Featured Publications
Integration of expression QTLs with fine mapping via SuSiE.
Zhang X, Jiang W, Zhao H. Integration of expression QTLs with fine mapping via SuSiE. PLOS Genetics 2024, 20: e1010929. PMID: 38271473, PMCID: PMC10846745, DOI: 10.1371/journal.pgen.1010929.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociGenome-wide association studiesFine-mapping methodsLinkage disequilibriumBody mass indexFine-mappingExpression quantitative trait loci informationGenome-wide association study resultsExpression quantitative trait loci analysisPresence of linkage disequilibriumExternal reference panelGenetic fine-mappingQuantitative trait lociPosterior inclusion probabilitiesInclusion probabilitiesAlzheimer's diseaseExpression QTLsLD patternsComplex traitsCandidate variantsAssociation studiesTrait lociAssociation to causationReference panelFunctional variantsLeveraging LD eigenvalue regression to improve the estimation of SNP heritability and confounding inflation
Song S, Jiang W, Zhang Y, Hou L, Zhao H. Leveraging LD eigenvalue regression to improve the estimation of SNP heritability and confounding inflation. American Journal Of Human Genetics 2022, 109: 802-811. PMID: 35421325, PMCID: PMC9118121, DOI: 10.1016/j.ajhg.2022.03.013.Peer-Reviewed Original ResearchConceptsLinkage disequilibrium score regressionComplex traitsSingle nucleotide polymorphismsSNP heritabilityGenome-wide association studiesDisequilibrium score regressionHigh-throughput technologiesHeritable phenotypesAssociation studiesGenetic studiesCryptic relatednessLD informationScore regressionHeritabilityGenetic contributionHeritability estimationPopulation stratificationDisease mechanismsTraitsLD matrixOnly summary statisticsUK BiobankPolygenicitySummary statisticsRelatednessSUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits
Zhang Y, Lu Q, Ye Y, Huang K, Liu W, Wu Y, Zhong X, Li B, Yu Z, Travers BG, Werling DM, Li JJ, Zhao H. SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits. Genome Biology 2021, 22: 262. PMID: 34493297, PMCID: PMC8422619, DOI: 10.1186/s13059-021-02478-w.Peer-Reviewed Original ResearchConceptsLocal genetic correlationsComplex traitsGenetic correlationsGenomic regionsLocal genetic correlation analysisGenome-wide association studiesLocal genomic regionsSpecific genomic regionsGenetic correlation analysisDistinct genetic signaturesGenetic similarityGenetic signaturesAssociation studiesTraitsSample overlapStatistical frameworkSummary statisticsDisequilibriumRegionAccurate estimationSimilarityTranscriptomic organization of the human brain in post-traumatic stress disorder
Girgenti MJ, Wang J, Ji D, Cruz DA, Stein M, Gelernter J, Young K, Huber B, Williamson D, Friedman M, Krystal J, Zhao H, Duman R. Transcriptomic organization of the human brain in post-traumatic stress disorder. Nature Neuroscience 2020, 24: 24-33. PMID: 33349712, DOI: 10.1038/s41593-020-00748-7.Peer-Reviewed Original ResearchMeSH KeywordsAdultAutopsyBrain ChemistryCohort StudiesDepressive Disorder, MajorFemaleGene Expression RegulationGene Regulatory NetworksGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansInterneuronsMaleMiddle AgedNerve Tissue ProteinsSex CharacteristicsStress Disorders, Post-TraumaticTranscriptomeYoung AdultConceptsGenome-wide association studiesSignificant gene networksDifferential gene expressionSystems-level evidenceSignificant genetic liabilityMajor depressive disorder cohortGene networksTranscriptomic organizationTranscriptomic landscapeDownregulated setsGenomic networksGene expressionAssociation studiesMolecular determinantsExtensive remodelingGenotype dataSexual dimorphismSignificant divergenceMolecular profileNetwork analysisELFN1TranscriptsDimorphismPostmortem tissueDivergence
2024
Phenome- and genome-wide analyses of retinal optical coherence tomography images identify links between ocular and systemic health
