2023
Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program
Wang X, Ryu J, Kim J, Ramirez A, Mayo K, Condon H, Vaitinadin N, Ohno-Machado L, Talavera G, Ellinor P, Lubitz S, Choi S. Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program. Journal Of Human Genetics 2023, 68: 565-570. PMID: 37072623, PMCID: PMC10524735, DOI: 10.1038/s10038-023-01147-z.Peer-Reviewed Original ResearchMeSH KeywordsCarrier ProteinsCoronary Artery DiseaseDiabetes Mellitus, Type 2Genetic Predisposition to DiseaseGenome-Wide Association StudyHumansPopulation HealthProprotein Convertase 9ConceptsDiverse human populationsGenomic dataGene-based burden testsWhole genome sequencesRare variant analysisHuman populationQuantitative traitsBurden testsRare lossLociComplex diseasesGenetic associationVariant analysisFunction variantsCardiometabolic traitsRare variantsTraitsBiomedical researchGIGYF1VariantsNPR2ACANSequencePopulationLDLR
2020
Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1
Rawat P, Brummel S, Singh K, Kim J, Frazer K, Nichols S, Seage G, Williams P, Van Dyke R, Harismendy O, Trout R, Spector S. Genomics Links Inflammation With Neurocognitive Impairment in Children Living With Human Immunodeficiency Virus Type-1. The Journal Of Infectious Diseases 2020, 224: 870-880. PMID: 33373444, PMCID: PMC8408770, DOI: 10.1093/infdis/jiaa792.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsChildChild, PreschoolFemaleGenome-Wide Association StudyGenomicsHIV InfectionsHIV-1HumansInfantInfectious Disease Transmission, VerticalInflammasomesInflammationIntracellular Signaling Peptides and ProteinsMaleMembrane ProteinsMicrogliaNeurocognitive DisordersReceptors, CCRConceptsWhole-exome sequencingValidation cohortNeurocognitive impairmentOdds ratioRisk of NCIHuman immunodeficiency virus type 1Immunodeficiency virus type 1Single nucleotide variantsAdjusted odds ratioIL-1β releaseVirus type 1Microglial releaseIL-1βHuman microgliaDecreased oddsType 1Logistic regressionCognitive scoresCCRL2MicrogliaFurther studiesHIVInflammationCsACohort
2018
Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki disease
Oyamada J, Shimizu C, Kim J, Williams M, Png E, Hibberd M, Tremoulet A, Perry J, Burns J. Bifid T waves on the ECG and genetic variation in calcium channel voltage‐dependent beta 2 subunit gene (CACNB2) in acute Kawasaki disease. Congenital Heart Disease 2018, 14: 213-220. PMID: 30395415, DOI: 10.1111/chd.12696.Peer-Reviewed Original ResearchConceptsBifid T wavesKawasaki diseaseT-wave morphologyKD subjectsT waveIndependent cohortKD susceptibilityAcute KD subjectsAcute Kawasaki diseaseSelf-limited vasculitisSubunit geneGenetic variantsGenotype/phenotype association studiesWide association study dataGenome-wide association study dataIntracellular calcium signalingPhenotype association studiesWave morphologyAssociation study dataCalcium channel geneCommon causeCardiac repolarizationMyocardial repolarizationCardiac diseaseAbnormal repolarization
2017
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 2017, 33: 3716-3725. PMID: 29036461, PMCID: PMC5860319, DOI: 10.1093/bioinformatics/btx470.Peer-Reviewed Original ResearchChildFamilyGenetic PrivacyGenome-Wide Association StudyHumansLinkage DisequilibriumParentsPolymorphism, Single NucleotideSoftwareWhole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
Kim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.Peer-Reviewed Original ResearchConceptsWhole genome sequencesGenome-wide association studiesToll-like receptor 6Single nucleotide variantsCommon disease-rare variant hypothesisExpression quantitative trait loci (eQTL) analysisDifferential expressionQuantitative trait locus (QTL) analysisCommon disease–common variantPathogen-associated molecular pattern recognitionIntegrative genomics approachIntronic single nucleotide variantsComplex genetic diseasesSequence quality scoresMolecular pattern recognitionWhole-genome sequencingGenomic approachesTranscriptome dataGenome sequenceSequence variationLocus analysisGenome sequencingAssociation studiesFunction of genotypeNucleotide variants
2013
Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)
Lin K, Tharp M, Conway M, Hsieh A, Ross M, Kim J, Kim H. Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP). PLOS ONE 2013, 8: e76384. PMID: 24058713, PMCID: PMC3776754, DOI: 10.1371/journal.pone.0076384.Peer-Reviewed Original Research