2025
Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion
Suhail Y, Du W, Afzal J, Wagner G, Kshitiz. Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion. Npj Systems Biology And Applications 2025, 11: 95. DOI: 10.1038/s41540-025-00577-z.Peer-Reviewed Original ResearchGene setsPlacental invasionHuman cancersResistance to invasionStromal genesStromal regulationCausal genesTranscriptional regulationHuman endometrial fibroblastsGenesStromal resistanceEpithelial invasionCancer malignancyEndometrial fibroblastsHuman fibroblastsCancer disseminationCancer invasionInvasionCancerFibroblastsJDP2EutheriansStage transitionsSurvey and Improvement Strategies for Gene Prioritization with Large Language Models
Neeley M, Qi G, Wang G, Tang R, Mao D, Liu C, Pasupuleti S, Yuan B, Xia F, Liu P, Liu Z, Hu X. Survey and Improvement Strategies for Gene Prioritization with Large Language Models. Bioinformatics Advances 2025, vbaf148. DOI: 10.1093/bioadv/vbaf148.Peer-Reviewed Original ResearchModeling thoracic aortic genetic variants in the zebrafish: useful for predicting clinical pathogenicity?
Prendergast A, Sheppard M, Famulski J, Nicoli S, Mukherjee S, Sips P, Elefteriades J. Modeling thoracic aortic genetic variants in the zebrafish: useful for predicting clinical pathogenicity? Frontiers In Cardiovascular Medicine 2025, 12: 1480407. PMID: 40066353, PMCID: PMC11892108, DOI: 10.3389/fcvm.2025.1480407.Peer-Reviewed Original ResearchPathogenicity of VUSProportion of variantsMedical genetic testingCausal genesPathogenicity assessmentClinical pathogensTested pathogensGenetic variantsCausative genesTAAD casesGenesGenetic defectsGenetic testingThoracic aortic aneurysmHeritable genetic defectsImpact cardiovascular morbidityPathogensVUSAortic aneurysmCardiovascular morbidityVariantsZebrafishTAADClinical applicationEnhance patient care
2024
W74. MULTI-OMICS ANALYSIS OF INTERMEDIATE PHENOTYPES REVEALS NEW RISK GENES AND PATHWAYS IN PSYCHOTIC DISORDERS
Xia C, Alliey-Rodriguez N, Tamminga C, Keshavan M, Pearlson G, Keedy S, Parker D, Bishop J, Chen C, Liu C, Gershon E. W74. MULTI-OMICS ANALYSIS OF INTERMEDIATE PHENOTYPES REVEALS NEW RISK GENES AND PATHWAYS IN PSYCHOTIC DISORDERS. European Neuropsychopharmacology 2024, 87: 141-142. DOI: 10.1016/j.euroneuro.2024.08.283.Peer-Reviewed Original ResearchTranscriptome-wide association studyGenome-wide complex trait analysisPotential causal genesQuantitative trait lociRisk genesEvent-related potentialsPolygenic risk scoresIntermediate phenotypesGene OntologyCase-control statusPsychotic disordersComplex trait analysisGenotype principal componentsIdentified risk genesGenetic correlationsMulti-omics analysisMendelian randomizationPRS-CSxPsychosis risk genesCausal genesAssociation studiesGenomic characteristicsDetect significant associationsGene associationsBipolar-Schizophrenia NetworkA genetic association study of circulating coagulation factor VIII and von Willebrand factor levels
de Vries P, Reventun P, Brown M, Heath A, Huffman J, Le N, Bebo A, Brody J, Temprano-Sagrera G, Raffield L, Ozel A, Thibord F, Jain D, Lewis J, Rodriguez B, Pankratz N, Taylor K, Polasek O, Chen M, Yanek L, Carrasquilla G, Marioni R, Kleber M, Trégouët D, Yao J, Li-Gao R, Joshi P, Trompet S, Martinez-Perez A, Ghanbari M, Howard T, Reiner A, Arvanitis M, Ryan K, Bartz T, Rudan I, Faraday N, Linneberg A, Ekunwe L, Davies G, Delgado G, Suchon P, Guo X, Rosendaal F, Klaric L, Noordam R, van Rooij F, Curran J, Wheeler M, Osburn W, O'Connell J, Boerwinkle