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
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 studiesGenetic 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 ResearchMeSH KeywordsAdultAgedAsia, EasternFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLymphoma, Large B-Cell, DiffuseMaleMiddle AgedPolymorphism, Single NucleotideVesicular Transport ProteinsConceptsLarge 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 populations
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 ResearchGene–environment interactions in severe intraventricular hemorrhage of preterm neonates
Ment LR, Ådén U, Lin A, Kwon SH, Choi M, Hallman M, Lifton RP, Zhang H, Bauer CR. Gene–environment interactions in severe intraventricular hemorrhage of preterm neonates. Pediatric Research 2013, 75: 241-250. PMID: 24192699, PMCID: PMC3946468, DOI: 10.1038/pr.2013.195.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApgar ScoreBlood CoagulationCerebral VentriclesCerebrovascular CirculationCollagen Type IVFactor VGene-Environment InteractionGenetic Predisposition to DiseaseGenetic VariationGestational AgeHumansHypoxia, BrainInfantInfant, PrematureInflammation MediatorsIntracranial HemorrhagesMethylenetetrahydrofolate Reductase (NADPH2)PhenotypePremature BirthPrognosisRisk FactorsConceptsIntraventricular hemorrhageCerebral injuryPreterm neonatesFactor V Leiden geneRisk of IVHEnvironmental triggersSevere intraventricular hemorrhageCerebral blood flowMethylenetetrahydrofolate reductase (MTHFR) variantsUnknown environmental triggersPresence of mutationsPeriventricular infarctionApgar scorePerinatal hypoxiaPreclinical dataFetal environmentGerminal matrixCerebral vasculatureBlood flowT polymorphismGene-environment interactionsMTHFR 677CHemorrhageNeonatesVascular pathwaysCommon PTP4A1‐PHF3‐EYS variants are specific for alcohol dependence
Zuo L, Wang K, Wang G, Pan X, Zhang X, Zhang H, Luo X. Common PTP4A1‐PHF3‐EYS variants are specific for alcohol dependence. American Journal On Addictions 2013, 23: 411-414. PMID: 24961364, PMCID: PMC4111256, DOI: 10.1111/j.1521-0391.2013.12115.x.Peer-Reviewed Original ResearchCandidate Gene Analysis: Severe Intraventricular Hemorrhage in Inborn Preterm Neonates
Ådén U, Lin A, Carlo W, Leviton A, Murray JC, Hallman M, Lifton RP, Zhang H, Ment LR, Group G. Candidate Gene Analysis: Severe Intraventricular Hemorrhage in Inborn Preterm Neonates. The Journal Of Pediatrics 2013, 163: 1503-1506.e1. PMID: 23896193, PMCID: PMC3812267, DOI: 10.1016/j.jpeds.2013.06.025.Peer-Reviewed Original ResearchMeSH KeywordsBirth WeightCase-Control StudiesCerebral HemorrhageFemaleGenetic Predisposition to DiseaseGenotypeHumansInfant, NewbornInfant, PrematureMaleMethylenetetrahydrofolate Reductase (NADPH2)SteroidsNKAIN1–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 casesGenome‐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
2011
A Novel, Functional and Replicable Risk Gene Region for Alcohol Dependence Identified by Genome-Wide Association Study
Zuo L, Zhang CK, Wang F, Li CS, Zhao H, Lu L, Zhang XY, Lu L, Zhang H, Zhang F, Krystal JH, Luo X. A Novel, Functional and Replicable Risk Gene Region for Alcohol Dependence Identified by Genome-Wide Association Study. PLOS ONE 2011, 6: e26726. PMID: 22096494, PMCID: PMC3210123, DOI: 10.1371/journal.pone.0026726.Peer-Reviewed Original ResearchStatistical Inference in Mixed Models and Analysis of Twin and Family Data
Wang X, Guo X, He M, Zhang H. Statistical Inference in Mixed Models and Analysis of Twin and Family Data. Biometrics 2011, 67: 987-995. PMID: 21306354, PMCID: PMC3129472, DOI: 10.1111/j.1541-0420.2010.01548.x.Peer-Reviewed Original ResearchMeSH KeywordsBiometryData Interpretation, StatisticalFamily HealthGenetic Diseases, InbornGenetic Predisposition to DiseaseHumansInheritance PatternsModels, StatisticalTwin Studies as TopicConceptsStandard regularity conditionsStatistical inferenceAsymptotic distributionRegularity conditionsSufficient conditionsCholesky decompositionLikelihood ratio testComputational softwareLinear modelAdvanced theoryFamily data analysisImportant exampleRatio testFamily dataKey ideaPrecise estimatesMixed-effects modelsTheoryMixed effects modelsData setsIdentifiabilityModelEstimatesMixed modelsGeneral linear modelThe Nuclear Transcription Factor PKNOX2 Is a Candidate Gene for Substance Dependence in European-Origin Women
