2025
Psychiatric genetics in the diverse landscape of Latin American populations
Bruxel E, Rovaris D, Belangero S, Chavarría-Soley G, Cuellar-Barboza A, Martínez-Magaña J, Nagamatsu S, Nievergelt C, Núñez-Ríos D, Ota V, Peterson R, Sloofman L, Adams A, Albino E, Alvarado A, Andrade-Brito D, Arguello-Pascualli P, Bandeira C, Bau C, Bulik C, Buxbaum J, Cappi C, Corral-Frias N, Corrales A, Corsi-Zuelli F, Crowley J, Cupertino R, da Silva B, De Almeida S, De la Hoz J, Forero D, Fries G, Gelernter J, González-Giraldo Y, Grevet E, Grice D, Hernández-Garayua A, Hettema J, Ibáñez A, Ionita-Laza I, Lattig M, Lima Y, Lin Y, López-León S, Loureiro C, Martínez-Cerdeño V, Martínez-Levy G, Melin K, Moreno-De-Luca D, Muniz Carvalho C, Olivares A, Oliveira V, Ormond R, Palmer A, Panzenhagen A, Passos-Bueno M, Peng Q, Pérez-Palma E, Prieto M, Roussos P, Sanchez-Roige S, Santamaría-García H, Shansis F, Sharp R, Storch E, Tavares M, Tietz G, Torres-Hernández B, Tovo-Rodrigues L, Trelles P, Trujillo-ChiVacuan E, Velásquez M, Vera-Urbina F, Voloudakis G, Wegman-Ostrosky T, Zhen-Duan J, Zhou H, Santoro M, Nicolini H, Atkinson E, Giusti-Rodríguez P, Montalvo-Ortiz J. Psychiatric genetics in the diverse landscape of Latin American populations. Nature Genetics 2025, 57: 1074-1088. PMID: 40175716, PMCID: PMC12133068, DOI: 10.1038/s41588-025-02127-z.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPsychiatric genomicsPsychiatric genome-wide association studiesLarge-scale genome-wide association studiesGenetic risk lociNon-European populationsGenetic diversityRisk lociGenetic admixtureBurden of psychiatric disordersAssociation studiesPsychiatric disordersEuropean ancestryPsychiatric geneticsGenomeHealthcare disparitiesConsortium effortLatin American populationsPromote equityEnvironmental factorsDiversityAmerican populationDiverse landscapeLociAncestryOptimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants
Yuan M, Goovaerts S, Lee M, Devine J, Richmond S, Walsh S, Shriver M, Shaffer J, Marazita M, Peeters H, Weinberg S, Claes P. Optimized phenotyping of complex morphological traits: enhancing discovery of common and rare genetic variants. Briefings In Bioinformatics 2025, 26: bbaf090. PMID: 40062617, PMCID: PMC11891655, DOI: 10.1093/bib/bbaf090.Peer-Reviewed Original ResearchConceptsRare variant association studiesGenome-wide association studiesComplex morphological traitsGenomic lociSNP heritabilityAssociation studiesRare variantsPhenotypic variationMorphological traitsAxes of phenotypic variationContext of genome-wide association studiesVariant association studiesIndividuals of European ancestryGene-based testsLinkage disequilibrium score regressionRare genetic variantsGenomic relatednessOptimal phenotypeUnrelated individualsGenetic variantsRelevant traitsEuropean ancestryScore regressionPhenotype distributionFamily dataA Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization
Koroglu M, Bilguvar K. A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization. Methods In Molecular Biology 2025, 2889: 207-233. PMID: 39745615, DOI: 10.1007/978-1-0716-4322-8_15.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyGenetic VariationGenomicsHigh-Throughput Nucleotide SequencingHumansMolecular Sequence AnnotationSoftwareConceptsGenomic dataHigh-throughput sequencing technologyGenomic data analysisField of genomicsNext-generation sequencingVariant callingNGS technologiesSequencing technologiesBioinformatics approachComprehensive computational approachSequenceComputational approachCancer researchGenomeTranscriptomeBioinformaticsNGSProteomicsNext-generationDNARNAEfficient sequenceAnnotationVariantsFragmentsCoupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits
