2025
Protocol for finding genetic variation associated with unmeasured traits through GenomicSEM common-factor GWAS
Johnston K, Signer R, Huckins L. Protocol for finding genetic variation associated with unmeasured traits through GenomicSEM common-factor GWAS. STAR Protocols 2025, 6: 103905. PMID: 40531628, PMCID: PMC12213288, DOI: 10.1016/j.xpro.2025.103905.Peer-Reviewed Original ResearchSex‐Specific Association Between Polymorphisms in Estrogen Receptor Alpha Gene (ESR1) and Depression: A Genome‐Wide Association Study of All of Us and UK Biobank Data
Hu Y, Che M, Zhang H. Sex‐Specific Association Between Polymorphisms in Estrogen Receptor Alpha Gene (ESR1) and Depression: A Genome‐Wide Association Study of All of Us and UK Biobank Data. Genetic Epidemiology 2025, 49: e70004. PMID: 40007508, PMCID: PMC11924109, DOI: 10.1002/gepi.70004.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesAlpha geneEstrogen receptor alpha geneGenetic risk factorsRisk lociGenomic associationsMajor depressive disorderMDD phenotypesGenetic studiesGenetic associationRisk factors of MDDGenesESR1 geneUK BiobankESR1Participant genotypesPolymorphismSex-SpecificSex-specific associationsDepressive disorderRacial/ethnic disparitiesFindings lack consistencyLength of lifeEmpowering genome-wide association studies via a visualizable test based on the regional association score
Jiang Y, Zhang H. Empowering genome-wide association studies via a visualizable test based on the regional association score. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2419721122. PMID: 39999171, PMCID: PMC11892588, DOI: 10.1073/pnas.2419721122.Peer-Reviewed Original Research
2024
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
Li K, Chaguza C, Stamp J, Chew Y, Chen N, Ferguson D, Pandya S, Kerantzas N, Schulz W, Initiative Y, Hahn A, Ogbunugafor C, Pitzer V, Crawford L, Weinberger D, Grubaugh N. Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. PLOS Computational Biology 2024, 20: e1012469. PMID: 39288189, PMCID: PMC11432881, DOI: 10.1371/journal.pcbi.1012469.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle-nucleotide polymorphismsAssociation studiesWhole-genome sequencingAmino acid changesSingle nucleotide polymorphismsPairs of substitutionsViral copiesEpistasis testsGenome sequenceGenetic variationSpike geneAcid changesViral genomeNucleotide polymorphismsSARS-CoV-2Detect interactionsHost factorsVirus copiesCopyInfection dynamicsRT-qPCRPolymorphismOmicron BASARS-CoV-2 infection
2023
A Polynesian-specific missense CETP variant alters the lipid profile
Moors J, Krishnan M, Sumpter N, Takei R, Bixley M, Cadzow M, Major T, Phipps-Green A, Topless R, Merriman M, Rutledge M, Morgan B, Carlson J, Zhang J, Russell E, Sun G, Cheng H, Weeks D, Naseri T, Reupena M, Viali S, Tuitele J, Hawley N, Deka R, McGarvey S, de Zoysa J, Murphy R, Dalbeth N, Stamp L, Taumoepeau M, King F, Wilcox P, Rapana N, McCormick S, Minster R, Merriman T, Leask M. A Polynesian-specific missense CETP variant alters the lipid profile. Human Genetics And Genomics Advances 2023, 4: 100204. PMID: 37250494, PMCID: PMC10209881, DOI: 10.1016/j.xhgg.2023.100204.Peer-Reviewed Original ResearchConceptsPopulation-specific genetic variantsGenomic studiesGenetic analysisFunction mutationsVariant altersGenetic determinantsGenetic variantsMinor alleleCETP deficiencyGenomicsHigher HDLLipid profileTraitsSequencingLow LDL-C levelsMutationsAllelesLDL-C levelsSerum lipid profileCopiesPolymorphismAssociatesLower LDLCardiovascular diseaseVariantsThe genomics of visuospatial neurocognition in obsessive-compulsive disorder: A preliminary GWAS