Zekavat S, Jorshery S, Rauscher F, Horn K, Sekimitsu S, Koyama S, Nguyen T, Costanzo M, Jang D, Burtt N, Kühnapfel A, Shweikh Y, Ye Y, Raghu V, Zhao H, Ghassemi M, Elze T, Segrè A, Wiggs J, Del Priore L, Scholz M, Wang J, Natarajan P, Zebardast N. Phenome- and genome-wide analyses of retinal optical coherence tomography images identify links between ocular and systemic health. Science Translational Medicine 2024, 16: eadg4517. PMID: 38266105, DOI: 10.1126/scitranslmed.adg4517.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesRetinal layer thicknessPhotoreceptor segmentsOptical coherence tomographyRetinal layersUK Biobank participantsLIFE-Adult-StudyInherited genetic lociGenome-wide associationGanglion cell complex layerRetinal optical coherence tomography imagesRetinal nerve fiber layerAge-related macular degenerationBiobank participantsEye careNerve fiber layerOptical coherence tomography imagesIncident mortalityMacular OCT imagesLIFE-AdultIndependent associationsAssociation studiesSystemic healthGenetic associationGenome-wide analysis
2023
Shared genetic architecture of blood eosinophil counts and asthma in UK Biobank
Li B, Wang Y, Wang Z, Li X, Kay S, Chupp G, Zhao H, Gomez J. Shared genetic architecture of blood eosinophil counts and asthma in UK Biobank. ERJ Open Research 2023, 9: 00291-2023. PMID: 37650091, PMCID: PMC10463033, DOI: 10.1183/23120541.00291-2023.Peer-Reviewed Original ResearchGenome-wide association studiesGenetic architectureGenetic correlation analysisUK BiobankGWAS resultsTranscription factorsInterleukin-4 SignalingBlood eosinophil countsAssociation studiesDoctor-diagnosed asthmaSignificant variantsEosinophil countEuropean ancestryTraitsPathwayGenetic linkType 2 immune responsesType 2 inflammationSignalingCritical associationImmune responseHeterogeneous diseaseTAGCSevere asthmaTherapeutic interventionsMulti-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program
Cheng Y, Dao C, Zhou H, Li B, Kember R, Toikumo S, Zhao H, Gelernter J, Kranzler H, Justice A, Xu K. Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program. Translational Psychiatry 2023, 13: 148. PMID: 37147289, PMCID: PMC10162964, DOI: 10.1038/s41398-023-02409-2.Peer-Reviewed Original ResearchConceptsSingle-trait genome-wide association studiesGenome-wide association studiesNovel lociPower of GWASJoint genome-wide association studyGenome-wide significant lociMillion Veteran ProgramGenome-wide associationSubstance use traitsGWAS summary statisticsNovel genetic variantsMulti-trait analysisFunctional annotationUse traitsSignificant lociHeritable traitMultiple lociAssociation studiesColocalization analysisLociPleiotropic effectsMTAgVeteran ProgramGenetic variantsTraitsA genome-wide association study of frailty identifies significant genetic correlation with neuropsychiatric, cardiovascular, and inflammation pathways
Ye Y, Noche R, Szejko N, Both C, Acosta J, Leasure A, Brown S, Sheth K, Gill T, Zhao H, Falcone G. A genome-wide association study of frailty identifies significant genetic correlation with neuropsychiatric, cardiovascular, and inflammation pathways. GeroScience 2023, 45: 2511-2523. PMID: 36928559, PMCID: PMC10651618, DOI: 10.1007/s11357-023-00771-z.Peer-Reviewed Original ResearchConceptsFried frailty scoreBiology of frailtyEuropean descent participantsOccurrence of frailtyGenome-wide association studiesMendelian randomization analysisFrailty scoreChronic painJoint disordersPolygenic risk scoresRespiratory diseaseInflammation pathwaysRisk scoreClinical phenotypeBrain tissueCausal associationFrailtyAge-related pathwaysRandomization analysisGenetic factorsAssociation studiesUK BiobankRetirement StudyPerson's vulnerabilitySignificant genetic correlationsWhole-Exome Sequencing Analyses Support a Role of Vitamin D Metabolism in Ischemic Stroke
Xie Y, Acosta J, Ye Y, Demarais Z, Conlon C, Chen M, Zhao H, Falcone G. Whole-Exome Sequencing Analyses Support a Role of Vitamin D Metabolism in Ischemic Stroke. Stroke 2023, 54: 800-809. PMID: 36762557, PMCID: PMC10467223, DOI: 10.1161/strokeaha.122.040883.Peer-Reviewed Original ResearchConceptsGene-based testingRare genetic variationGene-based analysisGenetic variationAssociation studiesGenome-wide association studiesSingle-variant association analysisWide significance levelSusceptibility risk lociWide association studyDeleterious missense variantsMissense rare variantsBonferroni-corrected thresholdWhole-exome sequencing dataRare variantsSingle variant analysisHeritable traitRisk lociExome-wide studySequencing dataExome sequencing analysisAssociation analysisSequencing analysisMissense variantsTraitsIdentification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans
Kimbrel N, Ashley-Koch A, Qin X, Lindquist J, Garrett M, Dennis M, Hair L, Huffman J, Jacobson D, Madduri R, Trafton J, Coon H, Docherty A, Mullins N, Ruderfer D, Harvey P, McMahon B, Oslin D, Beckham J, Hauser E, Hauser M, Agarwal K, Ashley-Koch A, Aslan M, Beckham J, Begoli E, Bhattacharya T, Brown B, Calhoun P, Cheung K, Choudhury S, Cliff A, Cohn J, Crivelli S, Cuellar-Hengartner L, Deangelis H, Dennis M, Dhaubhadel S, Finley P, Ganguly K, Garvin M, Gelernter J, Hair L, Harvey P, Hauser E, Hauser M, Hengartner N, Jacobson D, Jones P, Kainer D, Kaplan A, Katz I, Kember R, Kimbrel N, Kirby A, Ko J, Kolade B, Lagergren J, Lane M, Levey D, Levin D, Lindquist J, Liu X, Madduri R, Manore C, Martins S, McCarthy J, McDevitt-Cashman M, McMahon B, Miller I, Morrow D, Oslin D, Pavicic-Venegas M, Pestian J, Pyarajan S, Qin X, Rajeevan N, Ramsey C, Ribeiro R, Rodriguez A, Romero J, Santel D, Schaefferkoetter N, Shi Y, Stein M, Sullivan K, Sun N, Tamang S, Townsend A, Trafton J, Walker A, Wang X, Wangia-Anderson V, Yang R, Yoon H, Yoo S, Zamora-Resendiz R, Zhao H, Docherty A, Mullins N, Coleman J, Shabalin A, Kang J, Murnyak B, Wendt F, Adams M, Campos A, DiBlasi E, Fullerton J, Kranzler H, Bakian A, Monson E, Rentería M, Andreassen O, Bulik C, Edenberg H, Kessler R, Mann J, Nurnberger J, Pistis G, Streit F, Ursano R, Awasthi S, Bergen A, Berrettini W, Bohus M, Brandt H, Chang X, Chen H, Chen W, Christensen E, Crawford S, Crow S, Duriez P, Edwards A, Fernández-Aranda F, Fichter M, Galfalvy H, Gallinger S, Gandal M, Gorwood P, Guo Y, Hafferty J, Hakonarson H, Halmi K, Hishimoto A, Jain S, Jamain S, Jiménez-Murcia S, Johnson C, Kaplan A, Kaye W, Keel P, Kennedy J, Kim M, Klump K, Levey D, Li D, Liao S, Lieb K, Lilenfeld L, Lori A, Magistretti P, Marshall C, Mitchell J, Myers R, Okazaki S, Otsuka I, Pinto D, Powers A, Ramoz N, Ripke S, Roepke S, Rozanov V, Scherer S, Schmahl C, Sokolowski M, Starnawska A, Strober M, Su M, Thornton L, Treasure J, Ware E, Watson H, Witt S, Woodside D, Yilmaz Z, Zillich L, Agerbo E, Børglum A, Breen G, Demontis D, Erlangsen A, Esko T, Gelernter J, Glatt S, Hougaard D, Hwu H, Kuo P, Lewis C, Li Q, Liu C, Martin N, McIntosh A, Medland S, Mors O, Nordentoft M, Nurnberger J, Olsen C, Porteous D, Smith D, Stahl E, Stein M, Wasserman D, Werge T, Whiteman D, Willour V, Coon H, Ruderfer D, Dedert E, Elbogen E, Fairbank J, Hurley R, Kilts J, Martindale S, Marx C, McDonald S, Moore S, Morey R, Naylor J, Rowland J, Shura R, Swinkels C, Tupler L, Van Voorhees E, Yoash-Gantz R, Gaziano J, Muralidhar S, Ramoni R, Chang K, O’Donnell C, Tsao P, Breeling J, Hauser E, Sun Y, Huang G, Casas J, Moser J, Whitbourne S, Brewer J, Conner T, Argyres D, Stephens B, Brophy M, Humphries D, Selva L, Do N, Shayan S, Cho K, Churby L, Wilson P, McArdle R, Dellitalia L, Mattocks K, Harley J, Whittle J, Jacono F, Wells J, Gutierrez S, Gibson G, Hammer K, Kaminsky L, Villareal G, Kinlay S, Xu J, Hamner M, Mathew R, Bhushan S, Iruvanti P, Godschalk M, Ballas Z, Ivins D, Mastorides S, Moorman J, Gappy S, Klein J, Ratcliffe N, Florez H, Okusaga O, Murdoch M, Sriram P, Yeh S, Tandon N, Jhala D, Liangpunsakul S, Oursler K, Whooley M, Ahuja S, Constans J, Meyer P, Greco J, Rauchman M, Servatius R, Gaddy M, Wallbom A, Morgan T, Stapley T, Sherman S, Ross G, Strollo P, Boyko E, Meyer L, Gupta S, Huq M, Fayad J, Hung A, Lichy J, Hurley R, Robey B, Striker R. Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans. JAMA Psychiatry 2023, 80: 135-145. PMID: 36515925, PMCID: PMC9857322, DOI: 10.1001/jamapsychiatry.2022.3896.Peer-Reviewed Original ResearchConceptsMolecular genetic basisRisk lociSingle nucleotide variantsGWS lociGenetic basisGenomic risk lociRisk genesGenome-wide association studiesSignificant enrichmentGene-based analysisGenetic risk lociCandidate risk genesCyclic adenosine monophosphate (cAMP) signalingIdentification of novelPolygenic risk score analysisGene clusterFocal adhesionsGenetic substructureUbiquitination processChromosome 2Enrichment analysisAssociation studiesAxon guidanceAfrican ancestryNCAM1-TTC12Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression
Lin C, Liu W, Jiang W, Zhao H. Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression. Biology Methods And Protocols 2023, 8: bpad024. PMID: 37901453, PMCID: PMC10599978, DOI: 10.1093/biomethods/bpad024.Peer-Reviewed Original ResearchExpression quantitative trait lociGenome-wide association studiesComplex traitsGene expression regulationGenetic association signalsQuantitative trait lociScore regressionDisease-associated variantsSNP annotationGene annotationExpression regulationGWAS resultsTrait lociTrait heritabilityEQTL effectsAssociation signalsGene expressionAssociation studiesGene effectsSNP effectsHuman diseasesHeritabilityTraitsBiological realityAnnotation
