2020
Supervariants identification for breast cancer
Hu J, Li T, Wang S, Zhang H. Supervariants identification for breast cancer. Genetic Epidemiology 2020, 44: 934-947. PMID: 32808324, PMCID: PMC7924970, DOI: 10.1002/gepi.22350.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesCombination of allelesRare variantsNovel lociChromosome 2UK Biobank databaseChromosome 1Multiple lociAssociation studiesLociComplex diseasesGenesBiobank databaseAssociation methodGenomeVariantsTens of thousandsAllelesPolymorphismNovel resultsSignalsClassic conceptIdentification
2019
Common genetic variants have associations with human cortical brain regions and risk of schizophrenia
Bi X, Feng L, Wang S, Lin Z, Li T, Zhao B, Zhu H, Zhang H. Common genetic variants have associations with human cortical brain regions and risk of schizophrenia. Genetic Epidemiology 2019, 43: 548-558. PMID: 30941828, PMCID: PMC6559856, DOI: 10.1002/gepi.22203.Peer-Reviewed Original ResearchConceptsCortical regionsCortical brain regionsRisk of schizophreniaPrefrontal cortical regionsSymptom durationProdromal symptomsMental disordersSignificant associationBrain regionsCommon genetic variantsPhiladelphia Neurodevelopmental CohortPediatric imagingSchizophreniaNeurodevelopmental CohortCommon variantsHuman brainGenetic variantsHeritable mental disorderMagnetic resonanceAssociationWide association studyAssociation studiesGenetic effectsCohortSymptomsAn accurate and powerful method for copy number variation detection
Xiao F, Luo X, Hao N, Niu YS, Xiao X, Cai G, Amos CI, Zhang H. An accurate and powerful method for copy number variation detection. Bioinformatics 2019, 35: 2891-2898. PMID: 30649252, PMCID: PMC6735918, DOI: 10.1093/bioinformatics/bty1041.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAllelesData Interpretation, StatisticalDNA Copy Number VariationsGenome-Wide Association StudyPolymorphism, Single NucleotideSensitivity and SpecificitySoftwareConceptsHigh computational efficiency
2018
A univariate perspective of multivariate genome‐wide association analysis
Guo X, Zhu J, Fan Q, He M, Wang X, Zhang H. A univariate perspective of multivariate genome‐wide association analysis. Genetic Epidemiology 2018, 42: 470-479. PMID: 29781551, DOI: 10.1002/gepi.22128.Peer-Reviewed Original ResearchMeSH KeywordsComputer SimulationGenome-Wide Association StudyHumansModels, GeneticMultivariate AnalysisPhenotypeConceptsGenome-wide association studiesMultivariate genome-wide association studyMultivariate genome-wide association analysisGenome-wide association analysisMultiple correlated phenotypesGenetic signalsAssociation studiesCorrelated phenotypesAssociation analysisMultiple phenotypesSingle phenotypePhenotypeWhole genome association study of brain‐wide imaging phenotypes: A study of the ping cohort
Wen C, Mehta CM, Tan H, Zhang H. Whole genome association study of brain‐wide imaging phenotypes: A study of the ping cohort. Genetic Epidemiology 2018, 42: 265-275. PMID: 29411414, PMCID: PMC5851842, DOI: 10.1002/gepi.22111.Peer-Reviewed Original ResearchMeSH KeywordsBrainCognitionCohort StudiesDiffusion Tensor ImagingGenetic MarkersGenome-Wide Association StudyHumansMultivariate AnalysisPhenotypePolymorphism, Single NucleotideConceptsGenetic markersGenome-wide association study datasetWhole-genome association studiesComplex genetic basisGenome association studiesBrain-wide imaging phenotypesMultivariate phenotypesGenetic basisAssociation studiesGenetic studiesNeuropsychological disordersClinical diagnostic criteriaCovariance testBiological basisPhenotypeDiagnostic criteriaNeuroimaging biomarkersBrain functionBrain structuresPediatric imagingGWASImaging phenotypesDiffusion tensor
2017
Genome‐wide mediation analysis of psychiatric and cognitive traits through imaging phenotypes