Alemany-Navarro M, Tubío-Fungueiriño M, Almeida S, Cruz R, Lombroso A, Real E, Soria V, Bertolín S, Fernández-Prieto M, Alonso P, Menchón J, Carracedo A, Segalàs C. The genomics of visuospatial neurocognition in obsessive-compulsive disorder: A preliminary GWAS. Journal Of Affective Disorders 2023, 333: 365-376. PMID: 37094658, DOI: 10.1016/j.jad.2023.04.060.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsSuggestive signalsCase/control genome-wide association studyPreliminary genome-wide association studyGenome-wide levelGenome-wide significanceGenomic basisComplex traitsGenomic regionsWhole genomeGenetic basisAssociation studiesGenetic characterizationAssociation of SNPsNucleotide polymorphismsGenomicsTraitsGenomeGenesNeuropsychological traitsPolymorphismPromising avenueSignalsOCD casesMultivariate genome-wide association meta-analysis of over 1 million subjects identifies loci underlying multiple substance use disorders
Hatoum A, Colbert S, Johnson E, Huggett S, Deak J, Pathak G, Jennings M, Paul S, Karcher N, Hansen I, Baranger D, Edwards A, Grotzinger A, Tucker-Drob E, Kranzler H, Davis L, Sanchez-Roige S, Polimanti R, Gelernter J, Edenberg H, Bogdan R, Agrawal A. Multivariate genome-wide association meta-analysis of over 1 million subjects identifies loci underlying multiple substance use disorders. Nature Mental Health 2023, 1: 210-223. PMID: 37250466, PMCID: PMC10217792, DOI: 10.1038/s44220-023-00034-y.Peer-Reviewed Original ResearchGenome-wide associationGenetic risk lociIndependent single nucleotide polymorphismsProblematic tobacco useSingle nucleotide polymorphismsRisk lociHigh polygenicityLociReceptor geneAddiction risk factorsPolygenic risk scoresEuropean descentPolygenicityGenesSummary statisticsSubstance use disordersSomatic conditionsAncestryRegulationConfersUse disordersPolymorphismGenetic liabilityDopamine regulationPDE4BAssociation between Genetic Variants of CELSR2-PSRC1-SORT1 and Cardiovascular Diseases: A Systematic Review and Meta-Analysis
Castillo-Avila R, González-Castro T, Tovilla-Zárate C, Martínez-Magaña J, López-Narváez M, Juárez-Rojop I, Arias-Vázquez P, Borgonio-Cuadra V, Pérez-Hernández N, Rodríguez-Pérez J. Association between Genetic Variants of CELSR2-PSRC1-SORT1 and Cardiovascular Diseases: A Systematic Review and Meta-Analysis. Journal Of Cardiovascular Development And Disease 2023, 10: 91. PMID: 36975855, PMCID: PMC10056735, DOI: 10.3390/jcdd10030091.Peer-Reviewed Original ResearchCoronary artery diseaseCardiovascular diseaseArtery diseaseSystematic reviewCELSR2-PSRC1Total cholesterolEligible studiesRisk associationElectronic databasesMeta-analysisDiseaseTissue expressionPossible involvementGenetic variantsAssociationCluster variantsRs599839PheWAS analysesPolymorphismReviewCholesterol
2022
Exploring the genetic overlap between twelve psychiatric disorders
Romero C, Werme J, Jansen P, Gelernter J, Stein M, Levey D, Polimanti R, de Leeuw C, Posthuma D, Nagel M, van der Sluis S. Exploring the genetic overlap between twelve psychiatric disorders. Nature Genetics 2022, 54: 1795-1802. PMID: 36471075, DOI: 10.1038/s41588-022-01245-2.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsPleiotropic single nucleotide polymorphismsPositive genetic correlationStringent P-value thresholdGenetic architectureGenomic regionsGenetic covarianceBiological processesBiological pathwaysMolecular characterizationObserved phenotypicGenetic correlationsGenetic overlapBiological characterizationBiological mechanismsP-value thresholdOnly annotationGenesPleiotropicPairwise comparisonsPhenotypicPathwayAnnotationPolymorphismCharacterizationDeep Learning From Imaging Genetics for Schizophrenia Classification
Yu H, Florian T, Calhoun V, Ye D. Deep Learning From Imaging Genetics for Schizophrenia Classification. 2022, 00: 3291-3295. DOI: 10.1109/icip46576.2022.9897977.Peer-Reviewed Original ResearchSingle-nucleotide polymorphismsSingle nucleotide polymorphismsGenetic informationNucleotide polymorphismsGenetic changesGenetic disordersLayer-wise relevance propagationPatient's brainMorphological characteristicsPolymorphismStructural MRIMulti-modal deep learning approachExtract convolutional featuresA noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation
Yanchus C, Drucker K, Kollmeyer T, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo S, Ali A, Decker P, Kosel M, Panda A, Al-Zahrani K, Jiang L, Browning J, Lowden C, Geuenich M, Hernandez J, Gosio J, Ahmed M, Loganathan S, Berman J, Trcka D, Michealraj K, Fortin J, Carson B, Hollingsworth E, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He H, Murphy D, Wang L, Abyzov A, Dennis J, Maass P, Campbell K, Wilson M, Lachance D, Wrensch M, Wiencke J, Mak T, Pennacchio L, Dickel D, Visel A, Wrana J, Taylor M, Zadeh G, Dirks P, Eckel-Passow J, Attisano L, Pombo A, Ida C, Kvon E, Jenkins R, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022, 378: 68-78. PMID: 36201590, PMCID: PMC9926876, DOI: 10.1126/science.abj2890.Peer-Reviewed Original ResearchConceptsNoncoding single nucleotide polymorphismSingle nucleotide polymorphismsCausal variantsMolecular pathwaysIsocitrate dehydrogenaseLethal gliomaHeritable predispositionGlioma formationTumor developmentLow-grade gliomasMutant lower grade gliomasPolymorphismMouse modelPromoterLociEnhancerSixfold greater riskRs55705857PathwayMechanisticallyDehydrogenaseDisruptsExpressionPenetranceCancer risk
2021
STAT3 polymorphisms in North Africa and its implication in breast cancer
Ziadi W, Boussetta S, Elkamel S, Pakstis AJ, Kidd KK, Medimegh I, Elgaaied A, Cherni L. STAT3 polymorphisms in North Africa and its implication in breast cancer. Molecular Genetics & Genomic Medicine 2021, 9: e1744. PMID: 34251094, PMCID: PMC8404238, DOI: 10.1002/mgg3.1744.Peer-Reviewed Original ResearchConceptsNorth African populationsAfrican populationsSTAT3 regionSingle nucleotide polymorphismsRare haplotypesHsa-mirMiR databaseMajor haplotypesGenesNucleotide polymorphismsHaplotypesSNPsSTAT3Allele frequenciesRs7211777Tunisian populationPolymorphismPopulationDiversityNorth AfricaAllelesSignificant frequencyRecombinationAssaysCancerThe morphometry of left cuneus mediating the genetic regulation on working memory
He X, Li X, Fu J, Xu J, Liu H, Zhang P, Li W, Yu C, Ye Z, Qin W. The morphometry of left cuneus mediating the genetic regulation on working memory. Human Brain Mapping 2021, 42: 3470-3480. PMID: 33939221, PMCID: PMC8249898, DOI: 10.1002/hbm.25446.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsGenome-wide association study summary statisticsLinear mixed modelsIndependent single nucleotide polymorphismsSubgroup of CaucasiansAssociation studiesGenetic regulationAssociation analysisGenetic signaturesNucleotide polymorphismsGenetic variantsUK BiobankBiological pathwaysSummary statisticsImage-derived phenotypesPolymorphismMediation analysisCognitive functionPotential associationMixed modelsPathwayMRNA expressionDAAM1Human Connectome ProjectGenome-wide association study of psychiatric and substance use comorbidity in Mexican individuals
Martínez-Magaña JJ, Genis-Mendoza AD, Villatoro Velázquez JA, Bustos-Gamiño M, Juárez-Rojop IE, Tovilla-Zarate CA, Sarmiento E, Saucedo E, Rodríguez-Mayoral O, Fleiz-Bautista C, Camarena B, Aguilar A, Gonzalez-Castro TB, Medina-Mora ME, Nicolini H. Genome-wide association study of psychiatric and substance use comorbidity in Mexican individuals. Scientific Reports 2021, 11: 6771. PMID: 33762635, PMCID: PMC7990941, DOI: 10.1038/s41598-021-85881-4.Peer-Reviewed Original ResearchMeSH KeywordsAdultAllelesBiological Variation, PopulationComorbidityFemaleGenetic Association StudiesGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMaleMental DisordersMiddle AgedPolymorphism, Single NucleotidePublic Health SurveillanceQuantitative Trait LociRisk AssessmentRisk FactorsSubstance-Related DisordersYoung AdultConceptsGenome-wide association studiesGenome-wide correlationSingle nucleotide polymorphismsVertical pleiotropyAssociation studiesWide association signalsGenome-wide associationPolygenic risk scoresQuantitative lociAssociation signalsPhagocytosis pathwayNominal associationTraitsPleiotropyPathwayMeQTLMendelian randomizationGenesLociHigher polygenic risk scoreMicroarrayMultiple logistic modelMexican populationCommon comorbiditiesPolymorphism
2020
Lack of association between Mannose Binding Lectin-2 gene polymorphisms and periodontitis: A meta-analysis