2022
Genome-Wide Investigation of Maximum Habitual Alcohol Intake in US Veterans in Relation to Alcohol Consumption Traits and Alcohol Use Disorder
Deak JD, Levey DF, Wendt FR, Zhou H, Galimberti M, Kranzler HR, Gaziano JM, Stein MB, Polimanti R, Gelernter J, Muralidhar S, Moser J, Deen J, Gaziano J, Beckham J, Chang K, Tsao P, Luoh S, Casas J, Churby L, Whitbourne S, Brewer J, Brophy M, Selva L, Shayan S, Cho K, Pyarajan S, DuVall S, Connor T, Argyres D, Aslan M, Stephens B, Concato J, Gelernter J, Gleason T, Huang G, Koenen K, Marx C, Radhakrishnan K, Schork N, Stein M, Zhao H, Kaufman J, Nunez Y, Pietrzak R, Beck D, Cissell S, Crutchfield P, Lance W, Cheung K, Li Y, Sun N, Chen Q, Rajeevan N, Sayward F, Gagnon D, Harrington K, Quaden R, O'Leary T, Ramoni R. Genome-Wide Investigation of Maximum Habitual Alcohol Intake in US Veterans in Relation to Alcohol Consumption Traits and Alcohol Use Disorder. JAMA Network Open 2022, 5: e2238880. PMID: 36301540, PMCID: PMC9614582, DOI: 10.1001/jamanetworkopen.2022.38880.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGenome-wide significant lociGenomic structural equation modelingSignificant lociAlcohol traitsAssociation studiesAfrican ancestry participantsGenome-wide investigationAncestry-specific genome-wide association studiesGenetic correlationsPsychiatric traitsLinkage disequilibrium score regressionGenetic associationStrong genetic correlationSingle nucleotide variantsGenetic architectureGenetic association studiesGenetic lociTop associationsNegative rgEuropean ancestry participantsNucleotide variantsFunctional variantsScore regressionTraitsMendelian randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics
Hu X, Zhao J, Lin Z, Wang Y, Peng H, Zhao H, Wan X, Yang C. Mendelian randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2106858119. PMID: 35787050, PMCID: PMC9282238, DOI: 10.1073/pnas.2106858119.Peer-Reviewed Original Research
2021
Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors
Mullins N, Kang J, Campos AI, Coleman JRI, Edwards AC, Galfalvy H, Levey DF, Lori A, Shabalin A, Starnawska A, Su MH, Watson HJ, Adams M, Awasthi S, Gandal M, Hafferty JD, Hishimoto A, Kim M, Okazaki S, Otsuka I, Ripke S, Ware EB, Bergen AW, Berrettini WH, Bohus M, Brandt H, Chang X, Chen WJ, Chen HC, Crawford S, Crow S, DiBlasi E, Duriez P, Fernández-Aranda F, Fichter MM, Gallinger S, Glatt SJ, Gorwood P, Guo Y, Hakonarson H, Halmi KA, Hwu HG, Jain S, Jamain S, Jiménez-Murcia S, Johnson C, Kaplan AS, Kaye WH, Keel PK, Kennedy JL, Klump KL, Li D, Liao SC, Lieb K, Lilenfeld L, Liu CM, Magistretti PJ, Marshall CR, Mitchell JE, Monson ET, Myers RM, Pinto D, Powers A, Ramoz N, Roepke S, Rozanov V, Scherer SW, Schmahl C, Sokolowski M, Strober M, Thornton LM, Treasure J, Tsuang MT, Witt SH, Woodside DB, Yilmaz Z, Zillich L, Adolfsson R, Agartz I, Air TM, Alda M, Alfredsson L, Andreassen OA, Anjorin A, Appadurai V, Artigas M, Van der Auwera S, Azevedo MH, Bass N, Bau CHD, Baune BT, Bellivier F, Berger K, Biernacka JM, Bigdeli TB, Binder EB, Boehnke M, Boks MP, Bosch R, Braff DL, Bryant R, Budde M, Byrne EM, Cahn W, Casas M, Castelao E, Cervilla JA, Chaumette B, Cichon S, Corvin A, Craddock N, Craig D, Degenhardt F, Djurovic S, Edenberg HJ, Fanous AH, Foo JC, Forstner AJ, Frye M, Fullerton JM, Gatt JM, Gejman PV, Giegling I, Grabe HJ, Green MJ, Grevet EH, Grigoroiu-Serbanescu M, Gutierrez B, Guzman-Parra J, Hamilton SP, Hamshere ML, Hartmann A, Hauser J, Heilmann-Heimbach S, Hoffmann P, Ising M, Jones I, Jones LA, Jonsson L, Kahn RS, Kelsoe JR, Kendler KS, Kloiber S, Koenen KC, Kogevinas M, Konte B, Krebs MO, Landén M, Lawrence J, Leboyer M, Lee PH, Levinson DF, Liao C, Lissowska J, Lucae S, Mayoral F, McElroy SL, McGrath P, McGuffin P, McQuillin A, Medland SE, Mehta D, Melle I, Milaneschi Y, Mitchell PB, Molina E, Morken G, Mortensen PB, Müller-Myhsok B, Nievergelt C, Nimgaonkar V, Nöthen MM, O’Donovan M, Ophoff RA, Owen MJ, Pato C, Pato MT, Penninx BWJH, Pimm J, Pistis G, Potash JB, Power RA, Preisig M, Quested D, Ramos-Quiroga JA, Reif A, Ribasés M, Richarte