首页|inMTSCCA:An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics

inMTSCCA:An Integrated Multi-task Sparse Canonical Correlation Analysis for Multi-omic Brain Imaging Genetics

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Identifying genetic risk factors for Alzheimer's disease(AD)is an important research topic.To date,different endophenotypes,such as imaging-derived endophenotypes and proteomic expression-derived endophenotypes,have shown the great value in uncovering risk genes compared to case-control studies.Biologically,a co-varying pattern of different omics-derived endopheno-types could result from the shared genetic basis.However,existing methods mainly focus on the effect of endophenotypes alone;the effect of cross-endophenotype(CEP)associations remains lar-gely unexploited.In this study,we used both endophenotypes and their CEP associations of multi-omic data to identify genetic risk factors,and proposed two integrated multi-task sparse canonical correlation analysis(inMTSCCA)methods,i.e.,pairwise endophenotype correlation-guided MTSCCA(pcMTSCCA)and high-order endophenotype correlation-guided MTSCCA(hocMTSCCA).pcMTSCCA employed pairwise correlations between magnetic resonance imaging(MRI)-derived,plasma-derived,and cerebrospinal fluid(CSF)-derived endophenotypes as an addi-tional penalty.hocMTSCCA used high-order correlations among these multi-omic data for regular-ization.To figure out genetic risk factors at individual and group levels,as well as altered endophenotypic markers,we introduced sparsity-inducing penalties for both models.We compared pcMTSCCA and hocMTSCCA with three related methods on both simulation and real(consisting of neuroimaging data,proteomic analytes,and genetic data)datasets.The results showed that our methods obtained better or comparable canonical correlation coefficients(CCCs)and better feature subsets than benchmarks.Most importantly,the identified genetic loci and heterogeneous endophenotypic markers showed high relevance.Therefore,jointly using multi-omic endophenotypes and their CEP associations is promising to reveal genetic risk factors.The source code and manual of inMTSCCA are available at https://ngdc.cncb.ac.cn/biocode/tools/BT007330.

Brain imaging geneticsMulti-omic endophenotypeCross-endophenotype associationGenetic risk factorMedical image analysis

