2025
Copy Number Variations in the Brazilian High-Risk Cohort for Mental Conditions.
Arendt J, Zamariolli M, Almodobar L, Ito L, Ormond R, Oliveira A, Ota V, Rohde L, Miguel E, Pan P, Bressan R, Salum G, Belangero S, Santoro M. Copy Number Variations in the Brazilian High-Risk Cohort for Mental Conditions. Brazilian Journal Of Psychiatry 2025 PMID: 40014503, DOI: 10.47626/1516-4446-2024-3765.Peer-Reviewed Original ResearchCopy number variationsDatabase of Genomic VariantsNumber variationsMental health disordersCopy number variation studiesImpact of copy number variationsGenome Aggregation DatabasePennCNV softwareGenomic variantsGenetic variantsAggregation DatabaseAssociated with mental health disordersDevelopment of mental health disordersHigh-risk cohortInheritance patternMental conditionBrazilian High-Risk Cohort StudyHigh Risk Cohort StudyMild effect sizeCohort studyBrazilian cohortCopyHealth disordersDuplicationMeta-analysis
2024
Steering research on mRNA splicing in cancer towards clinical translation
Anczukow O, Allain F, Angarola B, Black D, Brooks A, Cheng C, Conesa A, Crosse E, Eyras E, Guccione E, Lu S, Neugebauer K, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks K, Yeo G, Thomas-Tikhonenko A. Steering research on mRNA splicing in cancer towards clinical translation. Nature Reviews Cancer 2024, 24: 887-905. PMID: 39384951, PMCID: PMC11698124, DOI: 10.1038/s41568-024-00750-2.Peer-Reviewed Original ResearchSplicing aberrationsMRNA splicingLong-read RNA sequencingRNA sequencingShort-read RNA sequencingCopy number variationsMis-spliced transcriptsRecurrent somatic mutationsSynthetic lethal approachSingle-cell levelSpliceosome componentsSplicing alterationsSplicing factorsCellular processesNumber variationsSpliceosome inhibitorsMRNA isoformsDNA repairSplicingSomatic mutationsTumor vulnerabilitiesLethal approachHuman cancersCancer initiationCancer progressionPrecision treatment paradigm: Genomic features and therapeutic implications in mesenchymal‐epithelial transition‐amplified gastric cancer
Yu Y, Zhang Z, Zhu M, Shan Y, Wang Y, Wei L, Huang X, Sun D, Peng Z, Liu T. Precision treatment paradigm: Genomic features and therapeutic implications in mesenchymal‐epithelial transition‐amplified gastric cancer. Clinical And Translational Discovery 2024, 4 DOI: 10.1002/ctd2.350.Peer-Reviewed Original ResearchSingle nucleotide variantsCopy number variationsGenomic featuresMET amplificationOverall survivalCohort 1TCGA cohortMesenchymal-epithelial transitionGastric cancerSignificant copy number variationsCohort 2Nucleotide variantsPI3K pathwayCancer Genome AtlasNumber variationsRNA dataExpression analysisMutational landscapeProgression-freeClinical responseK pathwayMET therapyChinese patientsKaplan-MeierTreated patientsEpigenetic heterogeneity hotspots in human liver disease progression
Hlady R, Zhao X, Khoury L, Wagner R, Luna A, Pham K, Pyrosopoulos N, Jain D, Wang L, Liu C, Robertson K. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology 2024, 81: 1197-1210. PMID: 39028883, PMCID: PMC11742070, DOI: 10.1097/hep.0000000000001023.Peer-Reviewed Original ResearchEpigenetic heterogeneityGenome-wide profiling of DNA methylationProfiling of DNA methylationDNA methylation landscapeGenome-wide profilingGene expression heterogeneityCopy number variationsMethylation landscapeOnset of liver cancerDNA methylationLiver disease developmentPhenotypic effectsNumber variationsGenetic heterogeneityTranscriptional heterogeneityFunctional screeningLiver disease progressionCopy numberExpression heterogeneityGene expressionTumor suppressorHuman diseasesGenesPathological phenotypesKey pathwaysGenome-wide analysis and visualization of copy number with CNVpytor in igv.js
