2025
Targeted analysis of dyslexia-associated regions on chromosomes 6, 12 and 15 in large multigenerational cohorts
Chapman N, Navas P, Dorschner M, Mehaffey M, Wigg K, Price K, Naumova O, Kerr E, Guger S, Lovett M, Grigorenko E, Berninger V, Barr C, Wijsman E, Raskind W. Targeted analysis of dyslexia-associated regions on chromosomes 6, 12 and 15 in large multigenerational cohorts. PLOS ONE 2025, 20: e0324006. PMID: 40424442, PMCID: PMC12112411, DOI: 10.1371/journal.pone.0324006.Peer-Reviewed Original ResearchConceptsEvidence of associationLarge-scale sequencing studiesCis-acting regulatory regionsGenome-wide association studiesAggregating rare variantsRare exonic variantsDetected significant evidenceSingle nucleotide polymorphismsGenomic variationDeleterious variantsAssociated with reduced performanceAssociation studiesLarge-effectRegulatory elementsTranscriptional regulationRegulatory regionsQuantitative phenotypesCandidate genesExonic variantsChromosome 6Sequencing studiesSingle variantsCoding exonsMultiple traitsGenetic basisDynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry
Mohsen H, Blenman K, Emani P, Morris Q, Carrot-Zhang J, Pusztai L. Dynamic clustering of genomics cohorts beyond race, ethnicity—and ancestry. BMC Medical Genomics 2025, 18: 87. PMID: 40375077, PMCID: PMC12082885, DOI: 10.1186/s12920-025-02154-z.Peer-Reviewed Original ResearchConceptsGenomic variationGenomic cohortsStudy of human genomic variationWhole exome sequencing datasetsTrait-specific lociHuman genomic variationCancer-relevant genesGenomic patternsGenomic signalsGenomic studiesSequencing datasetsCancer typesGermline variantsDisease predispositionBiological processesFunctional analysisGeographic scalesPhenotypic continuumClustering patternsPotential driversDiverse data collectionsRace categoriesLociGenesComplete portraitAdvancing translational exposomics: bridging genome, exposome and personalized medicine
Sarigiannis D, Karakitsios S, Anesti O, Stem A, Valvi D, Sumner S, Chatzi L, Snyder M, Thompson D, Vasiliou V. Advancing translational exposomics: bridging genome, exposome and personalized medicine. Human Genomics 2025, 19: 48. PMID: 40307849, PMCID: PMC12044731, DOI: 10.1186/s40246-025-00761-6.Peer-Reviewed Original ResearchConceptsExposome-wide association studyBridge genomicsLifestyle exposuresEnhancing causal inferencePublic health decision-makingEnvironmental health researchHealth decision-makingMulti-omics technologiesGenomic variationGenomic dataAssociation studiesHealth outcomesBioinformatics approachHealth researchPrecision preventionGenetic variabilityExposome dataExposure-response relationshipMulti-OmicsGenomeInternal exposomeVulnerable populationsComplex diseasesDisease phenotypePublic health
2024
A genotyping array for the globally invasive vector mosquito, Aedes albopictus
Cosme L, Corley M, Johnson T, Severson D, Yan G, Wang X, Beebe N, Maynard A, Bonizzoni M, Khorramnejad A, Martins A, Lima J, Munstermann L, Surendran S, Chen C, Maringer K, Wahid I, Mukherjee S, Xu J, Fontaine M, Estallo E, Stein M, Livdahl T, Scaraffia P, Carter B, Mogi M, Tuno N, Mains J, Medley K, Bowles D, Gill R, Eritja R, González-Obando R, Trang H, Boyer S, Abunyewa A, Hackett K, Wu T, Nguyễn J, Shen J, Zhao H, Crawford J, Armbruster P, Caccone A. A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors 2024, 17: 106. PMID: 38439081, PMCID: PMC10910840, DOI: 10.1186/s13071-024-06158-z.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingLow-coverage whole-genome sequencingSNP chipRepetitive elementsGenomic analysisNative rangePatterns of genomic variationWhole-genome sequencing dataSNP chip genotypesPopulation genomic analysesProtein-coding genesLevels of admixtureOrigin of invasionNon-coding regionsPercentage of repetitive elementsGenotyping of samplesChip genotypesGenetic clustersAncestry analysisGenomic variationGenotyping arraysGenotyping platformsMendelian genesGenetic variationGenotyping methods
2022
A phylogenetic approach to study the evolution of somatic mutational processes in cancer
