2020
Genotyping Array Design and Data Quality Control in the Million Veteran Program
Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji SG, Sun N, Webster T, Liem A, Hsieh P, Devineni P, Karnam P, Gong X, Radhakrishnan L, Schmidt J, Assimes TL, Huang J, Pan C, Humphries D, Brophy M, Moser J, Muralidhar S, Huang GD, Przygodzki R, Concato J, Gaziano JM, Gelernter J, O’Donnell C, Hauser ER, Zhao H, O’Leary T, Program V, Tsao PS, Pyarajan S. Genotyping Array Design and Data Quality Control in the Million Veteran Program. American Journal Of Human Genetics 2020, 106: 535-548. PMID: 32243820, PMCID: PMC7118558, DOI: 10.1016/j.ajhg.2020.03.004.Peer-Reviewed Original ResearchConceptsMillion Veteran ProgramGenome-wide association studiesGenome-wide scanHigh-quality genotypesArray-based genotypingWhole-genome sequencingNon-European individualsAssociation studiesGenetic markersOmics assaysAxiom arrayDownstream analysisVeteran ProgramCommon variantsGenetic associationAfrican American ancestryAmerican ancestryMVP cohortRare variantsSingle assayDiversityFurther data releasesLarge biobanksPromising resourceQuality control
2019
Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes
Chen J, Loukola A, Gillespie NA, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Jousilahti P, Hällfors J, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X. Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes. Nicotine & Tobacco Research 2019, 22: 900-909. PMID: 31294817, PMCID: PMC7249921, DOI: 10.1093/ntr/ntz099.Peer-Reviewed Original ResearchConceptsGenome-Wide Meta-AnalysisGene-based analysisChemokine signaling pathwaysGenetic architectureActin cytoskeletonNew lociReceptor recyclingMAPK signalingPathway interactionsBiological pathwaysSignaling pathwaysAxon guidanceNovel pathwayPhenotypeNovel candidatesEuropean ancestryPathwayReplication sampleNetwork analysisReplicationIno80CCytoskeletonCOPB2EndocytosisSORBS2
2017
Ancestry‐specific and sex‐specific risk alleles identified in a genome‐wide gene‐by‐alcohol dependence interaction study of risky sexual behaviors
Polimanti R, Zhao H, Farrer LA, Kranzler HR, Gelernter J. Ancestry‐specific and sex‐specific risk alleles identified in a genome‐wide gene‐by‐alcohol dependence interaction study of risky sexual behaviors. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2017, 174: 846-853. PMID: 28990359, PMCID: PMC5861711, DOI: 10.1002/ajmg.b.32604.Peer-Reviewed Original Research
2015
Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets
Vongpaisarnsin K, Listman JB, Malison RT, Gelernter J. Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets. Legal Medicine 2015, 17: 245-250. PMID: 25759192, PMCID: PMC4480199, DOI: 10.1016/j.legalmed.2015.02.004.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAncestry informative markersAssociation studiesGenome-wide association datasetInformative markersGenetic structureHapMap populationsSNP dataInternational HapMap databaseSuch SNPsEast Asian populationsHapMap databaseSNPsMarkersPopulationDiversityAsian populationsEfficient strategyThai population
2010
ADH1A variation predisposes to personality traits and substance dependence
Zuo L, Gelernter J, Kranzler HR, Stein MB, Zhang H, Wei F, Sen S, Poling J, Luo X. ADH1A variation predisposes to personality traits and substance dependence. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2010, 153B: 376-386. PMID: 19526455, PMCID: PMC2861415, DOI: 10.1002/ajmg.b.30990.Peer-Reviewed Original Research
2009
Measurement of admixture proportions and description of admixture structure in different U.S. populations
Halder I, Yang B, Kranzler HR, Stein MB, Shriver MD, Gelernter J. Measurement of admixture proportions and description of admixture structure in different U.S. populations. Human Mutation 2009, 30: 1299-1309. PMID: 19572378, PMCID: PMC2867064, DOI: 10.1002/humu.21045.Peer-Reviewed Original ResearchPopulation admixture modulates risk for alcohol dependence