Panda A, Suvakov M, Thorvaldsdottir H, Mesirov J, Robinson J, Abyzov A. Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. Bioinformatics 2024, 40: btae453. PMID: 39018173, PMCID: PMC11303504, DOI: 10.1093/bioinformatics/btae453.Peer-Reviewed Original ResearchMultiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability
Mihailovich M, Germain P, Shyti R, Pozzi D, Noberini R, Liu Y, Aprile D, Tenderini E, Troglio F, Trattaro S, Fabris S, Ciptasari U, Rigoli M, Caporale N, D’Agostino G, Mirabella F, Vitriolo A, Capocefalo D, Skaros A, Franchini A, Ricciardi S, Biunno I, Neri A, Kasri N, Bonaldi T, Aebersold R, Matteoli M, Testa G. Multiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability. Journal Of Clinical Investigation 2024, 134: e168982. PMID: 39007270, PMCID: PMC11245157, DOI: 10.1172/jci168982.Peer-Reviewed Original ResearchConceptsCopy number variationsWilliams-Beuren syndromeRibosome biogenesisP-RPS6Neurodevelopmental disordersRibosomal genesP-4EBPNumber variationsTranslation factorsMicroduplication syndromeMolecular mechanismsGenesNeuronal differentiationPatient-derivedIntrinsic excitabilityMTOR pathwayBiogenesisNeuronal maturationPhosphorylated rpS6Neuronal transmissionWilliams-BeurenPathophysiological relevanceNeurocognitive featuresIntellectual disabilityDisease modelsClinicopathological and molecular features of genome-stable colorectal cancers.
Jin L, Jin H, Kim Y, Cho N, Bae J, Kim J, Han S, Kim T, Kang G. Clinicopathological and molecular features of genome-stable colorectal cancers. Histology And Histopathology 2024, 40: 381-388. PMID: 38993017, DOI: 10.14670/hh-18-785.Peer-Reviewed Original ResearchConceptsCopy number variationsChromosomal instabilityColorectal cancerMicrosatellite instabilityMolecular featuresNumber variationsProportion of colorectal cancersDroplet digital PCRTCGA dataMutationsAberrant expressionGenesClinicopathological featuresNo significant differenceTumor nucleiBowel locationExpression of KRT7Proximal colonSurvival analysisSignificant differenceMicrosatelliteCopy number variation of metallothionein 1 (MT1) associates with MT1X isoform expression and the overall survival of hepatocellular carcinoma patients in Guangxi
Xu P, Al-Anesi M, Huang M, Wu S, Ge Y, Chai H, Li P, Hu Q. Copy number variation of metallothionein 1 (MT1) associates with MT1X isoform expression and the overall survival of hepatocellular carcinoma patients in Guangxi. Gene Reports 2024, 34: 101889. DOI: 10.1016/j.genrep.2024.101889.Peer-Reviewed Original ResearchHepatocellular carcinoma patientsOverall survivalHepatocellular carcinoma diagnosisCopy number variationsHepatocellular carcinomaCancer tissuesDown-regulationMetallothionein-1Survival of hepatocellular carcinoma patientsEffects of copy number variationPredictors of OSOverall survival of hepatocellular carcinoma patientsMetallothionein-1 geneMetallothionein-1 proteinSimultaneous down-regulationCarcinoma patientsACGH analysisTumor-suppressive effectsNumber variationsIsoform expressionTranslational levelPatientsCancerResults of RT-qPCRGenes
2023
FISH Panel for Leukemic Cutaneous T-Cell Lymphoma: Extended Patient Cohort Correlation with Blood Involvement and Clinical Outcomes