E, Beswick A, Psaty B, Kolcic I, Souto J, Becker L, Hansen T, Doyle M, Harris S, Moissl A, Deleuze J, Rich S, van Hylckama Vlieg A, Campbell H, Stott D, Soria J, de Maat M, Almasy L, Brody L, Auer P, Mitchell B, Ben-Shlomo Y, Fornage M, Hayward C, Mathias R, Kilpeläinen T, Lange C, Cox S, März W, Morange P, Rotter J, Mook-Kanamori D, Wilson C, van der Harst P, Jukema J, Ikram M, Blangero J, Kooperberg C, Desch K, Johnson A, Sabater-Lleal M, Lowenstein C, Smith A, Morrison A, 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 C, Johnson A, 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 E, Lange L, 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 J, Smith J, Smith N, Smith T, Smith E, 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 J, 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, Ziv E, Zody M, Zoellner S, Lindstrom S, Wang L, Smith N, Gordon W, van Hylckama Vlieg A, de Andrade M, Brody J, Pattee J, Haessler J, Brumpton B, Chasman D, Suchon P, Chen M, Turman C, Germain M, Wiggins K, MacDonald J, Braekkan S, Armasu S, Pankratz N, Jackson R, Nielsen J, Giulianini F, Puurunen M, Ibrahim M, Heckbert S, Bammler T, Frazer K, McCauley B, Taylor K, Pankow J, Reiner A, Gabrielsen M, Deleuze J, O'Donnell C, Kim J, McKnight B, Kraft P, Hansen J, Rosendaal F, Heit J, Psaty B, Tang W, Kooperberg C, Hveem K, Ridker P, Morange P, Johnson A, Kabrhel C, AlexandreTrégouët D, Smith N. A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels. Blood 2024, 143: 1845-1855. PMID: 38320121, PMCID: PMC11443575, DOI: 10.1182/blood.2023021452.Peer-Reviewed Original ResearchMendelian randomizationGene-based aggregation testingImputation of genotypesGene-based analysisMulti-phenotype analysisAssociations of factor VIIIGenetic association studiesHuman umbilical vein endothelial cellsCausal genesTrans-OmicsAssociation studiesB3GNT2Genetic associationVon Willebrand factorProtein von Willebrand factorLociIdentified associationsPDIA3Umbilical vein endothelial cellsIncreased riskMeta-analysisCarrier protein von Willebrand factorVein endothelial cellsPrecision medicineEndothelial cellsGenome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder
Nievergelt C, Maihofer A, Atkinson E, Chen C, Choi K, Coleman J, Daskalakis N, Duncan L, Polimanti R, Aaronson C, Amstadter A, Andersen S, Andreassen O, Arbisi P, Ashley-Koch A, Austin S, Avdibegoviç E, Babić D, Bacanu S, Baker D, Batzler A, Beckham J, Belangero S, Benjet C, Bergner C, Bierer L, Biernacka J, Bierut L, Bisson J, Boks M, Bolger E, Brandolino A, Breen G, Bressan R, Bryant R, Bustamante A, Bybjerg-Grauholm J, Bækvad-Hansen M, Børglum A, Børte S, Cahn L, Calabrese J, Caldas-de-Almeida J, Chatzinakos C, Cheema S, Clouston S, Colodro-Conde L, Coombes B, Cruz-Fuentes C, Dale A, Dalvie S, Davis L, Deckert J, Delahanty D, Dennis M, Desarnaud F, DiPietro C, Disner S, Docherty A, Domschke K, Dyb G, Kulenović A, Edenberg H, Evans A, Fabbri C, Fani N, Farrer L, Feder A, Feeny N, Flory J, Forbes D, Franz C, Galea S, Garrett M, Gelaye B, Gelernter J, Geuze E, Gillespie C, Goleva S, Gordon S, Goçi A, Grasser L, Guindalini C, Haas M, Hagenaars S, Hauser M, Heath A, Hemmings S, Hesselbrock V, Hickie I, Hogan K, Hougaard D, Huang H, Huckins L, Hveem K, Jakovljević M, Javanbakht A, Jenkins G, Johnson J, Jones I, Jovanovic T, Karstoft K, Kaufman M, Kennedy J, Kessler R, Khan A, Kimbrel N, King A, Koen N, Kotov R, Kranzler H, Krebs K, Kremen W, Kuan P, Lawford B, Lebois L, Lehto K, Levey D, Lewis C, Liberzon