Chen X, Cho K, Singer BH, Zhang H. The Nuclear Transcription Factor PKNOX2 Is a Candidate Gene for Substance Dependence in European-Origin Women. PLOS ONE 2011, 6: e16002. PMID: 21298047, PMCID: PMC3029286, DOI: 10.1371/journal.pone.0016002.Peer-Reviewed Original ResearchPropensity score‐based nonparametric test revealing genetic variants underlying bipolar disorder
Jiang Y, Zhang H. Propensity score‐based nonparametric test revealing genetic variants underlying bipolar disorder. Genetic Epidemiology 2011, 35: 125-132. PMID: 21254220, PMCID: PMC3077545, DOI: 10.1002/gepi.20558.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsGenetic variantsWellcome Trust Case Control ConsortiumRPGRIP1L geneGenetic studiesAssociation analysisHaplotype blocksChromosome 16Nucleotide polymorphismsComplex diseasesGenesComplex disorderStrong signalUnreported regionsVariantsImportant roleStrong evidencePolymorphismBipolar disorderRegionRegression and data mining methods for analyses of multiple rare variants in the Genetic Analysis Workshop 17 mini‐exome data
Bailey‐Wilson J, Brennan JS, Bull SB, Culverhouse R, Kim Y, Jiang Y, Jung J, Li Q, Lamina C, Liu Y, Mägi R, Niu YS, Simpson CL, Wang L, Yilmaz YE, Zhang H, Zhang Z. Regression and data mining methods for analyses of multiple rare variants in the Genetic Analysis Workshop 17 mini‐exome data. Genetic Epidemiology 2011, 35: s92-s100. PMID: 22128066, PMCID: PMC3360949, DOI: 10.1002/gepi.20657.Peer-Reviewed Original ResearchConceptsData mining methodsUse of machineMachine learning methodsMining methodsLearning methodsNovel methodGenetic Analysis Workshop 17 mini-exome dataGenetic Analysis Workshop 17Extreme locus heterogeneityDNA sequence dataLocus-specific heritabilityMultiple rare variantsPopulation-specific analysesRare variantsIndividual rare variantsRare genetic variantsRare causal variantsSubset of predictorsLarge numberMultiple variantsComplex traitsMachineSequence dataCausal variantsCausal mutations
2010
The Impact of Environmental and Genetic Factors on Neonatal Late-Onset Sepsis
Bizzarro MJ, Jiang Y, Hussain N, Gruen JR, Bhandari V, Zhang H. The Impact of Environmental and Genetic Factors on Neonatal Late-Onset Sepsis. The Journal Of Pediatrics 2010, 158: 234-238.e1. PMID: 20850766, PMCID: PMC3008342, DOI: 10.1016/j.jpeds.2010.07.060.Peer-Reviewed Original ResearchMeSH KeywordsAge of OnsetBirth WeightBlood-Borne PathogensCohort StudiesConfidence IntervalsCross InfectionEnvironmental ExposureFemaleGenetic Predisposition to DiseaseHospital MortalityHumansInfant, NewbornIntensive Care Units, NeonatalLogistic ModelsMalePrognosisRetrospective StudiesSepsisSurvival RateTime FactorsTwinsTwins, DizygoticTwins, MonozygoticConceptsLate-onset sepsisNewborn intensive care unitIntensive care unitCare unitBirth weightIntensive care unit populationNeonatal late-onset sepsisRetrospective cohort analysisTotal parenteral nutritionRespiratory distress syndromeGenetic factorsLogistic regression analysisMixed-effects logistic regressionNongenetic factorsMixed-effects logistic regression analysisSignificant genetic susceptibilityDistress syndromeParenteral nutritionGestational ageCohort analysisSepsisUnit populationConcordance rateGenetic susceptibilityLogistic regression
2009
The Genetic Susceptibility to Respiratory Distress Syndrome
Levit O, Jiang Y, Bizzarro MJ, Hussain N, Buhimschi CS, Gruen JR, Zhang H, Bhandari V. The Genetic Susceptibility to Respiratory Distress Syndrome. Pediatric Research 2009, 66: 693-697. PMID: 19687775, PMCID: PMC2796284, DOI: 10.1203/pdr.0b013e3181bbce86.Peer-Reviewed Original ResearchAnalysis of Twin Data Using SAS
Feng R, Zhou G, Zhang M, Zhang H. Analysis of Twin Data Using SAS. Biometrics 2009, 65: 584-589. PMID: 18647295, PMCID: PMC2700843, DOI: 10.1111/j.1541-0420.2008.01098.x.Peer-Reviewed Original Research