2020
Super‐variants identification for brain connectivity
Li T, Hu J, Wang S, Zhang H. Super‐variants identification for brain connectivity. Human Brain Mapping 2020, 42: 1304-1312. PMID: 33236465, PMCID: PMC7927294, DOI: 10.1002/hbm.25294.Peer-Reviewed Original ResearchConceptsCombination of allelesSingle nucleotide polymorphismsNovel lociBrain connectivityUK Biobank databaseChromosome 1Multiple lociGenetic effectsGenetic variantsNucleotide polymorphismsAssociation detectionLociGenetic associationGenesNeurodegenerative disordersBiobank databaseBrain issuesGenetic biomarkersBrain functionBrain structuresGenomeRSPO2Discovery phaseAssociationTMEM74Supervariants 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
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 alcoholism
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 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 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 analysisGeneticsVariantsGenetic 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
2011
A LASSO-based approach to analyzing rare variants in genetic association studies
Brennan JS, He Y, Calixte R, Nyirabahizi E, Jiang Y, Zhang H. A LASSO-based approach to analyzing rare variants in genetic association studies. BMC Proceedings 2011, 5: s100. PMID: 22373373, PMCID: PMC3287823, DOI: 10.1186/1753-6561-5-s9-s100.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 disorderRegion
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 toolGenotypesDetecting significant single-nucleotide polymorphisms in a rheumatoid arthritis study using random forests
Wang M, Chen X, Zhang M, Zhu W, Cho K, Zhang H. Detecting significant single-nucleotide polymorphisms in a rheumatoid arthritis study using random forests. BMC Proceedings 2009, 3: s69. PMID: 20018063, PMCID: PMC2795970, DOI: 10.1186/1753-6561-3-s7-s69.Peer-Reviewed Original ResearchSignificant single nucleotide polymorphismsGenome-wide dataGenetic Analysis Workshop 16 Problem 1 dataGenes/SNPsSNP markersSignificant SNPsSingle nucleotide polymorphismsGenetic association studiesWhole genomeChromosome 6Association studiesRheumatoid arthritis statusAntigen geneTraitsSNPsForestHLA-DRAArray experimentsGenomeMarkersHuman leukocyte antigen (HLA) genesGenesFurther analysisIndividual markersHigh levelsA 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 testGenesPhenotypeDetecting Genes and Gene–Gene Interactions for Age-Related Macular Degeneration with a Forest-based Approach
Wang M, Zhang M, Chen X, Zhang H. Detecting Genes and Gene–Gene Interactions for Age-Related Macular Degeneration with a Forest-based Approach. Statistics In Biopharmaceutical Research 2009, 1: 424-430. PMID: 20161521, PMCID: PMC2799940, DOI: 10.1198/sbr.2009.0046.Peer-Reviewed Original Research
2007
Polymorphisms of one-carbon-metabolizing genes and risk of breast cancer in a population-based study
Xu X, Gammon M, Zhang H, Wetmur J, Rao M, Teitelbaum S, Britton J, Neugut A, Santella R, Chen J. Polymorphisms of one-carbon-metabolizing genes and risk of breast cancer in a population-based study. Carcinogenesis 2007, 28: 1504-1509. PMID: 17372271, DOI: 10.1093/carcin/bgm061.Peer-Reviewed Original ResearchConceptsOne-carbon metabolismRate-limiting enzymeThymidylate synthaseRate-limiting genesOne-carbon pathwayDNA methylationEpigenetic processesSame pathwayGenesMethylenetetrahydrofolate reductaseDNA synthesisEnzymePathwayCritical rolePolymorphismSame populationCancer etiologyPopulation-based Long Island Breast Cancer Study ProjectMetabolismFunctional polymorphismsRepeat alleleMethylationReductaseAllelesSynthase
2006
Detection of Genes for Ordinal Traits in Nuclear Families and a Unified Approach for Association Studies
Zhang H, Wang X, Ye Y. Detection of Genes for Ordinal Traits in Nuclear Families and a Unified Approach for Association Studies. Genetics 2006, 172: 693-699. PMID: 16219774, PMCID: PMC1456175, DOI: 10.1534/genetics.105.049122.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsQuantitative traitsOrdinal traitsTraditional linkage studiesGenomewide association analysisAssociation of genesDetection of genesGametic disequilibriumLoci existAssociation studiesAssociation analysisGenesLinkage disequilibriumTraitsComplex diseasesLinkage studiesGrowth-associated protein 43Protein 43DisequilibriumPolymorphismFamilyMarkersNuclear families
2005
Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data
Zhong X, Zhang H. Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data. BMC Genomic Data 2005, 6: s31. PMID: 16451641, PMCID: PMC1866754, DOI: 10.1186/1471-2156-6-s1-s31.Peer-Reviewed Original ResearchConceptsLinkage analysisAssociation analysisSusceptibility genesGenetic Analysis Workshop 14Alcoholism dataCombination of linkageComplex disease mappingDisease susceptibility genesEntire genomeMean identityLinkage disequilibriumTransmission/disequilibrium testAssociation TestGenesPresence of linkageDisequilibrium testGenomeChromosomesGeneticsLinkageDisequilibriumAssociation strategyGreater numberRegionA genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking
Ye Y, Zhong X, Zhang H. A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking. BMC Genomic Data 2005, 6: s135. PMID: 16451594, PMCID: PMC1866801, DOI: 10.1186/1471-2156-6-s1-s135.Peer-Reviewed Original ResearchConceptsAssociation analysisGenetic Analysis Workshop 14Single nucleotide polymorphism dataJoint association analysisNew genesSingle nucleotide polymorphismsGenetic mechanismsPolymorphism dataAssociation studiesDeterministic forestsGenetics of AlcoholismGenesTreesUseful candidateGeneticsForestPolymorphismFuture studiesStudy of alcoholism
2004
Linkage analysis of ordinal traits for pedigree data
Feng R, Leckman JF, Zhang H. Linkage analysis of ordinal traits for pedigree data. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 16739-16744. PMID: 15548606, PMCID: PMC534720, DOI: 10.1073/pnas.0404623101.Peer-Reviewed Original ResearchConceptsLinkage analysisOrdinal traitsTourette Syndrome Association International ConsortiumLinkage analysis methodsQuantitative traitsEvidence of linkageGenome scanLinkage scanHuman diseasesAllele sharingTraitsPedigree dataInheritance patternDichotomous traitsSignificant allele sharingPhenotypeProportional odds logistic modelGENEHUNTERGenesGeneticsMarkersInternational Consortium
1997
Strategies to Identify Genes for Complex Diseases
Zhang H, Zhao H, Merikangas K. Strategies to Identify Genes for Complex Diseases. Annals Of Medicine 1997, 29: 493-498. PMID: 9562515, DOI: 10.3109/07853899709007473.Peer-Reviewed Original ResearchConceptsComplex diseasesNumerous human diseasesDisease-susceptible genesComplex human disordersHuman genomeGenetic basisHuman disordersHuman diseasesMolecular biologyGenesGenetic epidemiological studiesGenetic factorsComplex patternsDisease pathophysiologyGenomeBiologyTraitsInheritanceMultiple sclerosisBreast cancerEpidemiological studies