Avery J, Kim R, Cheng W, Foss F, Girardi M. FISH Panel for Leukemic Cutaneous T-Cell Lymphoma: Extended Patient Cohort Correlation with Blood Involvement and Clinical Outcomes. JID Innovations 2023, 3: 100212. PMID: 37674691, PMCID: PMC10477749, DOI: 10.1016/j.xjidi.2023.100212.Peer-Reviewed Original ResearchSignal transducerGene copy number variationActivator of transcriptionCopy number variationsGene copy number alterationsGenomic basisCopy number alterationsRelevant genesGenomic sequencingNumber variationsFISH panelNumber alterationsDe novoCost-effective panelFISH resultsAbnormal FISH resultsActivatorGene panelTranscriptionLeukemic cutaneous T-cell lymphomaCutaneous T-cell lymphomaGenesSequencingT-cell lymphomaDeletion
2022
Rare copy number variation in posttraumatic stress disorder
Maihofer A, Engchuan W, Huguet G, Klein M, MacDonald J, Shanta O, Thiruvahindrapuram B, Jean-louis M, Saci Z, Jacquemont S, Scherer S, Ketema E, Aiello A, Amstadter A, Avdibegović E, Babic D, Baker D, Bisson J, Boks M, Bolger E, Bryant R, Bustamante A, Caldas-de-Almeida J, Cardoso G, Deckert J, Delahanty D, Domschke K, Dunlop B, Dzubur-Kulenovic A, Evans A, Feeny N, Franz C, Gautam A, Geuze E, Goci A, Hammamieh R, Jakovljevic M, Jett M, Jones I, Kaufman M, Kessler R, King A, Kremen W, Lawford B, Lebois L, Lewis C, Liberzon I, Linnstaedt S, Lugonja B, Luykx J, Lyons M, Mavissakalian M, McLaughlin K, McLean S, Mehta D, Mellor R, Morris C, Muhie S, Orcutt H, Peverill M, Ratanatharathorn A, Risbrough V, Rizzo A, Roberts A, Rothbaum A, Rothbaum B, Roy-Byrne P, Ruggiero K, Rutten B, Schijven D, Seng J, Sheerin C, Sorenson M, Teicher M, Uddin M, Ursano R, Vinkers C, Voisey J, Weber H, Winternitz S, Xavier M, Yang R, McD Young R, Zoellner L, Salem R, Shaffer R, Wu T, Ressler K, Stein M, Koenen K, Sebat J, Nievergelt C. Rare copy number variation in posttraumatic stress disorder. Molecular Psychiatry 2022, 27: 5062-5069. PMID: 36131047, PMCID: PMC9763110, DOI: 10.1038/s41380-022-01776-4.Peer-Reviewed Original ResearchConceptsCopy number variationsCNV burdenInvestigation of copy number variationsNumber variationsRare copy number variationsRare genetic variationCNV regionsPopulation structureAssociation studiesGenetic variationGene setsGene pathwaysEuropean ancestryMicrodeletion regionPosttraumatic stress disorderPathway analysisGenesPosttraumatic stress disorder symptomsAnnotation resourcesEtiology of psychiatric disordersLogistic regression analysisStress disorderPathwayConsensus setAssociated with posttraumatic stress disorder
2021
Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers
Grant A, Xicola RM, Nguyen V, Lim J, Thorne C, Salhia B, Llor X, Ellis N, Padi M. Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers. Scientific Reports 2021, 11: 23507. PMID: 34873211, PMCID: PMC8648784, DOI: 10.1038/s41598-021-02806-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenomatous Polyposis ColiAdenomatous Polyposis Coli ProteinColorectal NeoplasmsDisease ProgressionDNA Copy Number VariationsDNA MethylationGenes, APCHumansMicrosatellite InstabilityMicrosatellite RepeatsMutationNeoplastic ProcessesPhenotypePromoter Regions, GeneticWnt Signaling PathwayConceptsAdenomatous polyposis coliMitochondrial activationDNA methylation profilesTumor suppressor gene adenomatous polyposis coliRNA expressionExpression of Axin2Cancer Genome AtlasIntracellular WntMethylation profilesAberrant regulationGene fusionsGenetic inactivationExtracellular WntNumber variationsGenome AtlasPolyposis coliSomatic mutationsAPC mutationsMutationsMolecular driversMutations of BRAFWntRSPO3Tumor progressionExpressionGenome structural variation in human evolution