Zuo L, Luo X, Listman JB, Kranzler HR, Wang S, Anton RF, Blumberg HP, Stein MB, Pearlson GD, Covault J, Charney DS, van Kammen DP, Price LH, Lappalainen J, Cramer J, Krystal JH, Gelernter J. Population admixture modulates risk for alcohol dependence. Human Genetics 2009, 125: 605-613. PMID: 19306106, PMCID: PMC2777998, DOI: 10.1007/s00439-009-0647-4.Peer-Reviewed Original ResearchAssociation of Markers in the 3′ Region of the GluR5 Kainate Receptor Subunit Gene to Alcohol Dependence
Kranzler HR, Gelernter J, Anton RF, Arias AJ, Herman A, Zhao H, Burian L, Covault J. Association of Markers in the 3′ Region of the GluR5 Kainate Receptor Subunit Gene to Alcohol Dependence. Alcohol Clinical And Experimental Research 2009, 33: 925-930. PMID: 19320626, PMCID: PMC2772659, DOI: 10.1111/j.1530-0277.2009.00913.x.Peer-Reviewed Original ResearchPro-Opiomelanocortin Gene Variation Related to Alcohol or Drug Dependence: Evidence and Replications Across Family- and Population-based Studies
Zhang H, Kranzler HR, Weiss RD, Luo X, Brady KT, Anton RF, Farrer LA, Gelernter J. Pro-Opiomelanocortin Gene Variation Related to Alcohol or Drug Dependence: Evidence and Replications Across Family- and Population-based Studies. Biological Psychiatry 2009, 66: 128-136. PMID: 19217079, PMCID: PMC2896237, DOI: 10.1016/j.biopsych.2008.12.021.Peer-Reviewed Original Research
2007
Interpopulation linkage disequilibrium patterns of GABRA2 and GABRG1 genes at the GABA cluster locus on human chromosome 4
Ittiwut C, Listman J, Mutirangura A, Malison R, Covault J, Kranzler HR, Sughondhabirom A, Thavichachart N, Gelernter J. Interpopulation linkage disequilibrium patterns of GABRA2 and GABRG1 genes at the GABA cluster locus on human chromosome 4. Genomics 2007, 91: 61-69. PMID: 17976953, PMCID: PMC2709929, DOI: 10.1016/j.ygeno.2007.08.007.Peer-Reviewed Original ResearchConceptsLinkage disequilibrium patternsDisequilibrium patternsHuman chromosome 4Intergenic distancesIntergenic regionHaplotype block structureChromosome 4Haplotype structureLD blocksFunctional variantsGamma 1 subunitChromosome 4pHigh LDGABRA2 locusGenetic associationGenesLociDifferent populationsAlpha 2GABRA2KbSubunitsPopulationReported associationsGABRG1CNR1 Variation Modulates Risk for Drug and Alcohol Dependence
Zuo L, Kranzler HR, Luo X, Covault J, Gelernter J. CNR1 Variation Modulates Risk for Drug and Alcohol Dependence. Biological Psychiatry 2007, 62: 616-626. PMID: 17509535, DOI: 10.1016/j.biopsych.2006.12.004.Peer-Reviewed Original ResearchMeSH KeywordsAdultAlcoholismBlack or African AmericanCase-Control StudiesChromosome MappingComorbidityFemaleGenetic MarkersGenetic Predisposition to DiseaseGenetic VariationGenotypeHumansMalePolymorphism, Single NucleotideReceptor, Cannabinoid, CB1Regression AnalysisRisk FactorsSubstance-Related DisordersWhite PeopleConceptsCannabinoid receptor 1Substance dependenceHealthy control subjectsHuman cannabinoid receptor 1Control subjectsSD patientsT genotypeProtective allelesAlcohol dependenceReceptor 1Disease riskModulate riskCNR1 geneCNR1 variationInitial reportCase-control sampleLarge case-control sampleRegression analysisRiskStrong genetic effectsMarkersSignificant interaction effectMultiple markersAncestry informative markersSNP8Markers in the 5′-Region of GABRG1 Associate to Alcohol Dependence and are in Linkage Disequilibrium with Markers in the Adjacent GABRA2 Gene
Covault J, Gelernter J, Jensen K, Anton R, Kranzler HR. Markers in the 5′-Region of GABRG1 Associate to Alcohol Dependence and are in Linkage Disequilibrium with Markers in the Adjacent GABRA2 Gene. Neuropsychopharmacology 2007, 33: 837-848. PMID: 17507911, PMCID: PMC2743531, DOI: 10.1038/sj.npp.1301456.Peer-Reviewed Original ResearchDemographic changes and marker properties affect detection of human population differentiation
Listman JB, Malison RT, Sughondhabirom A, Yang BZ, Raaum RL, Thavichachart N, Sanichwankul K, Kranzler HR, Tangwonchai S, Mutirangura A, Disotell TR, Gelernter J. Demographic changes and marker properties affect detection of human population differentiation. BMC Genomic Data 2007, 8: 21. PMID: 17498298, PMCID: PMC1876243, DOI: 10.1186/1471-2156-8-21.Peer-Reviewed Original ResearchCHRM2 variation predisposes to personality traits of agreeableness and conscientiousness