Bi X, Yang L, Li T, Wang B, Zhu H, Zhang H. Genome‐wide mediation analysis of psychiatric and cognitive traits through imaging phenotypes. Human Brain Mapping 2017, 38: 4088-4097. PMID: 28544218, PMCID: PMC5568842, DOI: 10.1002/hbm.23650.Peer-Reviewed Original Research
2016
A method for integrating neuroimaging into genetic models of learning performance
Mehta CM, Gruen JR, Zhang H. A method for integrating neuroimaging into genetic models of learning performance. Genetic Epidemiology 2016, 41: 4-17. PMID: 27859682, PMCID: PMC5154929, DOI: 10.1002/gepi.22025.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersChromosomes, Human, Pair 15FemaleGenome-Wide Association StudyHumansLearningLearning DisabilitiesMaleModels, GeneticNeuroimagingPhenotypePolymorphism, Single NucleotideRisk FactorsConceptsGenome-wide association studies
2015
Genes and environment in neonatal intraventricular hemorrhage
Ment LR, Ådén U, Bauer CR, Bada HS, Carlo WA, Kaiser JR, Lin A, Cotten CM, Murray J, Page G, Hallman M, Lifton RP, Zhang H, Network O. Genes and environment in neonatal intraventricular hemorrhage. Seminars In Perinatology 2015, 39: 592-603. PMID: 26516117, PMCID: PMC4668116, DOI: 10.1053/j.semperi.2015.09.006.Peer-Reviewed Original ResearchConceptsIntraventricular hemorrhagePreterm neonatesLow birth weight preterm neonatesSevere intraventricular hemorrhageWeight preterm neonatesNeonatal intraventricular hemorrhageCerebral blood flowBlood flowVascular pathwaysCandidate gene studiesGenetic factorsComplex disorderHemorrhageNeonatesAngiogenesisGene studiesGenome-wide association studiesAssociation Tests of Multiple Phenotypes: ATeMP
Guo X, Li Y, Ding X, He M, Wang X, Zhang H. Association Tests of Multiple Phenotypes: ATeMP. PLOS ONE 2015, 10: e0140348. PMID: 26479245, PMCID: PMC4610695, DOI: 10.1371/journal.pone.0140348.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyComputer SimulationGenome-Wide Association StudyGenotypeHumansModels, TheoreticalPhenotypeConceptsExtensive simulation studyStatistical literatureJoint association analysisMultiPhenSimulation studyEquivalence relationshipProportional odds modelReal case studyMeasurement errorMultivariate methodsOdds modelMultiple intermediate phenotypesJoint analysisMultiple phenotypesExplanatory variablesEquivalenceEstimationDistributionPhenotypic distributionATempSolutionErrorGenetic susceptibility to diffuse large B‐cell lymphoma in a pooled study of three Eastern Asian populations
Bassig BA, Cerhan JR, Au WY, Kim HN, Sangrajrang S, Hu W, Tse J, Berndt S, Zheng T, Zhang H, Pornsopone P, Lee JJ, Kim HJ, Skibola CF, Vijai J, Burdette L, Yeager M, Brennan P, Shin MH, Liang R, Chanock S, Lan Q, Rothman N. Genetic susceptibility to diffuse large B‐cell lymphoma in a pooled study of three Eastern Asian populations. European Journal Of Haematology 2015, 95: 442-448. PMID: 25611436, DOI: 10.1111/ejh.12513.Peer-Reviewed Original ResearchConceptsLarge B-cell lymphomaNon-Hodgkin lymphomaB-cell lymphomaDLBCL riskSimilar genetic risk factorsCommon NHL subtypesEuropean ancestryRisk of DLBCLGenetic risk factorsGenome-wide association studiesPooled studiesAggressive subtypeRisk factorsNHL subtypesStudy populationSignificant associationDLBCL casesGenetic susceptibilityGenome-wide significanceLymphomaAsian populationsPooled seriesDLBCLGenetic factorsEastern Asian populationsA Genome‐Wide Association Study of Early Spontaneous Preterm Delivery
Zhang H, Baldwin DA, Bukowski RK, Parry S, Xu Y, Song C, Andrews WW, Saade GR, Esplin MS, Sadovsky Y, Reddy UM, Ilekis J, Varner M, Biggio JR, Research F. A Genome‐Wide Association Study of Early Spontaneous Preterm Delivery. Genetic Epidemiology 2015, 39: 217-226. PMID: 25599974, PMCID: PMC4366311, DOI: 10.1002/gepi.21887.Peer-Reviewed Original ResearchConceptsSpontaneous preterm birthMaternal single nucleotide polymorphismsSPTB casesPreterm birthValidation cohortSingle nucleotide polymorphismsEarly spontaneous preterm deliveryP-valueTerm controlsTerm delivery controlsSpontaneous preterm deliveryMother-infant pairsCase-control studyIndependent validation cohortRace/ethnicityPreterm deliveryInfant morbidityMaternal ageControl groupMultiple testing adjustmentMultiple comparisonsCohortBirthNucleotide polymorphismsGenome-wide association studies