Hollox E, Zuccherato L, Tucci S. Genome structural variation in human evolution. Trends In Genetics 2021, 38: 45-58. PMID: 34284881, DOI: 10.1016/j.tig.2021.06.015.Peer-Reviewed Original ResearchConceptsRole of SVsStructural variationsHuman evolutionHuman structural variationGenomic structureGenomic regionsReference genomeSequencing technologiesGenome sequencingRecent large-scale studiesCopy numberNumber variationsGenomeSequencingFocused analysisEvolutionVariationLarge-scale studiesAdaptationInfectious diseasesMolecular Genetics and Complex Inheritance of Congenital Heart Disease
Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes 2021, 12: 1020. PMID: 34209044, PMCID: PMC8307500, DOI: 10.3390/genes12071020.Peer-Reviewed Original ResearchConceptsHigh-throughput genomic technologiesHigh-throughput sequencingGenetic architectureCHD familyGenetic variationSophisticated analysis strategiesCilia genesComplex inheritancePathway genesDe novo mutationsGenomic technologiesCauses of CHDMolecular geneticsBiological pathwaysMolecular diagnosisNumber variationsVEGF pathway genesGenesChromatinMutationsNovo mutationsGenetic etiologyTransmitted mutationsGenetic explanationSequencing
2020
Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry
Pathak GA, Polimanti R, Silzer TK, Wendt FR, Chakraborty R, Phillips NR. Genetically-regulated transcriptomics & copy number variation of proctitis points to altered mitochondrial and DNA repair mechanisms in individuals of European ancestry. BMC Cancer 2020, 20: 954. PMID: 33008348, PMCID: PMC7530964, DOI: 10.1186/s12885-020-07457-1.Peer-Reviewed Original ResearchConceptsWhole blood tissuesCopy number variationsNumber variationsGene expressionGenome-Wide Human SNP Array 6.0Mitochondrial apoptosis regulationRNA-seq informationGenetic variantsDNA repair mechanismsGene expression changesDNA repair processesGene expression associationsGene expression profilesGene network informationDNA repair genesCopy number dataCopy number analysisGene OntologyApoptosis regulationDNA repairEnriched pathwaysEnriched processesOrganismal injuryTranscriptomic profilesExpression changesMulti-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.Peer-Reviewed Original ResearchTriple-negative breast cancer cellsCancer cellsBreast cancer cellsStress response genesMulti-omics landscapeCell population compositionDrug-induced cell deathMulti-omics investigationsCell linesBCL2 family inhibitorsSingle-cell analysisChromatin accessibilityGenome structureMDA-MB-231 triple-negative breast cancer cellsChromatin structureMethylation stateResponse genesFamily inhibitorsCell deathTNBC cell linesNumber variationsDefense mechanismsResistance mechanismsNew therapeutic strategiesGenes
2019
Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk
Reid BM, Permuth JB, Chen YA, Fridley BL, Iversen ES, Chen Z, Jim H, Vierkant RA, Cunningham JM, Barnholtz-Sloan JS, Narod S, Risch H, Schildkraut JM, Goode EL, Monteiro AN, Sellers TA. Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk. Cancer Epidemiology Biomarkers & Prevention 2019, 28: 1117-1126. PMID: 30948450, PMCID: PMC6606353, DOI: 10.1158/1055-9965.epi-18-0833.Peer-Reviewed Original ResearchConceptsCommon CNV regionsCopy number variationsEOC susceptibilityNumber variationsTumor gene expressionGenome-wide analysisDNA copy number variationsWide association studyCommon copy number variationCancer Genome AtlasGenetic variationCNV regionsAssociation studiesFrequency variantsTCGA tumorsSomatic deletionGenome AtlasDeletionPhylogeny-based tumor subclone identification using a Bayesian feature allocation model
