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
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 ResearchConceptsGenome-wide association studiesMultivariate genome-wide association studyMultivariate genome-wide association analysisGenome-wide association analysisMultiple correlated phenotypesGenetic signalsAssociation studiesCorrelated phenotypesAssociation analysisMultiple phenotypesSingle phenotypePhenotype
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 ResearchConceptsGenome-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 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 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 ResearchConceptsGenome-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 alcoholismIdentifying Genetic Variants for Addiction via Propensity Score Adjusted Generalized Kendall’s Tau
Jiang Y, Li N, Zhang H. Identifying Genetic Variants for Addiction via Propensity Score Adjusted Generalized Kendall’s Tau. Journal Of The American Statistical Association 2014, 109: 905-930. PMID: 25382885, PMCID: PMC4219655, DOI: 10.1080/01621459.2014.901223.Peer-Reviewed Original ResearchGenome-wide association studiesGenetic variantsU-statisticsU-statistic methodNovel genetic variantsGWAS analysisPhenotype-genotype associationsEnvironmental factorsReplicable genetic variantsAssociation studiesSemiparametric methodAssociation analysisStatistical methodsStudy of AddictionParametric methodsGene-environment interactionsParametric estimatesInverse probability weightingSimulation resultsProbability weightingNull hypothesisVariantsKendall's tauGeneticsTraits
2013
NKAIN1–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 ResearchConceptsGenome-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 descentExpression
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 ResearchConceptsGenome-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 findingsLevels
2009
Memory management in genome-wide association studies
Chen X, Zhang M, Wang M, Zhu W, Cho K, Zhang H. Memory management in genome-wide association studies. BMC Proceedings 2009, 3: s54. PMID: 20018047, PMCID: PMC2795954, DOI: 10.1186/1753-6561-3-s7-s54.Peer-Reviewed Original ResearchGenome-wide association studiesAssociation studiesIdentification of genesNorth American Rheumatoid Arthritis Consortium studyGenome-wide associationMemory management toolsMemory management approachCentral processing unitLimited computer memorySignificant computational challengesMemory managementMemory usageProcessing unitMost usersComputational challengesPowerful toolComputer memoryGenesCommon diseaseManagement toolGenotypesA genome-wide association analysis of Framingham Heart Study longitudinal data using multivariate adaptive splines
Zhu W, Cho K, Chen X, Zhang M, Wang M, Zhang H. A genome-wide association analysis of Framingham Heart Study longitudinal data using multivariate adaptive splines. BMC Proceedings 2009, 3: s119. PMID: 20017984, PMCID: PMC2795891, DOI: 10.1186/1753-6561-3-s7-s119.Peer-Reviewed Original ResearchTraits of interestGenome-wide analysisGenome-wide association studiesWide association analysisGenome-wide dataMultivariate adaptive splinesAssociation studiesAssociation analysisGene-environment interactionsTraitsLongitudinal phenotypesGene-environment interaction effectsMasalFramingham Heart StudyPermutation testGenesPhenotypeMachine learning in genome‐wide association studies
Szymczak S, Biernacka JM, Cordell HJ, González‐Recio O, König IR, Zhang H, Sun YV. Machine learning in genome‐wide association studies. Genetic Epidemiology 2009, 33: s51-s57. PMID: 19924717, DOI: 10.1002/gepi.20473.Peer-Reviewed Original ResearchConceptsGenome-wide SNP dataSingle nucleotide polymorphismsSNP dataAssociation studiesGenome-wide association studiesOverall genetic architectureMachine learning approachesGenetic Analysis Workshop 16Wide association studyComplex human diseasesMain genetic effectsGenetic architectureLearning approachGenetic risk variantsEnsemble methodHuman diseasesGenetic effectsRisk variantsGenetic variantsComplex diseasesMachineNew variable selection procedureNetwork analysisVariable selection procedureDifferent approaches