Scherer N, Fässler D, Borisov O, Cheng Y, Schlosser P, Wuttke M, Haug S, Li Y, Telkämper F, Patil S, Meiselbach H, Wong C, Berger U, Sekula P, Hoppmann A, Schultheiss U, Mozaffari S, Xi Y, Graham R, Schmidts M, Köttgen M, Oefner P, Knauf F, Eckardt K, Grünert S, Estrada K, Thiele I, Hertel J, Köttgen A. Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. Nature Genetics 2025, 57: 193-205. PMID: 39747595, PMCID: PMC11735408, DOI: 10.1038/s41588-024-01965-7.Peer-Reviewed Original ResearchConceptsWhole-exome sequencing dataGene-metabolite associationsHuman traitsHuman metabolic reactionsSequence dataAllelic seriesGene functionExome sequencingFunctional variantsGenetic studiesInborn errors of metabolismHeterozygous variantsErrors of metabolismMusculoskeletal traitsMetabolic reactionsHuman heightUrine metabolitesHeterozygous stateSulfate reabsorptionInborn errorsTraitsAggregation testVariantsHuman metabolismMetabolomics
2024
cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation
Kalra S, Lanno S, Sanchez G, Coolon J. cis- and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation. Communications Biology 2024, 7: 1563. PMID: 39587248, PMCID: PMC11589579, DOI: 10.1038/s42003-024-07255-6.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDrosophilaDrosophila melanogasterFemaleGene Expression RegulationGenetic VariationMaleQuantitative Trait LociConceptsGene expression variationTrait variationExpression variationTrans-regulatory changesGene expression traitsSource of trait variationTrans-regulationExpression traitsDiverse organismsMolecular mechanismsDevelopmental stagesTransgenerational effectsGenesLife stagesTraitsDrosophilaGenomeEnvironmental responsibilityAssociated with changesMultiple different sourcesVariationPrioritizing disease-related rare variants by integrating gene expression data
Guo H, Urban A, Wong H. Prioritizing disease-related rare variants by integrating gene expression data. PLOS Genetics 2024, 20: e1011412. PMID: 39348415, PMCID: PMC11466430, DOI: 10.1371/journal.pgen.1011412.Peer-Reviewed Original ResearchMeSH KeywordsAlzheimer DiseaseComputer SimulationGene ExpressionGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansConceptsGene expression dataRare variantsExpression dataRare variant association methodsExcess of rare variantsImpact of rare variantsContext of human diseaseHuman genetic variationGenetic variationGene expressionComplex diseasesHuman diseasesGenesMolecular mechanismsFunctional consequencesRare variant typesAlzheimer's diseaseVariant typeVariantsAssociation methodStatistical frameworkSimulation studySample sizeOmicsAlzheimerA new lineage nomenclature to aid genomic surveillance of dengue virus