2014
TARV: Tree‐based Analysis of Rare Variants Identifying Risk Modifying Variants in CTNNA2 and CNTNAP2 for Alcohol Addiction
Song C, Zhang H. TARV: Tree‐based Analysis of Rare Variants Identifying Risk Modifying Variants in CTNNA2 and CNTNAP2 for Alcohol Addiction. Genetic Epidemiology 2014, 38: 552-559. PMID: 25041903, PMCID: PMC4154634, DOI: 10.1002/gepi.21843.Peer-Reviewed Original ResearchMeSH KeywordsAlcoholismAlpha CateninDatabases, GeneticFemaleGenetic VariationGenome-Wide Association StudyHumansMembrane ProteinsModels, GeneticNerve Tissue ProteinsOdds RatioRisk FactorsConceptsGenome-wide association studiesSequence kernel association testRare variant dataTree-based analysisRare variantsNext-generation sequencing technologiesVariant dataGeneration sequencing technologyKernel association testGene-gene interactionsSequencing technologiesMultiple genesAssociation studiesDisease modelsRisk genesCTNNA2Genetic variantsSAGE dataComplex disease modelsGenesStudy of AddictionComplex diseasesCommon variantsSpecific variantsRisk of alcoholism
2013
Sex chromosome-wide association analysis suggested male-specific risk genes for alcohol dependence
Zuo L, Wang K, Zhang X, Pan X, Wang G, Krystal JH, Zhang H, Luo X. Sex chromosome-wide association analysis suggested male-specific risk genes for alcohol dependence. Psychiatric Genetics 2013, 23: 233-238. PMID: 23907288, PMCID: PMC3941913, DOI: 10.1097/ypg.0b013e328364b8c7.Peer-Reviewed Original ResearchRare SERINC2 variants are specific for alcohol dependence in individuals of European descent
Zuo L, Wang KS, Zhang XY, Li CS, Zhang F, Wang X, Chen W, Gao G, Zhang H, Krystal JH, Luo X. Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent. Pharmacogenetics And Genomics 2013, 23: 395-402. PMID: 23778322, PMCID: PMC4287355, DOI: 10.1097/fpc.0b013e328362f9f2.Peer-Reviewed Original ResearchNKAIN1–SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent
Zuo L, Wang K, Zhang XY, Krystal JH, Li CS, Zhang F, Zhang H, Luo X. NKAIN1–SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent. Drug And Alcohol Dependence 2013, 129: 254-264. PMID: 23455491, PMCID: PMC3628730, DOI: 10.1016/j.drugalcdep.2013.02.006.Peer-Reviewed Original ResearchMeSH KeywordsAdultAlcoholismCarrier ProteinsCase-Control StudiesFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMaleMembrane ProteinsMiddle AgedWhite PeopleConceptsGenome-wide association studiesExpression quantitative loci (eQTL) analysisGene regionMetabolic pathwaysQuantitative loci analysisSNP-expression associationsCis-acting regulatory effectsDiscovery sampleSNP-disease associationsNumerous genesReplication sampleLocus analysisAssociation studiesAssociation analysisRisk SNPsTranscript expressionSNPsRegulatory effectsGenesPathwayEuropean descentExpressionNCK2 Is Significantly Associated with Opiates Addiction in African‐Origin Men
Liu Z, Guo X, Jiang Y, Zhang H. NCK2 Is Significantly Associated with Opiates Addiction in African‐Origin Men. The Scientific World JOURNAL 2013, 2013: 748979. PMID: 23533358, PMCID: PMC3603435, DOI: 10.1155/2013/748979.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsNCK2 geneGenome-wide significant associationGenome-wide significant levelWide association studyGene-based methodsNumerous genetic variantsGWAS discoveryChromosome 2Association studiesNck2Genetic variantsGenesNucleotide polymorphismsComplex diseasesFirst evidenceGenetic disordersDiscoverySignificant levelsPolymorphismVariantsSubstantial effort
2012