da Silva F, Leal A, Nibali L, Shin J, Carvalho M, Koga R, de Andrade Figueira M, Galeno J, Toro D, de Andrade Z, Batista N, Barcellos J. Lack of association between Mannose Binding Lectin-2 gene polymorphisms and periodontitis: A meta-analysis. Human Gene 2020, 26: 100757. DOI: 10.1016/j.mgene.2020.100757.Peer-Reviewed Original ResearchMBL-2Gene polymorphismsAssociated with susceptibility to periodontitisMeta-analysisNon-significant associationOdds ratioMBL-2 gene polymorphismsSusceptibility to periodontitisAssociated with periodontitisMBL-2 geneCalculation of odds ratiosConfidence intervalsBegg and Egger testsMutant allelesRs1800451 polymorphismLack of associationPeriodontitisStratified analysisEgger's testCaucasian groupGenotyping methodsRs1800450Publication biasMixed populationPolymorphismPolymorphisms in the interleukin genes and chronic periodontitis: A field synopsis and revaluation by Bayesian approaches
da Silva F, Pessoa L, Shin J, Alves E, Koga R, Smith C, Vasconcelos D, Pereira A. Polymorphisms in the interleukin genes and chronic periodontitis: A field synopsis and revaluation by Bayesian approaches. Cytokine 2020, 138: 155361. PMID: 33223448, DOI: 10.1016/j.cyto.2020.155361.Peer-Reviewed Original ResearchPathogenesis of Eosinophilic Esophagitis: A Comprehensive Review of the Genetic and Molecular Aspects
Ryu S, Lee K, Tizaoui K, Terrazzino S, Cargnin S, Effenberger M, Shin J, Kronbichler A. Pathogenesis of Eosinophilic Esophagitis: A Comprehensive Review of the Genetic and Molecular Aspects. International Journal Of Molecular Sciences 2020, 21: 7253. PMID: 33008138, PMCID: PMC7582808, DOI: 10.3390/ijms21197253.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesMultiple genome-wide association studiesGenetic lociAssociation studiesThymic stromal lymphopoietinGenetic polymorphismsMolecular aspectsGenetic riskLociPathophysiology of EoE.Pathophysiology of EoERisk of EoEReflux-like symptomsInterleukin (IL)-13Food impactionTh2 cellsEosinophilic esophagitisComprehensive pathophysiologyCellsEoEGeneticsPolymorphismEoE.The distinctive geographic patterns of common pigmentation variants at the OCA2 gene
Kidd KK, Pakstis AJ, Donnelly MP, Bulbul O, Cherni L, Gurkan C, Kang L, Li H, Yun L, Paschou P, Meiklejohn KA, Haigh E, Speed WC. The distinctive geographic patterns of common pigmentation variants at the OCA2 gene. Scientific Reports 2020, 10: 15433. PMID: 32963319, PMCID: PMC7508881, DOI: 10.1038/s41598-020-72262-6.Peer-Reviewed Original ResearchConceptsOculocutaneous albinism type 2Genetic variationOCA2 genePopulation genetic variationGeographic patternsNormal pigmentation variationPigmentation variationSingle nucleotide polymorphismsPositive selectionHypomorphic proteinEnhancer variantsPigmentation variantsGenesNucleotide polymorphismsDistinctive geographic patternsEye colorStrong selection effectsVariant frequencyPigmentationVariantsProteinAllelesVariationDifferent patternsPolymorphismThe NEMP family supports metazoan fertility and nuclear envelope stiffness
Tsatskis Y, Rosenfeld R, Pearson J, Boswell C, Qu Y, Kim K, Fabian L, Mohammad A, Wang X, Robson M, Krchma K, Wu J, Gonçalves J, Hodzic D, Wu S, Potter D, Pelletier L, Dunham W, Gingras A, Sun Y, Meng J, Godt D, Schedl T, Ciruna B, Choi K, Perry J, Bremner R, Schirmer E, Brill J, Jurisicova A, McNeill H. The NEMP family supports metazoan fertility and nuclear envelope stiffness. Science Advances 2020, 6: eabb4591. PMID: 32923640, PMCID: PMC7455189, DOI: 10.1126/sciadv.abb4591.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsNuclear envelopeHuman genome-wide association studiesGenome-wide association studiesGerm lineAssociation studiesGenetic studiesProteinCaenorhabditisNemp1ZebrafishFertilityHomologSterilityRoleBiochemicalPolymorphismEnvelopeFamilyComplexesMechanical stiffnessEarly lossLossSupervariants 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
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