V, Rietschel M, Rivera M, Roberts A, Roberts G, Rouleau GA, Rovaris DL, Rujescu D, Sánchez-Mora C, Sanders AR, Schofield PR, Schulze TG, Scott LJ, Serretti A, Shi J, Shyn SI, Sirignano L, Sklar P, Smeland OB, Smoller JW, Sonuga-Barke EJS, Spalletta G, Strauss JS, Świątkowska B, Trzaskowski M, Turecki G, Vilar-Ribó L, Vincent JB, Völzke H, Walters JTR, Weickert C, Weickert TW, Weissman MM, Williams LM, Wray NR, Zai CC, Ashley-Koch AE, Beckham JC, Hauser ER, Hauser MA, Kimbrel NA, Lindquist JH, McMahon B, Oslin DW, Qin X, Agerbo E, Børglum A, Breen G, Erlangsen A, Esko T, Gelernter J, Hougaard D, Kessler R, Kranzler H, Li Y, Martin N, McIntosh A, Mors O, Nordentoft M, Olsen C, Porteous D, Ursano R, Wasserman D, Werge T, Whiteman D, Bulik C, Coon H, Demontis D, Docherty A, Kuo P, Lewis G, Mann J, Rentería M, Smith D, Stahl E, Stein D, Streit F, Willour V, Ruderfer D, Wray N, Ripke S, Mattheisen M, Trzaskowski M, Byrne E, Abdellaoui A, Adams M, Agerbo E, Air T, Andlauer T, Bacanu S, Bækvad-Hansen M, Beekman A, Bigdeli T, Binder E, Bryois J, Buttenschøn H, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen J, Clarke T, Coleman J, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford G, Davies G, Degenhardt F, Derks E, Direk N, Dolan C, Dunn E, Eley T, Escott-Price V, Kiadeh F, Finucane H, Foo J, Forstner A, Frank J, Gaspar H, Gill M, Goes F, Gordon S, Weinsheimer S, Wellmann J, Willemsen G, Witt S, Wu Y, Xi H, Yang J, Zhang F, Arolt V, Baune B, Berger K, Boomsma D, Cichon S, Dannlowski U, de Geus E, Depaulo J, Domenici E, Domschke K, Esko T, Grabe H, Hamilton S, Grove J, Hall L, Hansen C, Hansen T, Herms S, Hickie I, Hoffmann P, Homuth G, Horn C, Hottenga J, Hougaard D, Howard D, Ising M, Jansen R, Jones I, Jones L, Jorgenson E, Knowles J, Kohane I, Kraft J, Kretzschmar W, Kutalik Z, Li Q, Lind P, MacIntyre D, MacKinnon D, Maier R, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland S, Mehta D, Middeldorp C, Mihailov E, Milaneschi Y, Milani L, Mondimore F, Montgomery G, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard M, Nyholt D, O’Reilly P, Oskarsson H, Hayward C, Heath A, Kendler K, Kloiber S, Lewis C, Li D, Lucae S, Madden P, Magnusson P, Martin N, McIntosh A, Metspalu A, Mors O, Mortensen P, Müller-Myhsok B, Nordentoft M, Nöthen M, O’Donovan M, Paciga S, Pedersen N, Owen M, Painter J, Pedersen C, Pedersen M, Peterson R, Peyrot W, Pistis G, Posthuma D, Quiroz J, Qvist P, Rice J, Riley B, Rivera M, Mirza S, Schoevers R, Schulte E, Shen L, Shi J, Shyn S, Sigurdsson E, Sinnamon G, Smit J, Smith D, Stefansson H, Steinberg S, Streit F, Strohmaier J, Tansey K, Teismann H, Teumer A, Thompson W, Thomson P, Thorgeirsson T, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden A, Umbricht D, Van der Auwera S, van Hemert A, Viktorin A, Visscher P, Wang Y, Webb B, Penninx B, Perlis R, Porteous D, Potash J, Preisig M, Rietschel M, Schaefer C, Schulze T, Smoller J, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman M, Werge T, Lewis C, Levinson D, Breen G, Børglum A, Sullivan P, Mullins N, Forstner A, O’Connell K, Coombes B, Coleman J, Qiao Z, Als T, Bigdeli T, Børte S, Bryois J, Charney A, Drange O, Gandal M, Hagenaars S, Ikeda M, Kamitaki N, Kim M, Krebs K, Panagiotaropoulou G, Schilder B, Sloofman L, Steinberg S, Trubetskoy V, Winsvold B, Won H, Abramova L, Adorjan K, Agerbo E, Al Eissa M, Albani D, Alliey-Rodriguez N, Anjorin A, Antilla V, Antoniou A, Awasthi S, Baek J, Bækvad-Hansen M, Bass N, Bauer M, Beins E, Bergen S, Birner A, Pedersen C, Bøen E, Boks M, Bosch R, Brum M, Brumpton B, Brunkhorst-Kanaan N, Budde M, Bybjerg-Grauholm J, Byerley W, Cairns M, Casas M, Cervantes P, Clarke T, Cruceanu C, Cuellar-Barboza A, Cunningham J, Curtis D, Czerski P, Dale A, Dalkner N, David F, Degenhardt F, Djurovic S, Dobbyn A, Douzenis A, Elvsåshagen T, Escott-Price V, Ferrier I, Fiorentino A, Foroud T, Forty L, Frank J, Frei O, Freimer N, Frisén L, Gade K, Garnham J, Gelernter J, Pedersen M, Gizer I, Gordon S, Gordon-Smith K, Greenwood T, Grove J, Guzman-Parra J, Ha K, Haraldsson M, Hautzinger M, Heilbronner U, Hellgren D, Herms S, Hoffmann P, Holmans P, Huckins L, Jamain S, Johnson J, Kalman J, Kamatani Y, Kennedy J, Kittel-Schneider S, Knowles J, Kogevinas M, Koromina M, Kranz T, Kranzler H, Kubo M, Kupka R, Kushner S, Lavebratt C, Lawrence J, Leber M, Lee H, Lee P, Levy