Large Scale Association Analysis for Drug Addiction: Results from SNP to Gene
Guo X, Liu Z, Wang X, Zhang H. Large Scale Association Analysis for Drug Addiction: Results from SNP to Gene. The Scientific World JOURNAL 2012, 2012: 939584. PMID: 23365539, PMCID: PMC3543790, DOI: 10.1100/2012/939584.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsChromosome MappingGenetic Predisposition to DiseaseGenome, HumanGenome-Wide Association StudyHumansModels, GeneticPolymorphism, Single NucleotideSubstance-Related DisordersConceptsGenome-wide association studiesAssociation studiesAssociation analysisGene-based association analysisLarge-scale association analysisSingle nucleotide polymorphism dataWide association studyComplex diseasesGene-based analysisGene-based methodsNucleotide polymorphism dataGenetic association studiesPolymorphism dataGene findingGenetic variantsIndividual SNPsStudy of AddictionSNPsGenetic etiologyGenesComprehensive analysisGeneticsVariantsGenome‐Wide Significant Association Signals in IPO11‐HTR1A Region Specific for Alcohol and Nicotine Codependence
Zuo L, Zhang X, Wang F, Li C, Lu L, Ye L, Zhang H, Krystal JH, Deng H, Luo X. Genome‐Wide Significant Association Signals in IPO11‐HTR1A Region Specific for Alcohol and Nicotine Codependence. Alcohol Clinical And Experimental Research 2012, 37: 730-739. PMID: 23216389, PMCID: PMC3610804, DOI: 10.1111/acer.12032.Peer-Reviewed Original ResearchMeSH KeywordsAdultAlcoholismBeta KaryopherinsBlack or African AmericanCase-Control StudiesChromosomes, Human, Pair 5FemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansMaleMiddle AgedPolymorphism, Single NucleotideQuantitative Trait LociReceptor, Serotonin, 5-HT1ATobacco Use DisorderWhite PeopleConceptsGenome-wide significance levelSingle nucleotide polymorphismsReplication cohortDiscovery cohortAlcohol dependenceExpression quantitative loci (eQTL) analysisPeripheral blood mononuclear cell samplesNeuropsychiatric disordersWide significant association signalsMononuclear cell samplesGenome-wide association studiesQuantitative loci analysisGene-disease association analysisCis-eQTL analysisTop single nucleotide polymorphismsCis-acting regulatory effectsSignificant association signalsBrain tissue samplesAmerican controlsEuropean American controlsRisk single nucleotide polymorphismsAfrican-American controlsSevere subtypeGenomic regionsAfrican American casesGenetic Association Test for Multiple Traits at Gene Level
Guo X, Liu Z, Wang X, Zhang H. Genetic Association Test for Multiple Traits at Gene Level. Genetic Epidemiology 2012, 37: 122-129. PMID: 23032486, PMCID: PMC3524409, DOI: 10.1002/gepi.21688.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesMultiple traitsGene levelSingle nucleotide polymorphismsGenetic association testsCommon genesAssociation studiesAssociation TestNucleotide polymorphismsTraitsStudy of AddictionComplex diseasesBiological mechanismsDisease of interestAssociation informationGenesGeneticsSuch studiesStrong evidencePolymorphismPrevious findingsLevelsGenome‐wide search for replicable risk gene regions in alcohol and nicotine co‐dependence
Zuo L, Zhang F, Zhang H, Zhang X, Wang F, Li C, Lu L, Hong J, Lu L, Krystal J, Deng H, Luo X. Genome‐wide search for replicable risk gene regions in alcohol and nicotine co‐dependence. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2012, 159B: 437-444. PMID: 22488850, PMCID: PMC3405545, DOI: 10.1002/ajmg.b.32047.Peer-Reviewed Original ResearchConceptsChromosome 3Genome-wide false discovery rateGene regionFalse discovery rateGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisRisk SNPsTranscript expressionGenome-wide association strategyGenome-wide searchCombined P valueSNP-disease associationsAssociation peakGenomic regionsEQTL analysisEuropean American casesCausal lociLocus analysisGene expressionAssociation analysisGenesSNPsRegulatory effectsDiscovery rate