2024
HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Cheng Y, Cai B, Li H, Zhang X, D’Souza G, Shrestha S, Edmonds A, Meyers J, Fischl M, Kassaye S, Anastos K, Cohen M, Aouizerat B, Xu K, Zhao H. HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data. Genome Biology 2024, 25: 273. PMID: 39407252, PMCID: PMC11476968, DOI: 10.1186/s13059-024-03411-7.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociQuantitative trait lociTrait lociMethylation dataFunctional annotation of genetic variantsAnnotation of genetic variantsGenetic variantsBisulfite sequencing dataEffects of genetic variantsBiologically relevant cell typesDNA methylation levelsCell typesFunctional annotationSequence dataComplex traitsMethylation datasetsRelevant cell typesMeQTLsMethylation levelsMethylation regulatorsReal data analysesLociVariantsMethylationDNA
2023
Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use
Fang F, Quach B, Lawrence K, van Dongen J, Marks J, Lundgren S, Lin M, Odintsova V, Costeira R, Xu Z, Zhou L, Mandal M, Xia Y, Vink J, Bierut L, Ollikainen M, Taylor J, Bell J, Kaprio J, Boomsma D, Xu K, Sandler D, Hancock D, Johnson E. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use. Molecular Psychiatry 2023, 29: 124-133. PMID: 37935791, PMCID: PMC11078760, DOI: 10.1038/s41380-023-02310-w.Peer-Reviewed Original ResearchEpigenome-wide association studiesDNA methylationCpG sitesDNA methylation changesEpigenome-wide associationSignificant CpG sitesMethylation changesBlood-based DNA methylationAssociation studiesSignificant CpGsEWAS analysisFalse discovery rateMethylationHealth outcomesLifetime cannabisCigarette smokingDiscovery rateMethylation scoreADGRF1APOBRACTN1SitesADAM12CpGEnvironmental exposures