2023
Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma
Recto K, Kachroo P, Huan T, Van Den Berg D, Lee G, Bui H, Lee D, Gereige J, Yao C, Hwang S, Joehanes R, Weiss S, Consortium N, Abe N, Abecasis G, Aguet F, Albert C, Almasy L, Alonso A, Ament S, Anderson P, Anugu P, Applebaum-Bowden D, Ardlie K, Arking D, Arnett D, Ashley-Koch A, Aslibekyan S, Assimes T, Auer P, Avramopoulos D, Ayas N, Balasubramanian A, Barnard J, Barnes K, Barr R, Barron-Casella E, Barwick L, Beaty T, Beck G, Becker D, Becker L, Beer R, Beitelshees A, Benjamin E, Benos T, Bezerra M, Bielak L, Bis J, Blackwell T, Blangero J, Blue N, Boerwinkle E, Bowden D, Bowler R, Brody J, Broeckel U, Broome J, Brown D, Bunting K, Burchard E, Bustamante C, Buth E, Cade B, Cardwell J, Carey V, Carrier J, Carson A, Carty C, Casaburi R, Romero J, Casella J, Castaldi P, Chaffin M, Chang C, Chang Y, Chasman D, Chavan S, Chen B, Chen W, Chen Y, Cho M, Choi S, Chuang L, Chung M, Chung R, Clish C, Comhair S, Conomos M, Cornell E, Correa A, Crandall C, Crapo J, Cupples L, Curran J, Curtis J, Custer B, Damcott C, Darbar D, David S, Davis C, Daya M, de Andrade M, de las Fuentes L, de Vries P, DeBaun M, Deka R, DeMeo D, Devine S, Dinh H, Doddapaneni H, Duan Q, Dugan-Perez S, Duggirala R, Durda J, Dutcher S, Eaton C, Ekunwe L, Boueiz A, Ellinor P, Emery L, Erzurum S, Farber C, Farek J, Fingerlin T, Flickinger M, Fornage M, Franceschini N, Frazar C, Fu M, Fullerton S, Fulton L, Gabriel S, Gan W, Gao S, Gao Y, Gass M, Geiger H, Gelb B, Geraci M, Germer S, Gerszten R, Ghosh A, Gibbs R, Gignoux C, Gladwin M, Glahn D, Gogarten S, Gong D, Goring H, Graw S, Gray K, Grine D, Gross C, Gu C, Guan Y, Guo X, Gupta N, Haessler J, Hall M, Han Y, Hanly P, Harris D, Hawley N, He J, Heavner B, Heckbert S, Hernandez R, Herrington D, Hersh C, Hidalgo B, Hixson J, Hobbs B, Hokanson J, Hong E, Hoth K, Hsiung C, Hu J, Hung Y, Huston H, Hwu C, Irvin M, Jackson R, Jain D, Jaquish C, Johnsen J, Johnson A, Johnson C, Johnston R, Jones K, Kang H, Kaplan R, Kardia S, Kelly S, Kenny E, Kessler M, Khan A, Khan Z, Kim W, Kimoff J, Kinney G, Konkle B, Kooperberg C, Kramer H, Lange C, Lange E, Lange L, Laurie C, Laurie C, LeBoff M, Lee J, Lee S, Lee W, LeFaive J, Levine D, Levy D, Lewis J, Li X, Li Y, Lin H, Lin H, Lin X, Liu S, Liu Y, Liu Y, Loos R, Lubitz S, Lunetta K, Luo J, Magalang U, Mahaney M, Make B, Manichaikul A, Manning A, Manson J, Martin L, Marton M, Mathai S, Mathias R, May S, McArdle P, McDonald M, McFarland S, McGarvey S, McGoldrick D, McHugh C, McNeil B, Mei H, Meigs J, Menon V, Mestroni L, Metcalf G, Meyers D, Mignot E, Mikulla J, Min N, Minear M, Minster R, Mitchell B, Moll M, Momin Z, Montasser M, Montgomery C, Muzny D, Mychaleckyj J, Nadkarni G, Naik R, Naseri T, Natarajan P, Nekhai S, Nelson S, Neltner B, Nessner C, Nickerson D, Nkechinyere O, North K, O'Connell J, O'Connor T, Ochs-Balcom H, Okwuonu G, Pack A, Paik D, Palmer N, Pankow J, Papanicolaou G, Parker C, Peloso G, Peralta J, Perez M, Perry J, Peters U, Peyser P, Phillips L, Pleiness J, Pollin T, Post W, Becker J, Boorgula M, Preuss M, Psaty B, Qasba P, Qiao D, Qin Z, Rafaels N, Raffield L, Rajendran M, Ramachandran V, Rao D, Rasmussen-Torvik L, Ratan