Miura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology 2022, 5: 617. PMID: 35732905, PMCID: PMC9217972, DOI: 10.1038/s42003-022-03560-0.Peer-Reviewed Original ResearchConceptsMutational processesPattern of conservationFalse-positive discovery rateCollection of mutationsSomatic mutational processesPhylogenetic approachGenomic variationSomatic variationCell lineagesMutational signaturesTumor evolutionMutation signaturesPhylogenyCancer cellsDiscovery rateMutationsComputer-simulated datasetsRelative activityLineagesComputational methodsSignaturesConservationDivergenceEvolutionJoint analysisThe Human Pangenome Project: a global resource to map genomic diversity
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison N, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D. The Human Pangenome Project: a global resource to map genomic diversity. Nature 2022, 604: 437-446. PMID: 35444317, PMCID: PMC9402379, DOI: 10.1038/s41586-022-04601-8.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHuman reference genomeReference genomeGenomic diversityGenomic variationHuman genomic variationGlobal genomic diversitySingle nucleotide variantsGene-disease associationsDiploid genomeGenetic resourcesGenomeGenomic researchFuture biomedical researchHigh-quality referenceStructural variantsHuman geneticsRoutine assemblyCommon variantsFunctional elementsPolymorphic regionDiversityBiomedical researchVariantsMajor updateGeneticsPopulation Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Frontiers In Medicine 2022, 9: 826746. PMID: 35265640, PMCID: PMC8899026, DOI: 10.3389/fmed.2022.826746.Peer-Reviewed Original ResearchPopulation genomic approachesStandard phylogenetic approachesGenome sequencing dataHaplotype networkGenomic approachesPhylogenetic approachTajima's DHigh-quality consensus sequencesGenetic diversityPopulation geneticsGenomic variationConsensus sequenceLineage expansionSequencing dataSARS-CoV-2 diversityGenetic characterizationLineage identificationDiversity landscapeInfection pathwaySARS-CoV-2 lineagesRecurrent mutationsGISAID databaseSARS-CoV-2DiversityPathogens
2020
Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders
Jourdon A, Mariani J, Scuderi S, Amiri A, Wu F, Yuen E, Abyzov A, Vaccarino F. Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders. 2020, 99-127. DOI: 10.1016/b978-0-12-814409-1.00005-7.ChaptersPluripotent stem cellsStem cellsStudy of speciesHuman neurodevelopmental disordersEpigenome analysisGene regulationIPSC fieldGenomic variationGene expressionGenetic backgroundDisease modelingStudies of neurodevelopmentIPSCsExperimental approachNeurodevelopmental disordersTranscriptomeGenomeCellsCell phenotypingSpeciesExperimental design issuesPhenotypeRegulationExpressionPhenotyping
2019
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Ghurye J, Koren S, Small S, Redmond S, Howell P, Phillippy A, Besansky N. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. GigaScience 2019, 8: giz063. PMID: 31157884, PMCID: PMC6545970, DOI: 10.1093/gigascience/giz063.Peer-Reviewed Original ResearchConceptsReference genomeHigh-quality reference genomeCurrent reference assemblyHaploid genome sizeMajor African malaria vector Anopheles funestusN50 scaffold sizeChromosome-scale assemblyReference genome assemblyN50 contig sizeChromosome-scale scaffoldsMalaria vector Anopheles funestusAfrican malaria vector Anopheles funestusMbp of sequenceSingle-molecule sequencingPrimary assemblyAnopheles funestusHi-C dataImportant disease vectorChromosome scaffoldingGenome sizeGenome assemblyContig sizeReference assemblyGenomic variationAssociation of phenotypicGuide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