Hill V, Cleemput S, Pereira J, Gifford R, Fonseca V, Tegally H, Brito A, Ribeiro G, de Souza V, Brcko I, Ribeiro I, De Lima I, Slavov S, Sampaio S, Elias M, Tran V, Kien D, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau G, Gregianini T, Godinho F, Vogels C, Breban M, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara L, Faria N, Carrington C, Hanley K, Holmes E, Dumon W, Lima A, de Oliveira T, Grubaugh N. A new lineage nomenclature to aid genomic surveillance of dengue virus. PLOS Biology 2024, 22: e3002834. PMID: 39283942, PMCID: PMC11426435, DOI: 10.1371/journal.pbio.3002834.Peer-Reviewed Original ResearchMeSH KeywordsDengueDengue VirusGenetic VariationGenome, ViralGenomicsGenotypeHumansPhylogenyTerminology as TopicConceptsGenomic surveillanceSub-genotype levelPartial genome sequencesDengue virusViral genomic diversityClade sizeGenome sequenceGenomic diversityPhylogenetic studiesPhylogenetic distanceSequence dataMinor lineageVirus classificationLineagesSurveillance of dengue virusDiversityAssignment toolComplex patternsVirusCladeSequenceGeographical areasGenotypesNomenclatureEndemic settingsDiversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Verma A, Huffman J, Rodriguez A, Conery M, Liu M, Ho Y, Kim Y, Heise D, Guare L, Panickan V, Garcon H, Linares F, Costa L, Goethert I, Tipton R, Honerlaw J, Davies L, Whitbourne S, Cohen J, Posner D, Sangar R, Murray M, Wang X, Dochtermann D, Devineni P, Shi Y, Nandi T, Assimes T, Brunette C, Carroll R, Clifford R, Duvall S, Gelernter J, Hung A, Iyengar S, Joseph J, Kember R, Kranzler H, Kripke C, Levey D, Luoh S, Merritt V, Overstreet C, Deak J, Grant S, Polimanti R, Roussos P, Shakt G, Sun Y, Tsao N, Venkatesh S, Voloudakis G, Justice A, Begoli E, Ramoni R, Tourassi G, Pyarajan S, Tsao P, O'Donnell C, Muralidhar S, Moser J, Casas J, Bick A, Zhou W, Cai T, Voight B, Cho K, Gaziano J, Madduri R, Damrauer S, Liao K. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science 2024, 385: eadj1182. PMID: 39024449, DOI: 10.1126/science.adj1182.Peer-Reviewed Original ResearchConceptsMillion Veteran ProgramNon-European populationsVeteran ProgramGenetic architectureAtlas of genetic associationsVeterans Affairs Million Veteran ProgramVA Million Veteran ProgramGenomic risk lociGenome-wide associationHuman genetic studiesHealth disparitiesUnited States veteransCausal variantsRisk lociGenetic insightsGenetic studiesGenetic associationGenetic causeStates veteransDiverse populationsDisease factorsLack of inclusionLongitudinal studyParticipantsTraitsGenomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon
Cabrera-Sosa L, Nolasco O, Kattenberg J, Fernandez-Miñope C, Valdivia H, Barazorda K, Arévalo de los Rios S, Rodriguez-Ferrucci H, Vinetz J, Rosanas-Urgell A, Van geertruyden J, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Scientific Reports 2024, 14: 16291. PMID: 39009685, PMCID: PMC11250820, DOI: 10.1038/s41598-024-66925-x.Peer-Reviewed Original ResearchConceptsPassive case detectionPf parasitesPersistent malaria transmissionPfhrp2/3 gene deletionsDeep sequencing assaySulfadoxine-pyrimethamineMalaria casesMalaria eliminationPlasmodium vivaxMalaria parasitesMalaria transmissionP. falciparumResistance mutationsImported infectionsMalariaPopulation genetic indicesSequencing assayCase detectionGene deletionPV populationResistance markersGenetic diversityPeruvian AmazonGenomic surveillanceGenetic indicesIdentification of rare genetic variants in the PCDH genetic family in a cohort of transgender women