Lei Du、Jin Zhang、Ying Zhao、Muheng Shang、Lei Guo、Junwei Han、The Alzheimer's Disease Neuroimaging Initiative、Michael W.Weiner、Norbert Schuff、Howard J.Rosen、Bruce L.Miller、David Perry、Arthur W.Toga、Lon S.Schneider、Sonia Pawluczyk、Mauricio Beccera、Liberty Teodoro、Bryan M.Spann、Karen Crawford、Scott Neu、Ronald Petersen、Bret Borowski、Jeff Gunter、Matt Senjem、Prashanthi Vemuri、David Jones、Kejal Kantarci、Chad Ward、Jack R.Clifford Jr.、Matthew Bernstein、Sara S.Mason、Colleen S.Albers、David Knopman、Kris Johnson、William Jagust、Susan Landau、John Q.Trojanowki、Leslie M.Shaw、Virginia Lee、Magdalena Korecka、Michal Figurski、Steven E.Arnold、Jason H.Karlawish、David A.Wolk、Christopher M.Clark、Laurel Beckett、Danielle Harvey、Evan Fletcher、Pauline Maillard、Charles DeCArli、John Olichney、Charles DeCarli、Owen Carmichael、Robert C.Green、Reisa A.Sperling、Keith A.Johnson、Gad Marshall、John Morris、Marc Raichle、David Holtzman、Nigel J.Cairns、Erin Franklin、Mark A.Mintun、Stacy Schneider、Angela Oliver、Lisa Taylor-Reinwald、Zaven Khachaturian、Greg Sorensen、Beau Ances、Maria Carroll、Mary L.Creech、Maria Carrillo、Lew Kuller、Chet Mathis、Oscar L.Lopez、Mary Ann Oakley、Donna M.Simpson、Steven Paul、Norman Relkin、Gloria Chaing、Michael Lin、Lisa Ravdin、Peter Davies、Howard Fillit、Franz Hefti、Marsel Mesulam、Emily Rogalski、Kristine Lipowski、Sandra Weintraub、Borna Bonakdarpour、Diana Kerwin、Chuang-Kuo Wu、Nancy Johnson、William Potter、Peter Snyder、Adam Schwartz、Tom Montine、Paul Aisen、Ronald G.Thomas、Michael Donohue、Sarah Walter、Devon Gessert、Tamie Sather、Gus Jiminez、Archana B.Balasubramanian、Leon Thai、Jennifer Mason、Iris Sim、James Brewer、Helen Vanderswag、Adam Fleisher、Nick Fox、Paul Thompson、Liana Apostolova、Kathleen Tingus、Ellen Woo、Daniel H.S.Silverman、Po H.Lu、George Bartzokis、Robert A.Koeppe、Judith L.Heidebrink、Joanne L.Lord、Norm Foster、Eric M.Reiman、Kewei Chen、Pierre Tariot、Anna Burke、Ann Marie Milliken、Nadira Trncic、Stephanie Reeder、Steven Potkin、Adrian Preda、Dana Nguyen、Neil Buckholtz、John Hsiao、Marilyn Albert、Chiadi Onyike、Daniel D'Agostino、Stephanie Kielb、Richard Frank、Jeffrey Kaye、Joseph Quinn、Lisa Silbert、Betty Lind、Raina Carter、Sara Dolen、Javier Villanueva-Meyer、Valory Pavlik、Victoria Shibley、Munir Chowdhury、Susan Rountree、Mimi Dang、Rachelle S.Doody、Yaakov Stern、Lawrence S.Honig、Daniel Marson、David Geldmacher、Marissa Natelson Love、Randall Griffith、David Clark、John Brockington、Erik Roberson、Karen L.Bell、Hillel Grossman、Effie Mitsis、Raj C.Shah、Leyla deToledo-Morrell、Ranjan Duara、Maria T.Greig-Custo、Warren Barker、Martin Sadowski、Mohammed O.Sheikh、Anaztasia Ulysse、Mrunalini Gaikwad、P.Murali Doraiswamy、Jeffrey R.Petrella、Salvador BorgesNeto、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、Kyle Womack、Dana Mathews、Mary Quiceno、Allan I.Levey、James J.Lah、Janet S.Cellar、Jeffrey M.Burns、Russell H.Swerdlow、William M.Brooks、Neill R Graff-Radford、Francine Parfitt、Kim Poki-Walker、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、Benita Mudge、Vesna Sossi、Howard Feldman、Michele Assaly、Elizabeth Finger、Stephen Pasternack、Irina Rachisky、John Rogers、Dick Trost、Andrew Kertesz、Charles Bernick、Donna Munic、Carl Sadowsky、Teresa Villena、Raymond Scott Turner、Kathleen Johnson、Brigid Reynolds、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、Smita Kittur、Michael Borrie、Ting-Yim Lee、Rob Bartha、Sterling Johnson、Sanjay Asthana、Cynthia M.Carlsson、Li Shen、Vernice Bates、Horacio Capote、Michelle Rainka、Douglas W.Scharre、Maria Kataki、Brendan Kelly、Earl A.Zimmerman、Dzintra Celmins、Alice D.Brown、Godfrey D.Pearlson、Karen Anderson、Laura A.Flashman、Marc Seltzer、Mary L.Hynes、Robert B.Santulli、Karen Blank、Kaycee M.Sink、Leslie Gordineer、Jeff D.Williamson、Pradeep Garg、Franklin Watkins、Brian R.Ott、Geoffrey Tremont、Stephen Salloway、Paul Malloy、Stephen Correia、Lori A.Daiello、Jacobo Mintzer、Kenneth Spicer、David Bachman、Nunzio Pomara、Raymundo Hernando、Antero Sarrael、Susan K.Schultz、Karen Ekstam Smith、Hristina Koleva、Ki Won Nam、Hyungsub Shim、Amanda Smith、Balebail Ashok Raj、Kristin Fargher、Tatiana M.Foroud、Kelley Faber、Sungeun Kim、Kwangsik Nho、Martin R.Farlow、Ann Marie Hake、Brandy R.Matthews、Jared R.Brosch、Scott Herring、Andrew J.Saykin

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Department of Intelligent Science and Technology,School of Automation,Northwestern Polytechnical University,Xi'an 710072,China

San Francisco Veterans Affairs Medical Center,University of California,San Francisco,CA 94107,USA

Reed Neurological Research Center,UCLA School of Medi-cine,Los Angeles,CA 90095,USA

Mayo Clinic Alzheimer's Disease Research Center,Rochester,MN 14607,USA

Helen Wills Neuroscience Institute,University of California,Berkeley,CA94704,USA

Center for Neurodegenerative Disease Researh,University of Pennsylvania,Philadelphia,PA 19019,USA

Department of Public Health Sciences,University of Califor-nia,Davis,CA 95616,USA

Brigham and Women's Hospital,Harvard Medical School,Boston,MA 02215,USA

Department of Pharmaceutical Chemistry,Washington Univer-sity,St.Louis,MO 63110,USA

Pitt Department of Psychiatry,University of Pittsburgh,Pitts-burgh,PA 20850,USA

Ruane Center for the Humanities,University of Pennsylvania,Philadelphia,PA 19104,USA

Alzheimer's Association,Chicago,IL 60631,USA

Radiology,University of Pittsburgh,Pittsburgh,PA 15213,USA

Cornell's Medical College,Cornell University,New York,NY 14853,USA

Albert Einstein College of Medicine,Yeshiva University,New York,NY 10461,USA

Steering Committee of the Milken Institute's Alliance to Improve Dementia Care,AD Drug Discovery Foundation,New York,NY 10019,USA

