard University, Case Western Reserve University, Dent Neurologic Institute, The Ohio State University, Albany Medical College, Hartford Hospital, Dartmouth–Hitchcock Medical Center, Wake Forest University Health Sciences, Rhode Island Hospital, Butler Hospital, Medical University of South Carolina, Nathan Kline Institute for Psychiatric Research, Cornell University, University of South Florida, USF Health Byrd Alzheimer's Institute
Language: English
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,690
Funders: National Science Foundation, 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, UC Davis Alzheimer's Disease Core Center, Indiana Alzheimer Disease Center, Bioinformatics Strategies for Multidimensional Brain Imaging Genetics, Genetic architecture of memory and executive functioning in Alzheimer's disease, G1554142629, G1593117279, G1650819308, G1654311910, G1823308732, G1880935189, III: Small: Collaborative Research: A Large-Scale Data Mining Framework for Genome-Wide Mapping of Multi-Modal Phenotypic Biomarkers and Outcome Prediction, Alzheimer's Disease Neuroimaging Initiative, G2022000225, G2100670906, G2105457377, G2152643862, G2189010064, G2340207221, G2423387114, G2471646051, G2522063444, G2536464517, G2554420656, Indiana Clinical and Translational Sciences Institute, G2772251316, 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, THE NCAA-DOD GRAND ALLIANCE: CONCUSSION ASSESSMENT, RESEARCH, AND EDUCATION (CARE) CONSORTIUM, G470063782, G4800177743, G4860885537, G5207404921, G5209990037, G528601746, G5324093878, 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, G5520316217, G5654639750, G5740349702, G5850682332, G5898594745, G613619302, G6173816828, G6210868510, G6213069043, G6371410416, G6412110892, G6447063303, G6719828067, G6792506723, G6899163935, G6948409098, G72415811, G7268282379, 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, G8107776361, G8151151163, G8228018387, Laboratory of Neuro Imaging Resource (LONIR), G8281378126, G8301434335, G839208290, G8632625050, G8852128998, G8895907669, G8897063270, G8957659042, G9000039018, G9000074849, G9000122335, G920654007
OpenAlex ID: W2607528709