Theisen J, Chorich L, Xu H, Knight J, Kim H, Layman L. Identification of rare genetic variants in the PCDH genetic family in a cohort of transgender women. F&S Science 2024, 5: 283-292. PMID: 38942387, DOI: 10.1016/j.xfss.2024.06.005.Peer-Reviewed Original ResearchMeSH KeywordsAdultCadherinsCohort StudiesExome SequencingFemaleGender IdentityGenetic VariationHumansMaleProtocadherinsTransgender PersonsConceptsIdentification of rare genetic variantsRare genetic variantsDatabase for AnnotationGenetic variantsExome sequencingSanger sequencingTransgender womenCisgender menPlasma membrane adhesion moleculesGenetic familiesFunctional classification analysisGene family membersIntegrated Discovery toolMembrane adhesion moleculesVariant confirmationPcdh genesGene familyPcdhRare variantsGene variantsDiscovery analysisExomeSequenceSangerGenesHigh-throughput assays to assess variant effects on disease
Ma K, Gauthier L, Cheung F, Huang S, Lek M. High-throughput assays to assess variant effects on disease. Disease Models & Mechanisms 2024, 17: dmm050573. PMID: 38940340, PMCID: PMC11225591, DOI: 10.1242/dmm.050573.Peer-Reviewed Original ResearchConceptsDeep mutational scanningGenetic variantsRare disease diagnosticsRare genetic variantsDisease mechanismsHigh-throughput assaySequencing effortsInvestigation of variantsMutational scanningModel cell lineVariant effectsMolecular toolsCell linesCell survival rateFunctional assaysDrug resistanceDisease diagnosticsDisease-relevant assaysVariantsClinical case reportBiological mechanismsAssayCase reportClinical reportsSurvival rateGenetic variants for head size share genes and pathways with cancer
Knol M, Poot R, Evans T, Satizabal C, Mishra A, Sargurupremraj M, van der Auwera S, Duperron M, Jian X, Hostettler I, van Dam-Nolen D, Lamballais S, Pawlak M, Lewis C, Carrion-Castillo A, van Erp T, Reinbold C, Shin J, Scholz M, Håberg A, Kämpe A, Li G, Avinun R, Atkins J, Hsu F, Amod A, Lam M, Tsuchida A, Teunissen M, Aygün N, Patel Y, Liang D, Beiser A, Beyer F, Bis J, Bos D, Bryan R, Bülow R, Caspers S, Catheline G, Cecil C, Dalvie S, Dartigues J, DeCarli C, Enlund-Cerullo M, Ford J, Franke B, Freedman B, Friedrich N, Green M, Haworth S, Helmer C, Hoffmann P, Homuth G, Ikram M, Jack C, Jahanshad N, Jockwitz C, Kamatani Y, Knodt A, Li S, Lim K, Longstreth W, Macciardi F, Consortium T, Amouyel P, Arfanakis K, Aribisala B, Bastin M, Chauhan G, Chen C, Cheng C, de Jager P, Deary I, Fleischman D, Gottesman R, Gudnason V, Hilal S, Hofer E, Janowitz D, Jukema J, Liewald D, Lopez L, Lopez O, Luciano M, Martinez O, Niessen W, Nyquist P, Rotter J, Rundek T, Sacco R, Schmidt H, Tiemeier H, Trompet S, van der Grond J, Völzke H, Wardlaw J, Yanek L, Yang J, Consortium T, Agartz I, Alhusaini S, Almasy L, Ames D, Amunts K, Andreassen O, Armstrong N, Bernard M, Blangero J, Blanken L, Boks M, Boomsma D, Brickman A, Brodaty H, Buckner R, Buitelaar J, Cannon D, Carr V, Catts S, Chakravarty M, Chen Q, Ching C, Corvin A, Crespo-Facorro B, Curran J, Davies G, de Geus E, de Zubicaray G, Braber A, Desrivières S, Dillman A, Djurovic S, Drevets W, Duggirala R, Ehrlich S, Erk S, Espeseth T, Fedko I, Fernández G, Fisher S, Foroud T, Ge T, Giddaluru S, Glahn D, Goldman A, Green R, Greven C, Grimm O, Hansell N, Hartman C, Hashimoto R, Heinz A, Henskens F, Hibar D, Ho B, Hoekstra P, Holmes A, Hoogman M, Hottenga J, Pol H, Jablensky A, Jenkinson M, Jia T, Jöckel K, Jönsson E, Kim S, Klein M, Kochunov P, Kwok J, Lawrie S, Le Hellard S, Lemaître H, Loughland C, Marquand A, Martin N, Martinot J, Matarin M, Mathalon D, Mather K, Mattay V, McDonald C, McMahon F, McMahon K, Rebekah E, McWhirter, Mecocci P, Melle I, Meyer-Lindenberg A, Michie P, Milaneschi Y, Morris D, Mowry