S, Lewis C, Liao C, Lucae S, Lundberg M, MacIntyre D, Magnusson S, Maier W, Maihofer A, Malaspina D, Maratou E, Martinsson L, Mattheisen M, McGregor N, McGuffin P, McKay J, Medeiros H, Medland S, Millischer V, Montgomery G, Moran J, Morris D, Mühleisen T, O’Brien N, O’Donovan C, Loohuis L, Oruc L, Papiol S, Pardiñas A, Perry A, Pfennig A, Porichi E, Potash J, Quested D, Raj T, Rapaport M, DePaulo J, Regeer E, Rice J, Rivas F, Rivera M, Roth J, Roussos P, Ruderfer D, Sánchez-Mora C, Schulte E, Senner F, Sharp S, Shilling P, Sigurdsson E, Sirignano L, Slaney C, Smeland O, Smith D, Sobell J, Hansen C, Artigas M, Spijker A, Stein M, Strauss J, Świątkowska B, Terao C, Thorgeirsson T, Toma C, Tooney P, Tsermpini E, Vawter P, Vedder H, Walters J, Witt S, Xi S, Xu W, Yang J, Young A, Young H, Zandi P, Zhou H, Zillich L, Psychiatry H, Adolfsson R, Agartz I, Alda M, Alfredsson L, Babadjanova G, Backlund L, Baune B, Bellivier F, Bengesser S, Berrettini W, Blackwood D, Boehnke M, Børglum A, Breen G, Carr V, Catts S, Corvin A, Craddock N, Dannlowski U, Dikeos D, Esko T, Etain B, Ferentinos P, Frye M, Fullerton J, Gawlik M, Gershon E, Goes F, Green M, Grigoroiu-Serbanescu M, Hauser J, Henskens F, Hillert J, Hong K, Hougaard D, Hultman C, Hveem K, Iwata N, Jablensky A, Jones I, Jones L, Kahn R, Kelsoe J, Kirov G, Landén M, Leboyer M, Lewis C, Li Q, Lissowska J, Lochner C, Loughland C, Martin N, Mathews C, Mayoral F, McElroy S, McIntosh A, McMahon F, Melle I, Michie P, Milani L, Mitchell P, Morken G, Mors O, Mortensen P, Mowry B, Müller-Myhsok B, Myers R, Neale B, Nievergelt C, Nordentoft M, Nöthen M, O’Donovan M, Oedegaard K, Olsson T, Owen M, Paciga S, Pantelis C, Pato C, Pato M, Patrinos G, Perlis R, Posthuma D, Ramos-Quiroga J, Reif A, Reininghaus E, Ribasés M, Rietschel M, Ripke S, Rouleau G, Saito T, Schall U, Schalling M, Schofield P, Schulze T, Scott L, Scott R, Serretti A, Weickert C, Smoller J, Stefansson H, Stefansson K, Stordal E, Streit F, Sullivan P, Turecki G, Vaaler A, Vieta E, Vincent J, Waldman I, Weickert T, Werge T, Wray N, Zwart J, Biernacka J, Nurnberger J, Cichon S, Edenberg H, Stahl E, McQuillin A, Di Florio A, Ophoff R, Andreassen O, Adan R, Alfredsson L, Ando T, Andreassen O, Aschauer H, Baker J, Bencko V, Bergen A, Berrettini W, Birgegård A, Boden J, Boehm I, Boni C, Perica V, Brandt H, Breen G, Bryois J, Buehren K, Bulik C, Burghardt R, Carlberg L, Cassina M, Cichon S, Clementi M, Coleman J, Cone R, Courtet P, Crawford S, Crow S, Crowley J, Danner U, Davis O, de Zwaan M, Dedoussis G, Degortes D, 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Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors. Biological Psychiatry 2021, 91: 313-327. PMID: 34861974, PMCID: PMC8851871, DOI: 10.1016/j.biopsych.2021.05.029.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGenetic architecturePsychiatric disordersGenetic correlationsRisk factorsGenome-wide significanceDivergent genetic architecturesGWAS summary statisticsShared genetic architectureStrong genetic correlationIntergenic lociSuicide attemptsReproductive traitsKnown Risk FactorsRisk lociPoor general healthChromosome 7Association studiesRelated psychiatric disordersMillion Veteran ProgramSuicide attempt casesLow socioeconomic statusLociNonfatal suicide attemptsGenetic effectsGenomics of Gulf War Illness in U.S. Veterans Who Served during the 1990–1991 Persian Gulf War: Methods and Rationale for Veterans Affairs Cooperative Study #2006
Radhakrishnan K, Hauser ER, Polimanti R, Helmer DA, Provenzale D, McNeil RB, Maffucci A, Quaden R, Zhao H, Whitbourne SB, Harrington KM, Vahey J, Gelernter J, Levey DF, Huang GD, Gaziano JM, Concato J, Aslan M. Genomics of Gulf War Illness in U.S. Veterans Who Served during the 1990–1991 Persian Gulf War: Methods and Rationale for Veterans Affairs Cooperative Study #2006. Brain Sciences 2021, 11: 845. PMID: 34202057, PMCID: PMC8301942, DOI: 10.3390/brainsci11070845.Peer-Reviewed Original ResearchGulf War IllnessMillion Veteran ProgramVeterans Affairs Cooperative StudyChronic multi-symptom illnessNon-deployed veteransHealth care utilizationMulti-symptom illnessGenome-wide association studiesChart reviewPersian Gulf WarCare utilizationCase definitionMedical recordsDiseases codesHealth QuestionnaireInternational ClassificationGene-environment interactionsLarger sample sizeCase statusU.S. veteransMVP participantsClinical diagnosisCooperative StudyIllnessHealth conditions
