2022
Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood
Li S, Mancuso N, Metayer C, Ma X, de Smith A, Wiemels J. Incorporation of DNA methylation quantitative trait loci (mQTLs) in epigenome-wide association analysis: application to birthweight effects in neonatal whole blood. Clinical Epigenetics 2022, 14: 158. PMID: 36457128, PMCID: PMC9714153, DOI: 10.1186/s13148-022-01385-6.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociSingle nucleotide polymorphismsDNA methylationGenetic variationDNA methylation quantitative trait lociGenetic effectsDiverse genetic ancestryEPIC arrayCpG island shore regionQuantitative trait lociDNA methylation dataEpigenome-wide association analysisTrait lociDevelopmental traitsEWAS resultsGenetic elementsGene expressionMethylation dataAssociation studiesK arrayAssociation analysisCertain lociMethylation levelsIllumina 450Top hits
2021
The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis
Muskens IS, Li S, Jackson T, Elliot N, Hansen HM, Myint SS, Pandey P, Schraw JM, Roy R, Anguiano J, Goudevenou K, Siegmund KD, Lupo PJ, de Bruijn MFTR, Walsh KM, Vyas P, Ma X, Roy A, Roberts I, Wiemels JL, de Smith AJ. The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nature Communications 2021, 12: 821. PMID: 33547282, PMCID: PMC7865055, DOI: 10.1038/s41467-021-21064-z.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCore Binding Factor Alpha 2 SubunitCpG IslandsDNA MethylationDown SyndromeEpigenesis, GeneticFemaleFetusGATA1 Transcription FactorGenome-Wide Association StudyGenome, HumanHematopoiesisHematopoietic Stem CellsHumansInfant, NewbornLiverMalePromoter Regions, GeneticProto-Oncogene Protein c-fli-1ConceptsDNA methylationGenome-wide impactGenome-wide effectsGenome-wide perturbationsPromoter/enhancer regionEpigenome-wide association studiesAssociation study resultsGene expression changesHematopoietic stem/progenitor cellsCell-type heterogeneityStem/progenitor cellsEpigenome-wide significant CpGsHematopoietic developmentDifferential methylationEpigenetic changesGene expressionPromoter regionEnhancer regionExpression changesAssociation studiesSignificant CpGsImportant regulatorSignificant hypermethylationHematopoietic cellsMethylation
2018
GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21
Wiemels JL, Walsh KM, de Smith AJ, Metayer C, Gonseth S, Hansen HM, Francis SS, Ojha J, Smirnov I, Barcellos L, Xiao X, Morimoto L, McKean-Cowdin R, Wang R, Yu H, Hoh J, DeWan AT, Ma X. GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. Nature Communications 2018, 9: 286. PMID: 29348612, PMCID: PMC5773513, DOI: 10.1038/s41467-017-02596-9.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentCaliforniaChild, PreschoolChromosomes, Human, Pair 17Chromosomes, Human, Pair 8FemaleGene FrequencyGenetic Predisposition to DiseaseGenome-Wide Association StudyHispanic or LatinoHumansInfantInfant, NewbornMalePolymorphism, Single NucleotidePrecursor Cell Lymphoblastic Leukemia-LymphomaRisk FactorsConceptsNew risk lociRisk lociGenome-wide association studiesGrowth regulation pathwaysGenetic associationAcute lymphoblastic leukemiaNovel genetic associationsChildhood acute lymphoblastic leukemiaGenetic Epidemiology ResearchTranscription factorsStrong genetic associationGene expressionAssociation studiesLymphocyte developmentMYC oncogeneChromosome 17q12Oncology GroupLymphoblastic leukemiaLociChildren's Oncology GroupCalifornia Childhood Leukemia StudyChildhood Leukemia StudyStructural contactsYear of birthNon-Latino whites
2014
PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia
Xiao J, Lee S, Xiao Y, Ma X, Houseman EA, Hsu L, Roy R, Wrensch M, de Smith A, Chokkalingam A, Buffler P, Wiencke JK, Wiemels JL. PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia. International Journal Of Cancer 2014, 135: 1101-1109. PMID: 24496747, PMCID: PMC4776754, DOI: 10.1002/ijc.28759.Peer-Reviewed Original ResearchMeSH KeywordsCell Transformation, NeoplasticChildChild, PreschoolDNA MethylationDNA-Binding ProteinsEnzyme ActivationEpigenesis, GeneticExtracellular Signal-Regulated MAP KinasesGene Expression Regulation, LeukemicHEK293 CellsHumansMutationPhosphorylationPrecursor Cell Lymphoblastic Leukemia-LymphomaPromoter Regions, GeneticRas ProteinsReceptor-Like Protein Tyrosine Phosphatases, Class 5Transcription FactorsTranscriptional ActivationConceptsDNA methylationPTPRG expressionDNA methylation profilesDNA methylation statusDephosphorylation of ERKMember genesEpigenetic mechanismsGene activationMutant RASRAS gene activationMethylation profilesGene expressionPtprg geneMethylation statusCell growthAdditional roleMethylationPotential therapeutic targetCell linesGenetic characteristicsGenesLeukemia phenotypeTherapeutic targetMutationsExpression