B, Nho K, Nichols T, Nöthen M, Olvera R, Oosterlaan J, Ophoff R, Pandolfo M, Pantelis C, Pappa I, Penninx B, Pike G, Rasser P, Rentería M, Reppermund S, Rietschel M, Risacher S, Romanczuk-Seiferth N, Rose E, Sachdev P, Sämann P, Saykin A, Schall U, Schofield P, Schramm S, Schumann G, Scott R, Shen L, Sisodiya S, Soininen H, Sprooten E, Srikanth V, Steen V, Strike L, Thalamuthu A, Toga A, Tooney P, Tordesillas-Gutiérrez D, Turner J, del C. Valdés Hernández M, van der Meer D, Van der Wee N, Van Haren N, van 't Ent D, Veltman D, Walter H, Weinberger D, Weiner M, Wen W, Westlye L, Westman E, Winkler A, Woldehawariat G, Wright M, Wu J, Mäkitie O, Mazoyer B, Medland S, Miyamoto S, Moebus S, Mosley T, Muetzel R, Mühleisen T, Nagata M, Nakahara S, Palmer N, Pausova Z, Preda A, Quidé Y, Reay W, Roshchupkin G, Schmidt R, Schreiner P, Setoh K, Shapland C, Sidney S, St Pourcain B, Stein J, Tabara Y, Teumer A, Uhlmann A, van der Lugt A, Vernooij M, Werring D, Windham B, Witte A, Wittfeld K, Yang Q, Yoshida K, Brunner H, Le Grand Q, Sim K, Stein D, Bowden D, Cairns M, Hariri A, Cheung C, Andersson S, Villringer A, Paus T, Cichon S, Calhoun V, Crivello F, Launer L, White T, Koudstaal P, Houlden H, Fornage M, Matsuda F, Grabe H, Ikram M, Debette S, Thompson P, Seshadri S, Adams H. Genetic variants for head size share genes and pathways with cancer. Cell Reports Medicine 2024, 5: 101529. PMID: 38703765, PMCID: PMC11148644, DOI: 10.1016/j.xcrm.2024.101529.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGene set enrichmentErbB signaling pathwayNear genesGenetic lociAssociation studiesCancer genesGenetic variantsSyndrome geneShared genesGenetic driversSize variantsGenesSignaling pathwayIntermediate progenitor cellsHeight variantsHead sizeVariantsNeural cellsPathwayWidespread effectsCellsLociP53Early brainIntegrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis
Ghouse J, Sveinbjörnsson G, Vujkovic M, Seidelin A, Gellert-Kristensen H, Ahlberg G, Tragante V, Rand S, Brancale J, Vilarinho S, Lundegaard P, Sørensen E, Erikstrup C, Bruun M, Jensen B, Brunak S, Banasik K, Ullum H, Verweij N, Lotta L, Baras A, Mirshahi T, Carey D, Kaplan D, Lynch J, Morgan T, Schwantes-An T, Dochtermann D, Pyarajan S, Tsao P, Laisk T, Mägi R, Kozlitina J, Tybjærg-Hansen A, Jones D, Knowlton K, Nadauld L, Ferkingstad E, Björnsson E, Ulfarsson M, Sturluson Á, Sulem P, Pedersen O, Ostrowski S, Gudbjartsson D, Stefansson K, Olesen M, Chang K, Holm H, Bundgaard H, Stender S. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis. Nature Genetics 2024, 56: 827-837. PMID: 38632349, PMCID: PMC11096111, DOI: 10.1038/s41588-024-01720-y.Peer-Reviewed Original ResearchMeSH KeywordsAlanine TransaminaseCarcinoma, HepatocellularCase-Control StudiesCohort StudiesFemalegamma-GlutamyltransferaseGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansLipaseLiver CirrhosisLiver NeoplasmsMaleMembrane ProteinsMultifactorial InheritancePolymorphism, Single NucleotideRisk FactorsConceptsMulti-ancestry genome-wide association studyPolygenic risk scoresRare variant analysisVariant analysisGenome-wide association studiesRare coding variantsHepatocellular carcinomaLow alanine aminotransferaseRisk associationAlcohol intakePrioritized genesGenetic architectureNear genesAlanine aminotransferaseRisk scoreHepatic lipid metabolismAssociation studiesLiver cirrhosisGenetic underpinningsPNPLA3 p.Cirrhosis to hepatocellular carcinomaRisk of cirrhosisLiver function testsLipid metabolismGenesRare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease
Bhattarai P, Gunasekaran T, Belloy M, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Turgutalp B, Sukumar G, Alba C, McGrath E, Hupalo D, Bacikova D, Le Guen Y, Lantigua R, Medrano M, Rivera D, Recio P, Nuriel T, Ertekin-Taner N, Teich A, Dickson D, Holley S, Greicius M, Dalgard C, Zody M, Mayeux R, Kizil C, Vardarajan B. Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease. Acta Neuropathologica 2024, 147: 70. PMID: 38598053, PMCID: PMC11006751, DOI: 10.1007/s00401-024-02721-1.Peer-Reviewed Original ResearchMeSH KeywordsAgedAlzheimer DiseaseAnimalsChild, PreschoolFibronectinsGenetic VariationGliosisHumansZebrafishConceptsLoss-of-functionWhole-genome sequencingFibronectin 1Genetic variationAlzheimer's diseaseAD riskRare coding variantsLoss-of-function variantsRare genetic variationGene Ontology termsFamily based studyIn vivo functional studiesAD-related pathologyAlpha 2 chainOntology termsPresence of cellular mechanismsProtective variantsECM proteinsAD pathologyPathway analysisFunctional studiesUnaffected carriersZebrafish modelAPOEe4 alleleProtein levels
2023
Genetic Variation and Sensory Perception of a Pediatric Formulation of Ibuprofen: Can a Medicine Taste Too Good for Some?
Mennella J, Kan M, Lowenthal E, Saraiva L, Mainland J, Himes B, Pepino M. Genetic Variation and Sensory Perception of a Pediatric Formulation of Ibuprofen: Can a Medicine Taste Too Good for Some? International Journal Of Molecular Sciences 2023, 24: 13050. PMID: 37685855, PMCID: PMC10487938, DOI: 10.3390/ijms241713050.Peer-Reviewed Original ResearchMeSH KeywordsAdministration, OralCohort StudiesDosage FormsGenetic VariationHumansIbuprofenPerceptionSensationTasteConceptsGenetic ancestryEuropean genetic ancestryTaste receptor genesIndependent of ancestryAfrican genetic ancestryGenetic variationFormulations of ibuprofenEpigenetic factorsAncestryReceptor geneDouble-blind cohort studyUrge to coughPerception of palatabilityRisk of accidental ingestionPersonality variationCohort studyPediatric formulationsSensory phenotypesThroat sensationChemesthetic sensationsMedicinal tasteTingling sensationPanelistsAdult panelistsDiverse populationsA draft human pangenome reference
Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Sirén J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Garrison N, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson N, Popejoy A, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Smith M, Sofia H, Abou Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Walenz B, Wood J, Zimin A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Wang T, Jarvis E, Miga K, Garrison E, Marschall T, Hall I, Li H, Paten B. A draft human pangenome reference. Nature 2023, 617: 312-324. PMID: 37165242, PMCID: PMC10172123, DOI: 10.1038/s41586-023-05896-x.Peer-Reviewed Original ResearchLeveraging base-pair mammalian constraint to understand genetic variation and human disease