Li J, Li Y, Li W, Luo H, Xi Y, Dong S, Gao M, Xu P, Zhang B, Liang Y, Zou Q, Hu X, Peng L, Zou D, Wang T, Yang H, Jiang C, Peng S, Wu F, Yu W. Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks. Genome Research 2019, 29: 270-280. PMID: 30670627, PMCID: PMC6360814, DOI: 10.1101/gr.240606.118.Peer-Reviewed Original ResearchConceptsWhole-genome bisulfite sequencingAberrant DNA methylationDNA methylationCell identityPredictor of gene expressionGenome-wide DNA methylationWhole-genome DNA methylationAberrant DNA methylation patternsDNA methylation patternsExpression of genes associated with immunityGenes associated with immunityAltering cell identityGene bodiesGC-richGenomic variationRepetitive regionsBisulfite sequencingMethylation patternsMethylation differencesGene expressionModulate expressionImmune surveillance networkLiver cancer developmentSequenceCancer development
2016
Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States
Carpi G, Walter KS, Mamoun CB, Krause PJ, Kitchen A, Lepore TJ, Dwivedi A, Cornillot E, Caccone A, Diuk-Wasser MA. Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States. BMC Genomics 2016, 17: 888. PMID: 27821055, PMCID: PMC5100190, DOI: 10.1186/s12864-016-3225-x.Peer-Reviewed Original ResearchConceptsStrong population structurePopulation structureGenome-wide diversityDifferentiated genetic clustersRecent population expansionB. microti samplesTick-borne apicomplexan parasiteB. microtiNortheastern USAGene flowEvolutionary originApicomplexan parasitesApicoplast genomeGenetic clustersGenomic variationPopulation expansionGeographic rangeRange expansionGenomic signaturesCurrent diversityHuman-derived samplesInfectious phenotypeTick vectorCapture strategyDiversityA map of human wanderlust
Tucci S, Akey JM. A map of human wanderlust. Nature 2016, 538: 179-180. PMID: 27654916, DOI: 10.1038/nature19472.Peer-Reviewed Original ResearchShifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma
Rubinstein JC, Brown TC, Christison-Lagay ER, Zhang Y, Kunstman JW, Juhlin CC, Nelson-Williams C, Goh G, Quinn CE, Callender GG, Udelsman R, Lifton RP, Korah R, Carling T. Shifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma. BMC Cancer 2016, 16: 646. PMID: 27538953, PMCID: PMC4989347, DOI: 10.1186/s12885-016-2665-7.Peer-Reviewed Original ResearchConceptsSingle nucleotide substitutionSomatic evolutionCommon ancestor cellGenomic changesNucleotide substitutionsTissue typesTissue-specific signaturesGenomic divergenceGenomic variationGenomic instabilityGenomic signaturesRisk of tumorigenesisSelective pressurePTC tumorigenesisTumor genomesAncestor cellsGenomeA transversionMethodsExome sequencingDiverse mutationsSomatic eventsMutational spectrumT transitionNovel patternTumorigenesisVectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity
Walter KS, Carpi G, Evans BR, Caccone A, Diuk-Wasser MA. Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity. PLOS Pathogens 2016, 12: e1005759. PMID: 27414806, PMCID: PMC4944968, DOI: 10.1371/journal.ppat.1005759.Peer-Reviewed Original ResearchConceptsPathogen diversityPositive selectionVertebrate hostsHost pathogen diversityLyme disease bacteriaNatural transmission cycleNatural populationsPathogen evolutionGenomic variationHost diversityMajority of ticksHost processesDiverse inoculumUndocumented levelEvolutionary processesTick diversityDisease vectorsMixed strain infectionsImmune complementIndividual ticksDiversityEpidemiological sentinelsTick vectorTransmission cycleHostDeciphering and Targeting Oncogenic Mutations and Pathways in Breast Cancer
Santarpia L, Bottai G, Kelly CM, Győrffy B, Székely B, Pusztai L. Deciphering and Targeting Oncogenic Mutations and Pathways in Breast Cancer. The Oncologist 2016, 21: 1063-1078. PMID: 27384237, PMCID: PMC5016060, DOI: 10.1634/theoncologist.2015-0369.Peer-Reviewed Original ResearchConceptsBreast cancerCancer-causing genesCopy number variationsRNA speciesRNA editingGenomic variationNext-generation sequencingRNA sequencingGenomic complexityGenomic portraitGreater genomic complexityOncogenic mutationsOncogenic eventsTarget profilingRare mutationsMutationsRecurrent mutationsSomatic variantsGenetic aberrationsFormal clinical trialsPotential therapeutic implicationsDriver mutationsSequencingGermline variantsMolecular abnormalities
2014
Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation
Guan L, Yang Q, Gu M, Chen L, Zhang X. Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation. Quantitative Biology 2014, 2: 71-79. DOI: 10.1007/s40484-014-0031-9.Peer-Reviewed Original ResearchExpression quantitative trait lociGenomic variationGene expressionAlternative splicingExpression QTL analysisRNA sequencing data setsPost-transcriptional regulationQuantitative trait lociLayer of regulationAlternative splicing isoformsExpression QTLsQTL analysisTrait lociSplicing isoformsMultiple isoformsSame geneExpression of exonsUbiquitous mechanismGene levelHapMap samplesSplicingRegulationExonsExpressionIsoformsComparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex
Sistrom M, Evans B, Bjornson R, Gibson W, Balmer O, Mäser P, Aksoy S, Caccone A. Comparative Genomics Reveals Multiple Genetic Backgrounds of Human Pathogenicity in the Trypanosoma brucei Complex. Genome Biology And Evolution 2014, 6: 2811-2819. PMID: 25287146, PMCID: PMC4224348, DOI: 10.1093/gbe/evu222.Peer-Reviewed Original ResearchConceptsT. brucei complexGenomic variationLife historyVariable life historiesAverage linkage disequilibriumTrypanosoma brucei complexGenome-wide studiesMeiotic reciprocal recombinationWhole genome sequencesMultiple genetic backgroundsHuman pathogenicityNumber of subspeciesHuman-infective parasiteNuclear genomeComparative genomicsChromosome sizeEukaryotic parasitesGenomic regionsHuman African trypanosomiasisRegulatory genesTaxonomic designationsDiverse hostsSingle nucleotide polymorphismsGenetic variationReciprocal recombinationGenome-Wide Association Study of Copy Number Variations (CNVs) with Opioid Dependence
Li D, Zhao H, Kranzler HR, Li MD, Jensen KP, Zayats T, Farrer LA, Gelernter J. Genome-Wide Association Study of Copy Number Variations (CNVs) with Opioid Dependence. Neuropsychopharmacology 2014, 40: 1016-1026. PMID: 25345593, PMCID: PMC4330517, DOI: 10.1038/npp.2014.290.Peer-Reviewed Original ResearchMeSH Keywordsalpha CateninChromosome DeletionChromosome DisordersChromosomes, Human, Pair 18DNA Copy Number VariationsFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansLeukocyte Common AntigensMaleMeta-Analysis as TopicOpioid-Related DisordersReceptor-Like Protein Tyrosine Phosphatases, Class 2ConceptsCopy number variationsAssociation studiesNumber variationsGenome-wide association studiesWide association studyUnique copy number variationsCommon copy number variationFirst GWASHarbor genesMissing heritabilityHuman genomeGenomic variationBiological importanceGenomeGenesGenetic risk factorsHeritabilitySubstance dependence riskGWASDuplicationDeletionReplicationPolymorphismVariationSmall proportion
2013
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
Preston M, Assefa S, Ocholla H, Sutherland C, Borrmann S, Nzila A, Michon P, Hien T, Bousema T, Drakeley C, Zongo I, Ouédraogo J, Djimde A, Doumbo O, Nosten F, Fairhurst R, Conway D, Roper C, Clark T. PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation. The Journal Of Infectious Diseases 2013, 209: 1808-1815. PMID: 24338354, PMCID: PMC4017360, DOI: 10.1093/infdis/jit812.Peer-Reviewed Original ResearchConceptsGenomic variationSingle nucleotide polymorphismsHigh-quality single nucleotide polymorphismsHigh-throughput sequencingInter-population differencesGenetic barcodesPlasmodium biologyGenetic variabilityGenomic dataInformative variantsDrug resistanceParasite populationsDifferential phenotypesLaboratory strainsMalaria parasitesNovel mutationsGlobal public health challengeNew insightsPf isolatesMalaria-endemic regionsPublic health challengePlasmodium falciparum speciesMedicine applicationsWeb-based resourcesClinical studies
2012
Impact of Retrotransposons in Pluripotent Stem Cells
Tanaka Y, Chung L, Park IH. Impact of Retrotransposons in Pluripotent Stem Cells. Molecules And Cells 2012, 34: 509-516. PMID: 23135636, PMCID: PMC3784326, DOI: 10.1007/s10059-012-0242-8.Peer-Reviewed Original Research
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