2020
A large-scale genome-wide association study meta-analysis of cannabis use disorder
Johnson EC, Demontis D, Thorgeirsson TE, Walters RK, Polimanti R, Hatoum AS, Sanchez-Roige S, Paul SE, Wendt FR, Clarke TK, Lai D, Reginsson GW, Zhou H, He J, Baranger DAA, Gudbjartsson DF, Wedow R, Adkins DE, Adkins AE, Alexander J, Bacanu SA, Bigdeli TB, Boden J, Brown SA, Bucholz KK, Bybjerg-Grauholm J, Corley RP, Degenhardt L, Dick DM, Domingue BW, Fox L, Goate AM, Gordon SD, Hack LM, Hancock DB, Hartz SM, Hickie IB, Hougaard DM, Krauter K, Lind PA, McClintick JN, McQueen MB, Meyers JL, Montgomery GW, Mors O, Mortensen PB, Nordentoft M, Pearson JF, Peterson RE, Reynolds MD, Rice JP, Runarsdottir V, Saccone NL, Sherva R, Silberg JL, Tarter RE, Tyrfingsson T, Wall TL, Webb BT, Werge T, Wetherill L, Wright MJ, Zellers S, Adams MJ, Bierut LJ, Boardman JD, Copeland WE, Farrer LA, Foroud TM, Gillespie NA, Grucza RA, Harris KM, Heath AC, Hesselbrock V, Hewitt JK, Hopfer CJ, Horwood J, Iacono WG, Johnson EO, Kendler KS, Kennedy MA, Kranzler HR, Madden PAF, Maes HH, Maher BS, Martin NG, McGue M, McIntosh AM, Medland SE, Nelson EC, Porjesz B, Riley BP, Stallings MC, Vanyukov MM, Vrieze S, Workgroup P, Walters R, Polimanti R, Johnson E, McClintick J, Hatoum A, He J, Wendt F, Zhou H, Adams M, Adkins A, Aliev F, Bacanu S, Batzler A, Bertelsen S, Biernacka J, Bigdeli T, Chen L, Clarke T, Chou Y, Degenhardt F, Docherty A, Edwards A, Fontanillas P, Foo J, Fox L, Frank J, Giegling I, Gordon S, Hack L, Hartmann A, Hartz S, Heilmann-Heimbach S, Herms S, Hodgkinson C, Hoffman P, Hottenga J, Kennedy M, Alanne-Kinnunen M, Konte B, Lahti J, Lahti-Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher B, Mbarek H, McIntosh A, McQueen M, Meyers J, Milaneschi Y, Palviainen T, Pearson J, Peterson R, Ripatti S, Ryu E, Saccone N, Salvatore J, Sanchez-Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang J, Webb B, Wedow R, Wetherill L, Wills A, Boardman J, Chen D, Choi D, Copeland W, Culverhouse R, Dahmen N, Degenhardt L, Domingue B, Elson S, Frye M, Gäbel W, Hayward C, Ising M, Keyes M, Kiefer F, Kramer J, Kuperman S, Lucae S, Lynskey M, Maier W, Mann K, Männistö S, Müller-Myhsok B, Murray A, Nurnberger J, Palotie A, Preuss U, Räikkönen K, Reynolds M, Ridinger M, Scherbaum N, Schuckit M, Soyka M, Treutlein J, Witt S, Wodarz N, Zill P, Adkins D, Boden J, Boomsma D, Bierut L, Brown S, Bucholz K, Cichon S, Costello E, de Wit H, Diazgranados N, Dick D, Eriksson J, Farrer L, Foroud T, Gillespie N, Goate A, Goldman D, Grucza R, Hancock D, Harris K, Heath A, Hesselbrock V, Hewitt J, Hopfer C, Horwood J, Iacono W, Johnson E, Kaprio J, Karpyak V, Kendler K, Kranzler H, Krauter K, Lichtenstein P, Lind P, McGue M, MacKillop J, Madden P, Maes H, Magnusson P, Martin N, Medland S, Montgomery G, Nelson E, Nöthen M, Palmer A, Pederson N, Penninx B, Porjesz B, Rice J, Rietschel M, Riley B, Rose R, Rujescu D, Shen P, Silberg J, Stallings M, Tarter R, Vanyukov M, Vrieze S, Wall T, Whitfield J, Zhao H, Neale B, Gelernter J, Edenberg H, Agrawal A, Davis L, Bogdan R, Gelernter J, Edenberg H, Stefansson K, Børglum A, Agrawal A. A large-scale genome-wide association study meta-analysis of cannabis use disorder. The Lancet Psychiatry 2020, 7: 1032-1045. PMID: 33096046, PMCID: PMC7674631, DOI: 10.1016/s2215-0366(20)30339-4.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesGenome-wide significant lociLarge-scale genome-wide association studiesGenetic correlationsChromosome 7 locusTraits of interestLarge genome-wide association studiesLinkage disequilibrium score regressionChromosome 8 locusDifferent genetic underpinningsDifferent genetic correlationsWellcome Trust Case Control ConsortiumDisequilibrium score regressionNovel genetic variantsStrong genetic componentSignificant lociGenetic lociGenetic underpinningsGenetic componentLociScore regressionGenetic variantsGenetic overlapIntegrative sequencingGenome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals
Xu K, Li B, McGinnis KA, Vickers-Smith R, Dao C, Sun N, Kember RL, Zhou H, Becker WC, Gelernter J, Kranzler HR, Zhao H, Justice AC. Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals. Nature Communications 2020, 11: 5302. PMID: 33082346, PMCID: PMC7598939, DOI: 10.1038/s41467-020-18489-3.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesLarge genome-wide association studiesMillion Veteran ProgramAssociation studiesExpression quantitative trait lociQuantitative trait lociChromatin interactionsComplex traitsFunctional annotationTrait lociSequencing ConsortiumDozen genesSignificant lociSmoking phenotypesLociMultiple populationsNew insightsPhenotypeVeteran ProgramGenetic vulnerabilityGenesTraitsAnnotationEuropean AmericansConsortiumGenome-Wide Association Studies of Schizophrenia and Bipolar Disorder in a Diverse Cohort of US Veterans
Bigdeli T, Fanous A, Li Y, Rajeevan N, Sayward F, Investigators G, Zhao H, Brophy M, Pyarajan S, O'Leary T, Gleason T, Przygodszki R, Muralidhar S, Gaziano J, Program M, Concato J, Siever L, Aslan M, Harvey P. Genome-Wide Association Studies of Schizophrenia and Bipolar Disorder in a Diverse Cohort of US Veterans. Biological Psychiatry 2020, 87: s178. DOI: 10.1016/j.biopsych.2020.02.468.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesStatistical Methods in Genome-Wide Association Studies
Sun N, Zhao H. Statistical Methods in Genome-Wide Association Studies. Annual Review Of Biomedical Data Science 2020, 3: 1-24. DOI: 10.1146/annurev-biodatasci-030320-041026.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesTraits of interestGenetic architectureIdentification of variantsGWAS dataStatistical methodologyStatistical challengesGenetic risk prediction modelsGenetic markersStatistical methodsHuman diseasesPhenotype informationGenetic variantsTraitsGenotype informationScientific goalsRecent progressGenesVariantsTens of thousandsHundreds of thousandsPrediction modelPathwayThousands
2019
International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci
Nievergelt CM, Maihofer AX, Klengel T, Atkinson EG, Chen CY, Choi KW, Coleman JRI, Dalvie S, Duncan LE, Gelernter J, Levey DF, Logue MW, Polimanti R, Provost AC, Ratanatharathorn A, Stein MB, Torres K, Aiello AE, Almli LM, Amstadter AB, Andersen SB, Andreassen OA, Arbisi PA, Ashley-Koch AE, Austin SB, Avdibegovic E, Babić D, Bækvad-Hansen M, Baker DG, Beckham JC, Bierut LJ, Bisson JI, Boks MP, Bolger EA, Børglum AD, Bradley B, Brashear M, Breen G, Bryant RA, Bustamante AC, Bybjerg-Grauholm J, Calabrese JR, Caldas- de- Almeida J, Dale AM, Daly MJ, Daskalakis NP, Deckert J, Delahanty DL, Dennis MF, Disner SG, Domschke K, Dzubur-Kulenovic A, Erbes CR, Evans A, Farrer LA, Feeny NC, Flory JD, Forbes D, Franz CE, Galea S, Garrett ME, Gelaye B, Geuze E, Gillespie C, Uka AG, Gordon SD, Guffanti G, Hammamieh R, Harnal S, Hauser MA, Heath AC, Hemmings SMJ, Hougaard DM, Jakovljevic M, Jett M, Johnson EO, Jones I, Jovanovic T, Qin XJ, Junglen AG, Karstoft KI, Kaufman ML, Kessler RC, Khan A, Kimbrel NA, King AP, Koen N, Kranzler HR, Kremen WS, Lawford BR, Lebois LAM, Lewis CE, Linnstaedt SD, Lori A, Lugonja B, Luykx JJ, Lyons MJ, Maples-Keller J, Marmar C, Martin AR, Martin NG, Maurer D, Mavissakalian MR, McFarlane A, McGlinchey RE, McLaughlin KA, McLean SA, McLeay S, Mehta D, Milberg WP, Miller MW, Morey RA, Morris CP, Mors O, Mortensen PB, Neale BM, Nelson EC, Nordentoft M, Norman SB, O’Donnell M, Orcutt HK, Panizzon MS, Peters ES, Peterson AL, Peverill M, Pietrzak RH, Polusny MA, Rice JP, Ripke S, Risbrough VB, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero K, Rung A, Rutten BPF, Saccone NL, Sanchez SE, Schijven D, Seedat S, Seligowski AV, Seng JS, Sheerin CM, Silove D, Smith AK, Smoller JW, Sponheim SR, Stein DJ, Stevens JS, Sumner JA, Teicher MH, Thompson WK, Trapido E, Uddin M, Ursano RJ, van den Heuvel LL, Van Hooff M, Vermetten E, Vinkers CH, Voisey J, Wang Y, Wang Z, Werge T, Williams MA, Williamson DE, Winternitz S, Wolf C, Wolf EJ, Wolff JD, Yehuda R, Young RM, Young KA, Zhao H, Zoellner LA, Liberzon I, Ressler KJ, Haas M, Koenen KC. International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci. Nature Communications 2019, 10: 4558. PMID: 31594949, PMCID: PMC6783435, DOI: 10.1038/s41467-019-12576-w.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesDisease genesAssociation studiesGenome-wide significant lociAfrican-ancestry analysesNon-coding RNAsGenetic risk lociParkinson's disease genesEuropean ancestry populationsNovel genesSignificant lociGenetic variationSpecific lociRisk lociAdditional lociLociAncestry populationsCommon variantsHeritability estimatesGenesGWASRNABiologySNPsPARK2