Sullivan P, Meadows J, Gazal S, Phan B, Li X, Genereux D, Dong M, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas M, Marinescu V, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins L, Lawler A, Keough K, Zheng Z, Zeng J, Wray N, Li Y, Johnson J, Chen J, Paten B, Reilly S, Hughes G, Weng Z, Pollard K, Pfenning A, Forsberg-Nilsson K, Karlsson E, Lindblad-Toh K, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science 2023, 380: eabn2937. PMID: 37104612, PMCID: PMC10259825, DOI: 10.1126/science.abn2937.Peer-Reviewed Original ResearchConceptsHuman genomeHuman diseasesCopy-number variationsHeritable human diseasesGenome annotationVariant annotationGenomic positionsGenomic regionsDisease heritabilityFunctional annotationEvolutionary constraintsAssociation studiesCopy-numberGenetic variationGenetic findingsGenomeCell typesRegulatory landscapeDisease mechanismsAnnotationBiological mechanismsCancer dataMammalsPredictor of functionHeritabilityGenetic Variation in Intercellular Adhesion Molecule-1 (ICAM-1) and Diastolic Heart Failure in the Black Population in the United States
Mezue K, Driggin E. Genetic Variation in Intercellular Adhesion Molecule-1 (ICAM-1) and Diastolic Heart Failure in the Black Population in the United States. Journal Of Cardiac Failure 2023, 29: 1173-1174. PMID: 37062471, DOI: 10.1016/j.cardfail.2023.03.021.Peer-Reviewed Original Research
2022
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis E, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger M, Porubsky D, Cheng H, Asri M, Logsdon G, Carnevali P, Chaisson M, Chin C, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton R, Fulton L, Garg S, Gerton J, Ghurye J, Granat A, Green R, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger E, Jain M, Kirsche M, Kolmogorov M, Korbel J, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell M, McDaniel J, Nie F, Olsen H, Olson N, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg S, Sanders A, Schatz M, Schmitt A, Schneider V, Selvaraj S, Shafin K, Shumate A, Stitziel N, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin A, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook J, Eichler E, Phillippy A, Paten B, Howe K, Miga K. Semi-automated assembly of high-quality diploid human reference genomes. Nature 2022, 611: 519-531. PMID: 36261518, PMCID: PMC9668749, DOI: 10.1038/s41586-022-05325-5.Peer-Reviewed Original ResearchConceptsDiploid genome assemblyGenome assemblyProtein-coding genesGlobal genetic variationCurrent human reference genomeDiploid human genomeHigh-quality assemblyAccurate long readsNon-synonymous amino acid changesHuman reference genomeAmino acid changesMost chromosomesReference assemblyReference genomeHuman genomeCentromeric regionsGenetic variationHigh diversityGenome sequencingLong readsSingle nucleotideGenomeAcid changesManual curationBiological genomesTemporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program
Gray R, Fusco N, Miller J, Tapia W, Mariani C, Caccone A, Jensen E. Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program. Integrative And Comparative Biology 2022, 62: 1864-1871. PMID: 35906184, DOI: 10.1093/icb/icac129.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsConservation of Natural ResourcesFemaleGenetic VariationGenomeMaleMicrosatellite RepeatsTurtlesConceptsCaptive breeding programsBreeding programsEffective population sizeGalapagos giant tortoisesCaptive breedingGenetic diversityGenetic trackingReproductive outputSpecies restorationGiant tortoisesConservation managersBreeding outcomesMicrosatellite markersGenetic analysisMore foundersBreeding cyclePopulation sizeBreeding facilitiesTortoisesValue of hybridsParentageOffspringGenomeHybridsBreeding
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