I, Linnstaedt S, Logue M, Lori A, Lu Y, Luft B, Lupton M, Luykx J, Makotkine I, Maples-Keller J, Marchese S, Marmar C, Martin N, Martínez-Levy G, McAloney K, McFarlane A, McLaughlin K, McLean S, Medland S, Mehta D, Meyers J, Michopoulos V, Mikita E, Milani L, Milberg W, Miller M, Morey R, Morris C, Mors O, Mortensen P, Mufford M, Nelson E, Nordentoft M, Norman S, Nugent N, O’Donnell M, Orcutt H, Pan P, Panizzon M, Pathak G, Peters E, Peterson A, Peverill M, Pietrzak R, Polusny M, Porjesz B, Powers A, Qin X, Ratanatharathorn A, Risbrough V, Roberts A, Rothbaum A, Rothbaum B, Roy-Byrne P, Ruggiero K, Rung A, Runz H, Rutten B, de Viteri S, Salum G, Sampson L, Sanchez S, Santoro M, Seah C, Seedat S, Seng J, Shabalin A, Sheerin C, Silove D, Smith A, Smoller J, Sponheim S, Stein D, Stensland S, Stevens J, Sumner J, Teicher M, Thompson W, Tiwari A, Trapido E, Uddin M, Ursano R, Valdimarsdóttir U, Van Hooff M, Vermetten E, Vinkers C, Voisey J, Wang Y, Wang Z, Waszczuk M, Weber H, Wendt F, Werge T, Williams M, Williamson D, Winsvold B, Winternitz S, Wolf C, Wolf E, Xia Y, Xiong Y, Yehuda R, Young K, Young R, Zai C, Zai G, Zervas M, Zhao H, Zoellner L, Zwart J, deRoon-Cassini T, van Rooij S, van den Heuvel L, Stein M, Ressler K, Koenen K. Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder. Nature Genetics 2024, 56: 792-808. PMID: 38637617, PMCID: PMC11396662, DOI: 10.1038/s41588-024-01707-9.Peer-Reviewed Original ResearchConceptsMeta-analysis of genome-wide association studiesGenome-wide significant lociMulti-ancestry meta-analysisGenome-wide association analysisGenome-wide association studiesIndividuals of European ancestryPotential causal genesNative American ancestryMulti-omics approachPost-traumatic stress disorderAdmixed individualsSignificant lociRisk lociCausal genesAssociation studiesAssociation analysisFunctional genesTranscription factorsGenetic studiesAmerican ancestryEuropean ancestryAxon guidanceSynaptic structureLociGenesA multi-ancestry genetic study of pain intensity in 598,339 veterans
Toikumo S, Vickers-Smith R, Jinwala Z, Xu H, Saini D, Hartwell E, Pavicic M, Sullivan K, Xu K, Jacobson D, Gelernter J, Rentsch C, Stahl E, Cheatle M, Zhou H, Waxman S, Justice A, Kember R, Kranzler H. A multi-ancestry genetic study of pain intensity in 598,339 veterans. Nature Medicine 2024, 30: 1075-1084. PMID: 38429522, PMCID: PMC12105102, DOI: 10.1038/s41591-024-02839-5.Peer-Reviewed Original ResearchPain intensityChronic painTreat chronic painCalcium channel blockersCross-ancestry meta-analysisGenome-wide association studiesExperience of painSamples of European ancestryPain phenotypesFunctional genomics dataGABAergic neuronsCalcium channelsAnalgesic effectB-blockersDrug groupMillion Veteran ProgramPainSubstance use disordersQuality of lifeDrug repurposing analysisOpioid crisisGenetic architectureCausal genesGenetic lociGenomic data
2023
Genome-wide association study of susceptibility to hospitalised respiratory infections
Williams A, Shrine N, Gijzel H, Betts J, Chen J, Hessel E, John C, Packer R, Reeve N, Yeo A, Abner E, Åsvold B, Auvinen J, Bartz T, Bradford Y, Brumpton B, Campbell A, Cho M, Chu S, Crosslin D, Feng Q, Esko T, Gharib S, Hayward C, Hebbring S, Hveem K, Järvelin M, Jarvik G, Landis S, Larson E, Liu J, Loos R, Luo Y, Moscati A, Mullerova H, Namjou B, Porteous D, Quint J, Center R, Ritchie M, Sliz E, Stanaway I, Thomas L, Wilson J, Hall I, Wain L, Michalovich D, Tobin M. Genome-wide association study of susceptibility to hospitalised