A, Redline S, Reed R, Reeves C, Regan E, Reiner A, Reupena M, Rice K, Rich S, Robillard R, Robine N, Roden D, Roselli C, Rotter J, Ruczinski I, Runnels A, Russell P, Ruuska S, Ryan K, Sabino E, Saleheen D, Salimi S, Salvi S, Salzberg S, Sandow K, Sankaran V, Santibanez J, Schwander K, Schwartz D, Sciurba F, Seidman C, Seidman J, Sériès F, Sheehan V, Sherman S, Shetty A, Shetty A, Sheu W, Shoemaker M, Silver B, Silverman E, Skomro R, Smith A, Smith J, Smith J, Smith N, Smith T, Smoller S, Snively B, Snyder M, Sofer T, Sotoodehnia N, Stilp A, Storm G, Streeten E, Su J, Sung Y, Sylvia J, Szpiro A, Taliun D, Tang H, Taub M, Taylor K, Taylor M, Taylor S, Telen M, Thornton T, Threlkeld M, Tinker L, Tirschwell D, Tishkoff S, Tiwari H, Tong C, Tracy R, Tsai M, Vaidya D, Van Den Berg D, VandeHaar P, Vrieze S, Walker T, Wallace R, Walts A, Wang F, Wang H, Wang J, Watson K, Watt J, Weeks D, Weinstock J, Weir B, Weiss S, Weng L, Wessel J, Willer C, Williams K, Williams L, Williams S, Wilson C, Wilson J, Winterkorn L, Wong Q, Wu B, Wu J, Xu H, Yanek L, Yang I, Yu K, Zekavat S, Zhang Y, Zhao S, Zhao W, Zhu X, Ziv E, Zody M, Zoellner S, O’Connor G, Levy D, DeMeo D. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma. EBioMedicine 2023, 95: 104758. PMID: 37598461, PMCID: PMC10462855, DOI: 10.1016/j.ebiom.2023.104758.Peer-Reviewed Original ResearchMeSH KeywordsAsthmaChildDNA MethylationEpigenomeFemaleGenome-Wide Association StudyHumansImmunoglobulin EMaleUbiquitin ThiolesteraseConceptsMethylation quantitative trait lociAssociation studiesNovel epigenetic signatureIdentifies novel targetsQuantitative trait lociTranscription factor bindingEpigenome-wide association studiesGene ontology analysisWide association studyClosest genesTrait lociCausal regulatorsDrug target analysisTranscription patternsOntology analysisDNA methylationEpigenetic signaturesFactor bindingGene expressionMolecular mechanismsMendelian randomizationCosta Rica StudyPotential therapeutic targetNovel targetGenetic epidemiologyMulti-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing
Chen F, Wang X, Jang S, Quach B, Weissenkampen J, Khunsriraksakul C, Yang L, Sauteraud R, Albert C, Allred N, Arnett D, Ashley-Koch A, Barnes K, Barr R, Becker D, Bielak L, Bis J, Blangero J, Boorgula M, Chasman D, Chavan S, Chen Y, Chuang L, Correa A, Curran J, David S, Fuentes L, Deka R, Duggirala R, Faul J, Garrett M, Gharib S, Guo X, Hall M, Hawley N, He J, Hobbs B, Hokanson J, Hsiung C, Hwang S, Hyde T, Irvin M, Jaffe A, Johnson E, Kaplan R, Kardia S, Kaufman J, Kelly T, Kleinman J, Kooperberg C, Lee I, Levy D, Lutz S, Manichaikul A, Martin L, Marx O, McGarvey S, Minster R, Moll M, Moussa K, Naseri T, North K, Oelsner E, Peralta J, Peyser P, Psaty B, Rafaels N, Raffield L, Reupena M, Rich S, Rotter J, Schwartz D, Shadyab A, Sheu W, Sims M, Smith J, Sun X, Taylor K, Telen M, Watson H, Weeks D, Weir D, Yanek L, Young K, Young K, Zhao W, Hancock D, Jiang B, Vrieze S, Liu D. Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nature Genetics 2023, 55: 291-300. PMID: 36702996, PMCID: PMC9925385, DOI: 10.1038/s41588-022-01282-x.Peer-Reviewed Original ResearchMeSH KeywordsBiologyDrug RepositioningGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansPolymorphism, Single NucleotideTobacco UseTranscriptomeConceptsTWAS methodsExpression quantitative trait loci (eQTL) dataQuantitative trait loci dataTranscriptome-wide associationWide association studyGenome-wide association study summary statisticsWhole genome sequencesSubsequent fine mappingEQTL datasetNew genesLoci dataFine mappingPhenotypic effectsTobacco use phenotypesDiverse ancestryAssociation studiesBiological relevanceEuropean ancestryGenesAncestryGWASSummary statisticsBiologyDrug repurposingDiversity
2022
Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension
Kelly TN, Sun X, He KY, Brown MR, Taliun SAG, Hellwege JN, Irvin MR, Mi X, Brody JA, Franceschini N, Guo X, Hwang SJ, de Vries PS, Gao Y, Moscati A, Nadkarni GN, Yanek LR, Elfassy T, Smith JA, Chung RH, Beitelshees AL, Patki A, Aslibekyan S, Blobner BM, Peralta JM, Assimes TL, Palmas WR, Liu C, Bress AP, Huang Z, Becker LC, Hwa CM, O’Connell J, Carlson JC, Warren HR, Das S, Giri A, Martin LW, Johnson W, Fox ER, Bottinger EP, Razavi AC, Vaidya D, Chuang LM, Chang YC, Naseri T, Jain D, Kang HM, Hung AM, Srinivasasainagendra V, Snively BM, Gu D, Montasser ME, Reupena M, Heavner BD, LeFaive J, Hixson JE, Rice KM, Wang FF, Nielsen JB, Huang J, Khan AT, Zhou W, Nierenberg JL, Laurie CC, Armstrong ND, Shi M, Pan Y, Stilp AM, Emery L, Wong Q, Hawley NL, Minster RL, Curran JE, Munroe PB, Weeks DE, North KE, Tracy RP, Kenny EE, Shimbo D, Chakravarti A, Rich SS, Reiner AP, Blangero J, Redline S, Mitchell BD, Rao DC, Chen Y, Kardia SLR, Kaplan RC, Mathias RA, He J, Psaty BM, Fornage M, Loos RJF, Correa A, Boerwinkle E, Rotter JI, Kooperberg C, Edwards TL, Abecasis GR, Zhu X, Levy D, Arnett DK, Morrison AC. Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension. Hypertension 2022, 79: 1656-1667. PMID: 35652341, PMCID: PMC9593435, DOI: 10.1161/hypertensionaha.122.19324.Peer-Reviewed Original ResearchMeSH KeywordsBlood PressureGenome-Wide Association StudyGenomicsHumansHypertensionPolymorphism, Single NucleotidePrecision MedicineConceptsDiastolic blood pressureSystolic blood pressureBlood pressureSequencing dataNovel common variantsWhole-genome sequencing dataGenome-wide significanceAllele frequency spectrumGenome sequencing studiesWhole-genome sequencing analysisLower systolic blood pressureWhole-exome sequencing dataStage 1Future blood pressureNovel lociTrans-OmicsIntergenic variantsVariant findingsSequencing studiesMillion Veteran ProgramUK Biobank participantsSequencing analysisCommon variantsBlood pressure signalsStroke participants
2021
Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease
Katz D, Tahir U, Bick A, Pampana A, Ngo D, Benson M, Yu Z, Robbins J, Chen Z, Cruz D, Deng S, Farrell L, Sinha S, Schmaier A, Shen D, Gao Y, Hall M, Correa A, Tracy R, Durda P, Taylor K, Liu Y, Johnson W, Guo X, Yao J, Ida Chen Y, Manichaikul A, Jain D, Bouchard C, Sarzynski M, Rich S, Rotter J, Wang T, Wilson J, Natarajan P, Gerszten R, Abe N, Abecasis G, Aguet F, Albert C, Almasy L, Alonso A, Ament S, Anderson P, Anugu P, Applebaum-Bowden D, Ardlie K, Arking D, Arnett D, Ashley-Koch A, Aslibekyan S, Assimes T, Auer P, Avramopoulos D, Ayas N, Balasubramanian