Luo X, Kranzler HR, Zuo L, Zhang H, Wang S, Gelernter J. CHRM2 variation predisposes to personality traits of agreeableness and conscientiousness. Human Molecular Genetics 2007, 16: 1557-1568. PMID: 17468496, DOI: 10.1093/hmg/ddm104.Peer-Reviewed Original Research
2006
Diplotype Trend Regression Analysis of the ADH Gene Cluster and the ALDH2 Gene: Multiple Significant Associations with Alcohol Dependence
Luo X, Kranzler HR, Zuo L, Wang S, Schork NJ, Gelernter J. Diplotype Trend Regression Analysis of the ADH Gene Cluster and the ALDH2 Gene: Multiple Significant Associations with Alcohol Dependence. American Journal Of Human Genetics 2006, 78: 973-987. PMID: 16685648, PMCID: PMC1474098, DOI: 10.1086/504113.Peer-Reviewed Original ResearchConceptsADH gene clusterGene clusterAldehyde dehydrogenase geneStructured association analysisConventional association methodsALDH2 geneAlcohol dehydrogenaseAdh geneDehydrogenase geneAssociation analysisSusceptibility lociGenesRisk genesFunctional variantsDisease allelesFunctional complexityCase-control sampleAncestry informative markersHardy-Weinberg equilibrium testDisequilibrium measuresMultiple significant associationsAllelesAlcohol-metabolizing enzymesConventional case-control comparisonsUnlinked ancestry-informative markers
2005
Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment
Yang BZ, Zhao H, Kranzler HR, Gelernter J. Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment. BMC Genomic Data 2005, 6: 50. PMID: 16225681, PMCID: PMC1285360, DOI: 10.1186/1471-2156-6-50.Peer-Reviewed Original ResearchADH4 Gene Variation is Associated with Alcohol Dependence and Drug Dependence in European Americans: Results from HWD Tests and Case–Control Association Studies
Luo X, Kranzler HR, Zuo L, Lappalainen J, Yang BZ, Gelernter J. ADH4 Gene Variation is Associated with Alcohol Dependence and Drug Dependence in European Americans: Results from HWD Tests and Case–Control Association Studies. Neuropsychopharmacology 2005, 31: 1085-1095. PMID: 16237392, DOI: 10.1038/sj.npp.1300925.Peer-Reviewed Original ResearchAdultAlcohol DehydrogenaseAlcohol-Induced Disorders, Nervous SystemAlcoholismAmericasDNA Mutational AnalysisEuropeFemaleGenes, RecessiveGenetic MarkersGenetic Predisposition to DiseaseGenetic TestingGenetic VariationGenotypeHaplotypesHumansLinkage DisequilibriumMaleMiddle AgedPolymorphism, Single NucleotidePromoter Regions, GeneticSubstance-Related DisordersWhite PeoplePractical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE
Yang B, Zhao H, Kranzler HR, Gelernter J. Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE. Genetic Epidemiology 2005, 28: 302-312. PMID: 15782414, DOI: 10.1002/gepi.20070.Peer-Reviewed Original Research
2004
Confirmation and fine mapping of the chromosome 1 alcohol dependence risk locus
Lappalainen J, Kranzler HR, Petrakis I, Somberg LK, Page G, Krystal JH, Gelernter J. Confirmation and fine mapping of the chromosome 1 alcohol dependence risk locus. Molecular Psychiatry 2004, 9: 312-319. PMID: 15094791, DOI: 10.1038/sj.mp.4001429.Peer-Reviewed Original ResearchConceptsTransmission disequilibrium testNovel candidate genesSTR markersTransmission disequilibriumShort tandem repeat markersGenetic linkage studiesFine mappingRepeat markersTandem repeat markersCandidate genesChromosome 1Linkage signalMap intervalSmall nuclear familiesBase pairsGenesLinkage disequilibriumLinkage findingsSusceptibility genesDNA base pairsLinkage studiesSupport intervalBP intervalChromosome 1pDisequilibrium testGenome-Wide Linkage Scan for Loci Predisposing to Social Phobia: Evidence for a Chromosome 16 Risk Locus
Gelernter J, Page GP, Stein MB, Woods SW. Genome-Wide Linkage Scan for Loci Predisposing to Social Phobia: Evidence for a Chromosome 16 Risk Locus. American Journal Of Psychiatry 2004, 161: 59-66. PMID: 14702251, DOI: 10.1176/appi.ajp.161.1.59.Peer-Reviewed Original ResearchConceptsGenome-wide linkage scanLinkage scanChromosome 16LOD scoreGenetic linkage analysisNorepinephrine transporter proteinLinkage genome scanGenomic locationEntire genomeChromosome 16 markersGenome scanMultipoint LOD scoreRisk lociTransporter proteinsGenetic markersLinkage analysisSusceptibility lociChromosome 9Physiological candidatesLocus predisposingLociZlr scoreAmerican pedigreesX softwareD16S415