2025
Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants
Yuan M, Goovaerts S, Lee M, Devine J, Richmond S, Walsh S, Shriver M, Shaffer J, Marazita M, Peeters H, Weinberg S, Claes P. Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants. Briefings In Bioinformatics 2025, 26: bbaf090. PMID: 40062617, PMCID: PMC11891655, DOI: 10.1093/bib/bbaf090.Peer-Reviewed Original ResearchConceptsRare variant association studiesGenome-wide association studiesComplex morphological traitsGenomic lociSNP heritabilityAssociation studiesRare variantsPhenotypic variationMorphological traitsAxes of phenotypic variationContext of genome-wide association studiesVariant association studiesIndividuals of European ancestryGene-based testsLinkage disequilibrium score regressionRare genetic variantsGenomic relatednessOptimal phenotypeUnrelated individualsGenetic variantsRelevant traitsEuropean ancestryScore regressionPhenotype distributionFamily dataNongenetic adaptation by collective migration
Vo L, Avgidis F, Mattingly H, Edmonds K, Burger I, Balasubramanian R, Shimizu T, Kazmierczak B, Emonet T. Nongenetic adaptation by collective migration. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2423774122. PMID: 39970001, PMCID: PMC11874451, DOI: 10.1073/pnas.2423774122.Peer-Reviewed Original ResearchConceptsGene regulationCollective migrationPhenotype distributionPhenotypic compositionStress response pathwaysSwimming phenotypeCell populationsBacterial populationsStress responseAbundance distributionMultidimensional phenotypesGenetic mutationsPhenotypeDiverse environmentsEnvironmental conditionsGenesMutationsSwimming behaviorChanging environmentDoubling timeMigrating populationCellsRegulationMigrationAdaptation
2022
Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies
Zhuang Y, Wolford B, Nam K, Bi W, Zhou W, Willer C, Mukherjee B, Lee S. Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies. Bioinformatics 2022, 38: 4337-4343. PMID: 35876838, PMCID: PMC9477535, DOI: 10.1093/bioinformatics/btac459.Peer-Reviewed Original ResearchConceptsEmpirical saddlepoint approximationFamily disease historyCase-control imbalanceSaddlepoint approximationGenome-wide association analysisPopulation-based genetic association studiesGenetic association testsVariant-phenotype associationsDisease historyGenetic association studiesLow detection powerType I error inflationCorrelation of phenotypesWhite British sampleSupplementary dataAssociation studiesPopulation-based biobanksIncreased phenotypic correlationsKorean GenomeSimulation studyPhenotype distributionPhenotypeAssociation TestBioinformaticsPhenotypic correlations
2021
Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes
Bi W, Zhou W, Dey R, Mukherjee B, Sampson J, Lee S. Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes. American Journal Of Human Genetics 2021, 108: 825-839. PMID: 33836139, PMCID: PMC8206161, DOI: 10.1016/j.ajhg.2021.03.019.Peer-Reviewed Original ResearchConceptsOrdinal categorical phenotypesGenome-wide association studiesCategorical phenotypesGenome-wide significant variantsRare variantsPhenotype distributionControlled type I error ratesType I error rateMixed model approachArray genotypingAssociation studiesCommon variantsQuantitative traitsSignificant variantsLogistic mixed modelsLack of analysis toolsUK BiobankLinear mixed model approachPhenotypeAssociation TestVariantsMixed modelsSignificance levelMAFTraits
2019
Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use
Wu W, Wang Z, Xu K, Zhang X, Amei A, Gelernter J, Zhao H, Justice AC, Wang Z. Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use. Genetics 2019, 213: 1225-1236. PMID: 31591132, PMCID: PMC6893384, DOI: 10.1534/genetics.119.302598.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation analysisGenome-wide association analysisCase-control genome-wide association studyPhenotype model misspecificationImportant locusGenetic architectureComplex traitsGenetic association analysisGene mappingGenome scanPathway analysisAssociation studiesAxonal guidanceGenetic variantsBinary traitsAssociation TestElectronic health record-based studiesPathwayImportant pathwayLociTraitsPhenotype distributionLongitudinal phenotypesPhenotype
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