respiratory infections. Wellcome Open Research 2023, 6: 290. PMID: 39220670, PMCID: PMC11362726, DOI: 10.12688/wellcomeopenres.17230.2.Peer-Reviewed Original ResearchGenome-wide significant signalsExpression quantitative trait lociGenome-wide association studiesStage 1 analysisAssociation studiesRespiratory infection susceptibilityTranscription factor binding activityHomeodomain-containing transcription factorQuantitative trait lociFactor binding activityInverse variance-weighted meta-analysesExpression of PBX3Biological mechanismsGenome-wideUK BiobankCausal genesRespiratory infection casesTrait lociInfection susceptibilityWell-imputedTranscription factor 3Transcription factorsRespiratory infectionsSignificant signalsGenetic determinantsT102. IDENTIFYING NEW TREATMENT TARGETS FOR ALCOHOL USE DISORDER THROUGH GENETIC AND ELECTRONIC HEALTH RECORDS DATA APPROACHES
Gray J, Kranzler H, Leggio L, Piserchia Z, Winterlind E, Setzer M, Rentsch C. T102. IDENTIFYING NEW TREATMENT TARGETS FOR ALCOHOL USE DISORDER THROUGH GENETIC AND ELECTRONIC HEALTH RECORDS DATA APPROACHES. European Neuropsychopharmacology 2023, 75: s217. DOI: 10.1016/j.euroneuro.2023.08.386.Peer-Reviewed Original ResearchSeed genesGenome-wide significant lociL-type calcium channel blockerDisease-associated genesCalcium channel blockersAlcohol use disorderTargets of approved drugsPeripheral genesSignificant lociCausal genesGene identificationGene inputNetwork genesGenetic supportBiological networksChannel blockersGenesUse disorderDisease mechanismsFDA-approved drugsL-type calcium channelsRegulate dopamine activityImprove drug developmentAlpha-adrenergic receptorsSevere side effects9. THE GENETIC ARCHITECTURE OF PAIN INTENSITY IN THE MILLION VETERAN PROGRAM
Toikumo S, Vickers-Smith R, Jinwala Z, Xu H, Saini D, Hartwell E, Pavicic M, Sullivan K, Jacobson D, Cheatle M, Zhou H, Waxman S, Justice A, Kember R, Kranzler H. 9. THE GENETIC ARCHITECTURE OF PAIN INTENSITY IN THE MILLION VETERAN PROGRAM. European Neuropsychopharmacology 2023, 75: s60-s61. DOI: 10.1016/j.euroneuro.2023.08.120.Peer-Reviewed Original ResearchIndependent lociGenetic architectureMillion Veteran ProgramGenome-wide association testingIndependent genetic lociLinkage disequilibrium score regressionDrug-gene interaction databaseDisequilibrium score regressionNovel genetic variantsPotential drug targetsComplex traitsGWAS resultsCausal genesDruggable genomeDrug repurposing analysisGenetic lociDruggable genesInteraction databasesDrug targetsGenetic correlationsMolecular contributorsAssociation testingLociPsychiatric traitsScore regressionSingle‐Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population‐Level scRNA‐Seq Studies
Dillard L, Rosenow W, Calabrese G, Mesner L, Al‐Barghouthi B, Abood A, Farber E, Onengut‐Gumuscu S, Tommasini S, Horowitz M, Rosen C, Yao L, Qin L, Farber C. Single‐Cell Transcriptomics of Bone Marrow Stromal Cells in Diversity Outbred Mice: A Model for Population‐Level scRNA‐Seq Studies. Journal Of Bone And Mineral Research 2023, 38: 1350-1363. PMID: 37436066, PMCID: PMC10528806, DOI: 10.1002/jbmr.4882.Peer-Reviewed Original ResearchConceptsGene regulatory networksMesenchymal lineage cellsBone marrow-derived stromal cellsGenome-wide association studiesOsteocyte-like cellsLineage cellsOsteogenic conditionsTranscriptomic profilesSingle-cell RNA-seqCell typesTranscriptomic data setsGenetics of osteoporosisDisease-Associated VariantsSingle-cell levelMarrow-derived stromal cellsTranscriptomic perspectiveRegulatory networksCausal genesRNA-seqTranscriptomic dataScRNA-seqMesenchymal progenitorsAssociation studiesGenetic studiesLineage precursorsDepression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses
Als T, Kurki M, Grove J, Voloudakis G, Therrien K, Tasanko E, Nielsen T, Naamanka J, Veerapen K, Levey D, Bendl J, Bybjerg-Grauholm J, Zeng B, Demontis D, Rosengren A, Athanasiadis G, Bækved-Hansen M, Qvist P, Bragi Walters G, Thorgeirsson T, Stefánsson H, Musliner K, Rajagopal V, Farajzadeh L, Thirstrup J, Vilhjálmsson B, McGrath J, Mattheisen M, Meier S, Agerbo E, Stefánsson K, Nordentoft M, Werge T, Hougaard D, Mortensen P, Stein M, Gelernter J, Hovatta I, Roussos P, Daly M, Mors O, Palotie A, Børglum A. Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses. Nature Medicine 2023, 29: 1832-1844. PMID: 37464041, PMCID: PMC10839245, DOI: 10.1038/s41591-023-02352-1.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphism heritabilityGenome-wide analysisLikely causal genesFunctional genomics dataRisk variantsWide association studyPolygenic burdenPsychiatric disordersCausal genesPolygenic architectureGenomic dataRisk lociAssociation studiesSubgroups of depressionCause of disabilityDepression genetic riskCommon psychiatric disordersPrecision medicine approachCases of depressionOligodendrocyte lineageGenesLociConsiderable sex differencesGABAergic neuronsPsychiatric comorbidity
2022
Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases
Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax 2022, 78: 792-798. PMID: 36216496, PMCID: PMC10083187, DOI: 10.1136/thorax-2021-217703.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association analysisLocal genetic correlationsSingle-cell expression dataCandidate genesTranscription factorsIntegrative analysisGenomic regionsGenetic correlationsExpression dataTF target genesComplex genetic architectureTF binding sitesWide association studyPower of GWASSpecific DEGsGenetic architectureNew genesNovel genesCausal genesTarget genesGenetic basisEnrichment analysisAssociation studiesRegulatory roleAssociation analysisMutation spectrum of congenital heart disease in a consanguineous Turkish population
Dong W, Kaymakcalan H, Jin SC, Diab NS, Tanıdır C, Yalcin ASY, Ercan‐Sencicek A, Mane S, Gunel M, Lifton RP, Bilguvar K, Brueckner M. Mutation spectrum of congenital heart disease in a consanguineous Turkish population. Molecular Genetics & Genomic Medicine 2022, 10: e1944. PMID: 35481623, PMCID: PMC9184665, DOI: 10.1002/mgg3.1944.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingLaterality defectsUnique genetic architectureCongenital heart diseaseConsanguineous familyGenetic architectureCausal genesCHD genesGenome analysisHomozygous variantGenetic landscapeGenetic lesionsGenomic alterationsHeart diseaseConsanguineous populationFunction variantsRecessive variantsCHD probandsGenesType of CHDMutation spectrumStructural congenital heart diseaseVariantsCHD subjectsAdditional patients
2021
A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR
Xu M, Mehl L, Zhang T, Thakur R, Sowards H, Myers T, Jessop L, Chesi A, Johnson M, Wells A, Michael H, Bunda P, Jones K, Higson H, Hennessey R, Jermusyk A, Kovacs M, Landi M, Iles M, Goldstein A, Consortium M, Choi J, Chanock S, Grant S, Chari R, Merlino G, Law M, Brown K. A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR. American Journal Of Human Genetics 2021, 108: 1611-1630. PMID: 34343493, PMCID: PMC8456165, DOI: 10.1016/j.ajhg.2021.07.002.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBasic Helix-Loop-Helix Transcription FactorsCarcinogenesisCarcinoma, Squamous CellChromatinChromosomes, Human, Pair 7Gene Expression RegulationGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyGenome, HumanHumansMelanocytesMelanomaPolychlorinated DibenzodioxinsPolymorphism, Single NucleotidePrimary Cell CulturePromoter Regions, GeneticReceptors, Aryl HydrocarbonSkin NeoplasmsSunbathingUltraviolet RaysConceptsGenome-wide association studiesAryl hydrocarbon receptorMelanoma genome‐wide association studiesCellular responsesFunctional variantsLikely causal genesChromatin state annotationCandidate causal variantsHydrocarbon receptorMelanoma susceptibility genesGrowth phenotypeAhR expressionCausal genesPrimary melanocytesCausal variantsLead SNPRisk lociAhR bindingAssociation studiesGrowth arrestLuciferase assaySusceptibility genesCell growthKey environmental exposuresLociIntegrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization
Pathak GA, Singh K, Miller-Fleming TW, Wendt FR, Ehsan N, Hou K, Johnson R, Lu Z, Gopalan S, Yengo L, Mohammadi P, Pasaniuc B, Polimanti R, Davis LK, Mancuso N. Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization. Nature Communications 2021, 12: 4569. PMID: 34315903, PMCID: PMC8316582, DOI: 10.1038/s41467-021-24824-z.Peer-Reviewed Original ResearchConceptsPutative causal genesGenome-wide association studiesUnderstanding of genesIntegrative genomic analysisTrans-ethnic studiesAssociation scanCausal genesGenomic analysisAssociation studiesDiverse ancestral backgroundsGenesSusceptibility genesBiobank JapanHost geneticsProtein levelsAncestral backgroundPathwayExpressionMRNA expressionSplicingRapid progressPhenomeGeneticsHost inflammatory responseCoagulation pathway
2020
A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer
Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt S, Borgida A, Bracci PM, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Canzian F, Childs EJ, Cotterchio M, Du M, Duell EJ, Fuchs C, Gallinger S, Gaziano JM, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Holly EA, Klein EA, Kogevinas M, Kurtz RJ, LeMarchand L, Malats N, Männistö S, Milne R, Neale RE, Ng K, Obazee O, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Rothman N, Scelo G, Sesso HD, Severi G, Sieri S, Silverman D, Sund M, Tjønneland A, Thornquist MD, Tobias GS, Trichopoulou A, Van Den Eeden SK, Visvanathan K, Wactawski-Wende J, Wentzensen N, White E, Yu H, Yuan C, Zeleniuch-Jacquotte A, Hoover R, Brown K, Kooperberg C, Risch HA, Jacobs EJ, Li D, Yu K, Shu XO, Chanock SJ, Wolpin BM, Stolzenberg-Solomon RZ, Chatterjee N, Klein AP, Smith JP, Kraft P, Shi J, Petersen GM, Zheng W, Amundadottir LT. A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. Journal Of The National Cancer Institute 2020, 112: 1003-1012. PMID: 31917448, PMCID: PMC7566474, DOI: 10.1093/jnci/djz246.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association studyCancer risk lociRisk lociAssociation studiesPancreatic cancer susceptibility lociGene expression prediction modelsNovel candidate susceptibility genesPossible causal genesGenome-wide association studiesGenome-wide associationCancer susceptibility lociCandidate susceptibility genesNormal pancreatic tissue samplesFunctional genesTranscriptome dataCausal genesNovel lociCandidate genesGene expressionSusceptibility lociGenesGenotype dataLociSusceptibility genesDifferent tissuesApplying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy
Lek A, Zhang Y, Woodman KG, Huang S, DeSimone AM, Cohen J, Ho V, Conner J, Mead L, Kodani A, Pakula A, Sanjana N, King OD, Jones PL, Wagner KR, Lek M, Kunkel LM. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Science Translational Medicine 2020, 12 PMID: 32213627, PMCID: PMC7304480, DOI: 10.1126/scitranslmed.aay0271.Peer-Reviewed Original ResearchConceptsGenome-wide CRISPRCellular hypoxia responseFacioscapulohumeral muscular dystrophyHypoxia responseCell deathTherapeutic discoveryGenome-wide perturbationsComplex genetic diseasesEmergence of CRISPRUnbiased genetic screeningSelection assaysGene-editing technologyDUX4 proteinCausal genesDUX4 expressionZebrafish modelEpigenetic changesProtein turnoverMuscular dystrophyCRISPRMyogenic lineDUX4Genetic diseasesGenesMechanistic understandingGenome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis
Allen RJ, Guillen-Guio B, Oldham JM, Ma SF, Dressen A, Paynton ML, Kraven LM, Obeidat M, Li X, Ng M, Braybrooke R, Molina-Molina M, Hobbs BD, Putman RK, Sakornsakolpat P, Booth HL, Fahy WA, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Whyte MKB, Zhang Y, Kaminski N, Adegunsoye A, Strek ME, Neighbors M, Sheng XR, Gudmundsson G, Gudnason V, Hatabu H, Lederer DJ, Manichaikul A, Newell JD, O’Connor G, Ortega VE, Xu H, Fingerlin TE, Bossé Y, Hao K, Joubert P, Nickle DC, Sin DD, Timens W, Furniss D, Morris AP, Zondervan KT, Hall IP, Sayers I, Tobin MD, Maher TM, Cho MH, Hunninghake GM, Schwartz DA, Yaspan BL, Molyneaux PL, Flores C, Noth I, Jenkins RG, Wain LV. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2020, 201: 564-574. PMID: 31710517, PMCID: PMC7047454, DOI: 10.1164/rccm.201905-1017oc.Peer-Reviewed Original ResearchMeSH KeywordsAgedCase-Control StudiesCell Cycle ProteinsFemaleGene ExpressionGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansIdiopathic Pulmonary FibrosisIntracellular Signaling Peptides and ProteinsKinesinsMaleMiddle AgedRisk AssessmentSignal TransductionSpindle ApparatusTOR Serine-Threonine KinasesConceptsGenome-wide association studiesAssociation studiesIPF susceptibilityNew genome-wide significant signalsGenome-wide significant signalsGenome-wide analysisCell-cell adhesionLarge genome-wide association studiesImportance of mTORPolygenic risk score analysisTelomere maintenanceCausal genesFunctional analysisSusceptibility variantsRisk score analysisMultiple pathwaysGenetic associationGenesHost defensePolygenic risk scoresIndependent studiesPossible roleExpression associatesSignificant signalRecent studies
2019
Cell-Autonomous Hedgehog Signaling Is Not Required for Cyst Formation in Autosomal Dominant Polycystic Kidney Disease
Ma M, Legué E, Tian X, Somlo S, Liem KF. Cell-Autonomous Hedgehog Signaling Is Not Required for Cyst Formation in Autosomal Dominant Polycystic Kidney Disease. Journal Of The American Society Of Nephrology 2019, 30: 2103-2111. PMID: 31451534, PMCID: PMC6830786, DOI: 10.1681/asn.2018121274.Peer-Reviewed Original ResearchConceptsHedgehog pathwayPolycystin-1Polycystin-2Autosomal dominant polycystic kidney diseaseMain causal genePolycystic kidney diseaseKidney cyst formationEpithelial cellsLevels of HedgehogCiliary genesDominant polycystic kidney diseaseMutant mouse kidneysRenal epithelial cellsCausal genesSignal transductionCell signalingGenetic manipulationPrimary ciliaCyst formationMultipass transmembraneHedgehog signalingConditional inactivationUnknown pathwayHedgehogKidney phenotype
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