2020
Genotyping Array Design and Data Quality Control in the Million Veteran Program
Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji SG, Sun N, Webster T, Liem A, Hsieh P, Devineni P, Karnam P, Gong X, Radhakrishnan L, Schmidt J, Assimes TL, Huang J, Pan C, Humphries D, Brophy M, Moser J, Muralidhar S, Huang GD, Przygodzki R, Concato J, Gaziano JM, Gelernter J, O’Donnell C, Hauser ER, Zhao H, O’Leary T, Program V, Tsao PS, Pyarajan S. Genotyping Array Design and Data Quality Control in the Million Veteran Program. American Journal Of Human Genetics 2020, 106: 535-548. PMID: 32243820, PMCID: PMC7118558, DOI: 10.1016/j.ajhg.2020.03.004.Peer-Reviewed Original ResearchConceptsMillion Veteran ProgramGenome-wide association studiesGenome-wide scanHigh-quality genotypesArray-based genotypingWhole-genome sequencingNon-European individualsAssociation studiesGenetic markersOmics assaysAxiom arrayDownstream analysisVeteran ProgramCommon variantsGenetic associationAfrican American ancestryAmerican ancestryMVP cohortRare variantsSingle assayDiversityFurther data releasesLarge biobanksPromising resourceQuality control
2017
Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence
Hancock DB, Guo Y, Reginsson GW, Gaddis NC, Lutz SM, Sherva R, Loukola A, Minica CC, Markunas CA, Han Y, Young KA, Gudbjartsson DF, Gu F, McNeil DW, Qaiser B, Glasheen C, Olson S, Landi MT, Madden PAF, Farrer LA, Vink J, Saccone NL, Neale MC, Kranzler HR, McKay J, Hung RJ, Amos CI, Marazita ML, Boomsma DI, Baker TB, Gelernter J, Kaprio J, Caporaso NE, Thorgeirsson TE, Hokanson JE, Bierut LJ, Stefansson K, Johnson EO. Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence. Molecular Psychiatry 2017, 23: 1911-1919. PMID: 28972577, PMCID: PMC5882602, DOI: 10.1038/mp.2017.193.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesGenotype-Tissue Expression (GTEx) projectDNA methyltransferase genesAcetylcholine receptor genesNicotine dependenceMethyltransferase geneExpression projectCHRNB4 genesHeritable traitAdditional lociProxy phenotypeSequence variantsDNMT3B expressionGenesReceptor geneSquamous cell lung carcinomaCHRNA5-CHRNA3African American ancestryNovel associationsInternational Lung Cancer ConsortiumCell lung carcinomaLociAmerican ancestryAdult cerebellum