Zeng L, Warren J, Zhao H. Phylogeny-based tumor subclone identification using a Bayesian feature allocation model. The Annals Of Applied Statistics 2019, 13: 1212-1241. DOI: 10.1214/18-aoas1223.Peer-Reviewed Original ResearchCopy number variationsCourse of evolutionSubgroup of cellsWhole-genome sequencing samplesTumor subclonesBayesian feature allocation modelPhylogenetic structureDifferent genetic alterationsPhylogeny structureSequencing depthFeature allocation modelNumber variationsSequencing samplesTree sizeDistinct genotypesGenetic alterationsSubclonesResult of competitionTumor progressionBayesian modelEstimation accuracySifADrug resistanceCellsSimulation study
2018
Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells
Chen L, Fakiola M, Staines K, Butter C, Kaufman J. Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells. Frontiers In Immunology 2018, 9: 930. PMID: 29765375, PMCID: PMC5938342, DOI: 10.3389/fimmu.2018.00930.Peer-Reviewed Original ResearchConceptsCopy number variationsBG genesB12 haplotypeCytoplasmic tailFunctional allelesB2 haplotypeClosely-related genesUnequal crossing-overTruncated cytoplasmic tailPeripheral T cellsGene familyCoiled-coilAlternative splicingButyrophilin familyHeptad repeatNumber variationsCrossing-overHaplotypesPolar residuesGenesButyrophilinAllelesT cell ligandsCell typesT cellsPatient-derived conditionally reprogrammed cells maintain intra-tumor genetic heterogeneity
Correa BRS, Hu J, Penalva LOF, Schlegel R, Rimm DL, Galante PAF, Agarwal S. Patient-derived conditionally reprogrammed cells maintain intra-tumor genetic heterogeneity. Scientific Reports 2018, 8: 4097. PMID: 29511269, PMCID: PMC5840339, DOI: 10.1038/s41598-018-22427-1.Peer-Reviewed Original ResearchConceptsDrug target identificationNon-small cell lung cancerCancer cell biologyIntra-tumor genetic heterogeneityDrug discovery effortsMutant-allele tumor heterogeneity (MATH) scoreCell biologyWhole-exome sequencingCell heterogeneityNumber variationsPatient-derived cell culturesDiscovery effortsCR cellsCancer cell linesIntra-tumoral heterogeneityGenetic heterogeneityCell linesExome sequencingTarget identificationCell lung cancerLung cancer modelBiologyCell culturesMolecular characteristicsPrimary cultures
2017
Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma.
Berry JL, Xu L, Murphree AL, Krishnan S, Stachelek K, Zolfaghari E, McGovern K, Lee TC, Carlsson A, Kuhn P, Kim JW, Cobrinik D, Hicks J. Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma. JAMA Ophthalmology 2017, 135: 1221-1230. PMID: 29049475, PMCID: PMC5710399, DOI: 10.1001/jamaophthalmol.2017.4097.Peer-Reviewed Original ResearchConceptsTumor-derived DNACell-free DNARB eyesIntravitreous injectionAqueous humorAH samplesCopy number variationsSalvage therapyRB1 mutationsTumor biopsiesNumber variationsTertiary care hospitalCase series studyDNA copy number variationsDNA copy number alterationsCopy number variation profilesHigh-sensitivity kitChromosomal copy number variationsTumor DNA fractionPolymerase chain reaction primersWhole-genome sequencingPrimary enucleationCare hospitalDisease courseNumber variation profiles
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