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 hitsInvestigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia
Xu K, Li S, Pandey P, Kang AY, Morimoto LM, Mancuso N, Ma X, Metayer C, Wiemels JL, de Smith AJ. Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia. Human Molecular Genetics 2022, 31: 3741-3756. PMID: 35717575, PMCID: PMC9616572, DOI: 10.1093/hmg/ddac137.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesSingle nucleotide polymorphismsGenetic risk lociDNA methylationRisk single nucleotide polymorphismsRisk lociAssociation studiesHeritable genetic variationGenome-wide association studiesMost single nucleotide polymorphismsDNA methylation differencesNon-European populationsEpigenetic mechanismsGenetic variationMethylation differencesSignificant DMPsPromoter regionFunctional pathwaysCpG positionsAssociation analysisFunctional roleMethylationNucleotide polymorphismsLociBlood DNA
2018
BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia
de Smith AJ, Walsh KM, Francis SS, Zhang C, Hansen HM, Smirnov I, Morimoto L, Whitehead TP, Kang A, Shao X, Barcellos LF, McKean‐Cowdin R, Zhang L, Fu C, Wang R, Yu H, Hoh J, Dewan AT, Metayer C, Ma X, Wiemels JL. BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia. International Journal Of Cancer 2018, 143: 2647-2658. PMID: 29923177, PMCID: PMC6235695, DOI: 10.1002/ijc.31622.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultCaliforniaCell Cycle ProteinsChildChromosome MappingChromosomes, Human, Pair 10Core Binding Factor Alpha 1 SubunitEnhancer Elements, GeneticFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansK562 CellsLinkage DisequilibriumLogistic ModelsMalePhosphotransferases (Alcohol Group Acceptor)Polycomb Repressive Complex 1Polymorphism, Single NucleotidePrecursor Cell Lymphoblastic Leukemia-LymphomaTrans-ActivatorsYoung AdultConceptsFunctional variantsSingle nucleotide polymorphism (SNP) imputationGenome-wide significant associationGenome-wide association studiesStem cell enhancerPutative functional variantsChIP-seq dataRegion of associationGenetic Epidemiology ResearchChromosome 10p12Transcription factorsAdmixed AmericansCell enhancerLead SNPAssociation studiesSNP associationsAssociation analysisLinkage disequilibriumBMI1SNPsTight linkage disequilibriumPIP4K2APreferential bindingRisk allelesVariants