A, Barnard J, Barnes K, Barr R, Barron-Casella E, Barwick L, Beaty T, Beck G, Becker D, Becker L, Beer R, Beitelshees A, Benjamin E, Benos T, Bezerra M, Bielak L, Bis J, Blackwell T, Blangero J, Boerwinkle E, Bowden D, Bowler R, Brody J, Broeckel U, Broome J, Brown D, Bunting K, Burchard E, Bustamante C, Buth E, Cade B, Cardwell J, Carey V, Carrier J, Carson A, Carty C, Casaburi R, Casas Romero J, Casella J, Castaldi P, Chaffin M, Chang C, Chang Y, Chasman D, Chavan S, Chen B, Chen W, Chen Y, Cho M, Choi S, Chuang L, Chung M, Chung R, Clish C, Comhair S, Conomos M, Cornell E, Correa A, Crandall C, Crapo J, Cupples L, Curran J, Curtis J, Custer B, Damcott C, Darbar D, David S, Davis C, Daya M, de Andrade M, de las Fuentes L, de Vries P, DeBaun M, Deka R, DeMeo D, Devine S, Dinh H, Doddapaneni H, Duan Q, Dugan-Perez S, Duggirala R, Durda J, Dutcher S, Eaton C, Ekunwe L, El Boueiz A, Ellinor P, Emery L, Erzurum S, Farber C, Farek J, Fingerlin T, Flickinger M, Fornage M, Franceschini N, Frazar C, Fu M, Fullerton S, Fulton L, Gabriel S, Gan W, Gao S, Gao Y, Gass M, Geiger H, Gelb B, Geraci M, Germer S, Gerszten R, Ghosh A, Gibbs R, Gignoux C, Gladwin M, Glahn D, Gogarten S, Gong D, Goring H, Graw S, Gray K, Grine D, Gross C, Gu C, Guan Y, Guo X, Gupta N, Haas D, Haessler J, Hall M, Han Y, Hanly P, Harris D, Hawley N, He J, Heavner B, Heckbert S, Hernandez R, Herrington D, Hersh C, Hidalgo B, Hixson J, Hobbs B, Hokanson J, Hong E, Hoth K, Hsiung C, Hu J, Hung Y, Huston H, Hwu C, Irvin M, Jackson R, Jain D, Jaquish C, Johnsen J, Johnson A, Johnson C, Johnston R, Jones K, Kang H, Kaplan R, Kardia S, Kelly S, Kenny E, Kessler M, Khan A, Khan Z, Kim W, Kimoff J, Kinney G, Konkle B, Kooperberg C, Kramer H, Lange C, Lange E, Lange L, Laurie C, Laurie C, LeBoff M, Lee J, Lee S, Lee W, LeFaive J, Levine D, Levy D, Lewis J, Li X, Li Y, Lin H, Lin H, Lin X, Liu S, Liu Y, Liu Y, Loos R, Lubitz S, Lunetta K, Luo J, Magalang U, Mahaney M, Make B, Manichaikul A, Manning A, Manson J, Martin L, Marton M, Mathai S, Mathias R, May S, McArdle P, McDonald M, McFarland S, McGarvey S, McGoldrick D, McHugh C, McNeil B, Mei H, Meigs J, Menon V, Mestroni L, Metcalf G, Meyers D, Mignot E, Mikulla J, Min N, Minear M, Minster R, Mitchell B, Moll M, Momin Z, Montasser M, Montgomery C, Muzny D, Mychaleckyj J, Nadkarni G, Naik R, Naseri T, Natarajan P, Nekhai S, Nelson S, Neltner B, Nessner C, Nickerson D, Nkechinyere O, North K, O’Connell J, O’Connor T, Ochs-Balcom H, Okwuonu G, Pack A, Paik D, Palmer N, Pankow J, Papanicolaou G, Parker C, Peloso G, Peralta J, Perez M, Perry J, Peters U, Peyser P, Phillips L, Pleiness J, Pollin T, Post W, Powers Becker J, Preethi Boorgula M, Preuss M, Psaty B, Qasba P, Qiao D, Qin Z, Rafaels N, Raffield L, Rajendran M, Ramachandran V, Rao D, Rasmussen-Torvik L, Ratan A, Redline S, Reed R, Reeves C, Regan E, Reiner A, Reupena M, Rice K, Rich S, Robillard R, Robine N, Roden D, Roselli C, Rotter J, Ruczinski I, Runnels A, Russell P, Ruuska S, Ryan K, Sabino E, Saleheen D, Salimi S, Salvi S, Salzberg S, Sandow K, Sankaran V, Santibanez J, Schwander K, Schwartz D, Sciurba F, Seidman C, Seidman J, Sériès F, Sheehan V, Sherman S, Shetty A, Shetty A, Sheu W, Shoemaker