Acumen Pharmaceuticals,Livermore,CA 94551,USA

Cognitive Neurology and Alzheimer's Disease Center,North-western University,Chicago,IL 60611,USA

National Institute of Mental Health,Bethesda,MD 20892,USA

Department of Neurology,Brown University,Providence,RI 02912,USA

Tailored Therapeutics,Eli Lilly and Company,Indianapolis,IN 46285,USA

Department of Pathology,University of Washington,Seattle,WA 98195,USA

University of California San Diego,La Jolla,CA 92093,USA

Department of Behavioural and Social Sciences,University of London,London WC1E 6BT,UK

University of California,Los Angeles,Torrance,CA 90509,USA

Department of Radiology,University of Michigan,Ann Arbor,MI 48109-2800,USA

Department of Neurology,University of Utah,Salt Lake City,UT 84112,USA

Banner Alzheimer's Institute,Phoenix,AZ 85006,USA

University of California Irvine,Orange,CA 92868,USA

National Institute on Aging,Baltimore,MD 21202,USA

Department of Neurology,Johns Hopkins University,Balti-more,MD 21205,USA

Richard Frank Consulting,New York,NY 13340,USA

Oregon Health and Science University,Portland,OR 97239,USA

Baylor College of Medicine,Houston,TX 75835,USA

Columbia University Medical Center,New York,NY 10027,USA

Department of Neurology,University of Alabama,Birming-ham,AL 35201,USA

Department of Neurology,Mount Sinai School of Medicine,New York,NY 75835,USA

Rush University Medical Center,Chicago,IL 60612,USA

Wien Center,Miami Beach,FL 33140,USA

School of Informatics and Computing,Indiana University-Purdue University,Indianapolis,IN 46202,USA

Departments of Radiology,Duke University Medical Center,Durham,NC 27710,USA

Department of Neurology and Sanders-Brown Center on Aging,University of Kentucky,Lexington,KY 40292,USA

Department of Psychiatry,University of Rochester School of Medicine and Dentistry,Rochester,NY 14642,USA

Department of Neuroloy,University of Texas Southwestern Medical School,Galveston,TX 77555,USA

Department of Neurology,Emory University,Atlanta,GA 30307,USA

University of Kansas Medical Center,Kansas City,KS 66160,USA

Mayo Clinic,Jacksonville,FL 28546,USA

Yale University School of Medicine,New Haven,CT 201942,USA

Montreal-Jewish General Hospital,Montreal,PQ H3A 2A7,Canada

Sunnybrook Health Sciences,Toronto,ON M5S 1A5,Canada

UBC Clinic for AD and Related Disorders,Vancouver,BC V6T 1Z2,Canada

St.Joseph's Health Care,London,ON N6A 4H1,Canada

Cleveland Clinic Lou Ruvo Center for Brain Health,Las Vegas,NV 89106,USA

Premiere Research Inst(Palm Beach Neurology),West Palm Beach,FL 33413,USA

Georgetown University Medical Center,Washington,DC 20007,USA

Department of Psychiatry and Behavioral Sciences,Stanford University,Stanford,CA 94305,USA

Veterans Affairs Boston Healthcare System,Boston Univer-sity,Boston,MA 02215,USA

Howard University,Washington,DC 98195,USA

Department of Neurology,Case Western Reserve University,Cleveland,OH 44106,USA

Neurological Care of CNY,Liverpool,NY 13088,USA

Joseph,s Health Care,The University of Western Ontario,London,ON 77842,Canada

Department of Biostatistics,Epidemiology and Informatics Perelman School of Medicine University of Pennsylvania,Philadelphia,PA 19104,USA

Dent Neurologic Institute,Amherst,NY 14226,USA

Department of Neurology,Ohio State University,Columbus,OH 43210,USA

Albany Medical College,Albany,NY 12208,USA

Hartford Hospital Olin Neuropsychiatry Research Center,Hartford,CT 06114,USA

Dartmouth-Hitchcock Medical Center,Lebanon,NH 97355,USA

Wake Forest School of Medicine,Winston-Salem,NC 27109,USA

Alpert Medical School,Brown University,Providence,RI 02912,USA

Department of Neurology,Warren Alpert Medical School of Brown University,Providence,RI 02912,USA

Medical University South Carolina,Charleston,SC 29425,USA

Nathan Kline Institute,Orangeburg,New York,NY 10962,USA

University of Iowa College of Medicine,Iowa City,I A 52242,USA

USF Health Byrd Alzheimer's Institute,University of South Florida,Tampa,FL 33613,USA

Department of Medical and Molecular Genetics,Indiana University School of Medicine,Indianapolis,IN 46202,USA

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STI2030-Major ProjectsNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNatural Science Basic Research Program of ShaanxiInnovation Foundation for Doctor Dissertation at Northwestern Polytechnical University,China

2022ZD02137006213600461973255619360072020JM-142CX2023062

2023

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子:0.495
ISSN:1672-0229
年,卷(期):2023.21(2)
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