M, Silver B, Silverman E, Skomro R, Smith A, Smith J, Smith J, Smith N, Smith T, Smoller S, Snively B, Snyder M, Sofer T, Sotoodehnia N, Stilp A, Storm G, Streeten E, Su J, Sung Y, Sylvia J, Szpiro A, Taliun D, Tang H, Taub M, Taylor K, Taylor M, Taylor S, Telen M, Thornton T, Threlkeld M, Tinker L, Tirschwell D, Tishkoff S, Tiwari H, Tong C, Tracy R, Tsai M, Vaidya D, Van Den Berg D, VandeHaar P, Vrieze S, Walker T, Wallace R, Walts A, Wang F, Wang H, Wang J, Watson K, Watt J, Weeks D, Weinstock J, Weir B, Weiss S, Weng L, Wessel J, Willer C, Williams K, Williams L, Wilson C, Wilson J, Winterkorn L, Wong Q, Wu J, Xu H, Yanek L, Yang I, Yu K, Zekavat S, Zhang Y, Zhao S, Zhao W, Zhu X, Zody M, Zoellner S. Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease. Circulation 2021, 145: 357-370. PMID: 34814699, PMCID: PMC9158509, DOI: 10.1161/circulationaha.121.055117.Peer-Reviewed Original ResearchMeSH KeywordsAdultBlack PeopleCardiovascular DiseasesFemaleGenome-Wide Association StudyHumansMaleProteomeConceptsWhole genome sequence analysisGenome sequence analysisWhole genome sequencing association analysisPlasma proteomeSequence analysisNovel pleiotropic lociNovel genetic determinantsNew protein associationsNew biological mechanismsGenetic architectureNon-European populationsPleiotropic lociGenotyping arraysProtein associationProteomic profilingGene locusGenetic regionsProteomics platformFunctional importanceAssociation analysisProteomeAfrican ancestryGenetic determinantsNovel insightsProtein
2020
Genome-wide association studies in Samoans give insight into the genetic architecture of fasting serum lipid levels
Carlson JC, Weeks DE, Hawley NL, Sun G, Cheng H, Naseri T, Reupena M, Tuitele J, Deka R, McGarvey ST, Minster RL. Genome-wide association studies in Samoans give insight into the genetic architecture of fasting serum lipid levels. Journal Of Human Genetics 2020, 66: 111-121. PMID: 32759990, PMCID: PMC7785639, DOI: 10.1038/s10038-020-0816-9.Peer-Reviewed Original ResearchMeSH KeywordsAdultApolipoprotein A-IApolipoproteins ECholesterol Ester Transfer ProteinsCholesterol, HDLCholesterol, LDLCohort StudiesFastingFemaleGenetic MarkersGenome-Wide Association StudyHumansLipid MetabolismLipidsMaleMiddle AgedPolymorphism, Single NucleotideQuantitative Trait LociSamoaTriglyceridesConceptsGenome-wide association studiesGenetic architectureAssociation studiesGenome-wide significant associationDifferent association signalsUnique population historyPopulation bottlenecksLipid lociPopulation historyAssociation signalsSuggestive associationRab21Current understandingMGAT1Association of variantsReplication cohortLipidsBiological foundationsVariantsLociLow-density lipoproteinInsightsPopulationLipid levelsHigh-density lipoprotein
2016
A thrifty variant in CREBRF strongly influences body mass index in Samoans
Minster RL, Hawley NL, Su CT, Sun G, Kershaw EE, Cheng H, Buhule OD, Lin J, Reupena MS, Viali S, Tuitele J, Naseri T, Urban Z, Deka R, Weeks DE, McGarvey ST. A thrifty variant in CREBRF strongly influences body mass index in Samoans. Nature Genetics 2016, 48: 1049-1054. PMID: 27455349, PMCID: PMC5069069, DOI: 10.1038/ng.3620.Peer-Reviewed Original Research