2024
Noninvasive single‐cell‐based prenatal genetic testing: A proof of concept clinical study
Bellair M, Amaral E, Ouren M, Roark C, Kim J, O'Connor A, Soriano A, Schindler M, Wapner R, Stone J, Tavella N, Merriam A, Perley L, Breman A, Beaudet A. Noninvasive single‐cell‐based prenatal genetic testing: A proof of concept clinical study. Prenatal Diagnosis 2024, 44: 304-316. PMID: 38411249, DOI: 10.1002/pd.6529.Peer-Reviewed Original ResearchConceptsNoninvasive prenatal genetic testingLow-risk pregnanciesConcept clinical studyCopy number analysisPrenatal genetic testingNext-generation sequencingPlacental mosaicismMaternal bloodAneuploidy resultsMeasures of test performanceCK stainingCVS casesClinical studiesGenetic testingNucleated cellsTrophoblastRed cellsNumber analysisPregnancyBloodDeletions/duplicationsAneuploidyDeletionAmniocentesisCells
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 changes
2017
De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome
Wang Q, Geng Q, Zhou Q, Luo F, Li P, Xie J. De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome. Molecular Cytogenetics 2017, 10: 46. PMID: 29270226, PMCID: PMC5738159, DOI: 10.1186/s13039-017-0347-z.Peer-Reviewed Original ResearchBeckwith-Wiedemann syndromeMethylation profilingGenome-wide copy number analysisGain of methylationAberrant methylation patternsIntegrated molecular approachSingle gene mutationsCopy number analysisSegmental uniparental disomyMethylation patternsGenetic mechanismsChromosome 11p15.5Genetic analysisTelomeric endMicroarray analysisMolecular approachesMolecular etiologyDuplicationBWS patientsNumber changesUniparental disomyGenetic defectsChromosome microarray analysisNumber analysisPaternal originGenome-wide copy number analysis of cell-free DNA from patients with chemotherapy-resistant metastatic triple-negative breast cancer.
Stover D, Parsons H, Ha G, Freeman S, Barry W, Guo H, Gydush G, Reed S, Rhoades J, Rotem D, Hughes M, Krop I, Tolaney S, Wagle N, Getz G, Meyerson M, Love J, Winer E, Lin N, Adalsteinsson V. Genome-wide copy number analysis of cell-free DNA from patients with chemotherapy-resistant metastatic triple-negative breast cancer. Journal Of Clinical Oncology 2017, 35: 1092-1092. DOI: 10.1200/jco.2017.35.15_suppl.1092.Peer-Reviewed Original ResearchTriple-negative breast cancerMetastatic triple-negative breast cancerCell-free DNAMetastatic TNBCFirst blood drawCopy number alterationsOverall survivalBlood drawBreast cancerPrimary triple-negative breast cancerTumor fractionMedian overall survivalBreast cancer subsetsIndependent prognostic markerPlasma samplesNovel therapeutic targetCopy number analysisNumber alterationsHazard ratioLiver metastasesGenome-wide copy number analysisMetastatic diagnosisBRCA statusPrognostic markerCancer subsets
2014
Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers
Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Alves M, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers. Clinical Cancer Research 2014, 20: 3842-3848. PMID: 24874835, PMCID: PMC4102633, DOI: 10.1158/1078-0432.ccr-14-0565.Peer-Reviewed Original ResearchConceptsSquamous cell carcinomaOlder patientsOral tongueYounger patientsCell carcinomaWhole-exome sequencingOlder smokersSimilar patientsTongue tumorsNon smokersIncreasing incidenceEpidemiologic studiesIndependent cohortPatientsSCCOTSmokingTumorsCohortAlteration frequencyGenomic effectsTCGA dataCopy number analysisGene-specific mutationsOlder cohortTypes of mutations
2012
Integrated analysis of tumor samples sheds light on tumor heterogeneity.
Parisi F, Micsinai M, Strino F, Ariyan S, Narayan D, Bacchiocchi A, Cheng E, Xu F, Li P, Kluger H, Halaban R, Kluger Y. Integrated analysis of tumor samples sheds light on tumor heterogeneity. The Yale Journal Of Biology And Medicine 2012, 85: 347-61. PMID: 23012583, PMCID: PMC3447199.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorChromosome MappingChromosomes, HumanDNA Copy Number VariationsEvolution, MolecularGene Expression ProfilingGene Expression Regulation, NeoplasticGenes, NeoplasmHumansIntercellular Signaling Peptides and ProteinsKaryotypingMelanomaMutationOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideProto-Oncogene Proteins B-rafConceptsHigh-throughput profilingGene expression levelsExpression levelsDifferent gene expression levelsGene expression profilingCopy number analysisExpression profilingSNP arrayPathway analysisCopy number statusWnt pathwayTumor samplesNumber alteration profilesTumor heterogeneityTumor evolutionCopy number alteration profilesGenomic aberrationsIntegrated analysisCell linesTumor subclonesNumber analysisNumber statusProfilingDriver mutationsRecurrent associationAttenuation of the Retinoblastoma Pathway in Pancreatic Neuroendocrine Tumors Due to Increased Cdk4/Cdk6
Tang L, Contractor T, Clausen R, Klimstra D, Du Y, Allen P, Brennan M, Levine A, Harris C. Attenuation of the Retinoblastoma Pathway in Pancreatic Neuroendocrine Tumors Due to Increased Cdk4/Cdk6. Clinical Cancer Research 2012, 18: 4612-4620. PMID: 22761470, DOI: 10.1158/1078-0432.ccr-11-3264.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overAnimalsCell ProliferationCyclin D1Cyclin-Dependent Kinase 4Cyclin-Dependent Kinase 6Cyclin-Dependent KinasesDNA Copy Number VariationsFemaleGene Expression Regulation, NeoplasticGenes, Tumor SuppressorHumansKaplan-Meier EstimateMaleMetabolic Networks and PathwaysMiceMiddle AgedMutationNeoplasm StagingNeuroendocrine TumorsPancreatic NeoplasmsPiperazinesPyridinesRetinoblastoma ProteinTransplantation, HeterologousConceptsRetinoblastoma pathwayPancreatic neuroendocrine tumorsGenome-wide sequencing studiesPan-NETsTumor suppressor pathwayCyclin D1Copy number analysisRetinoblastoma tumor suppressor pathwayNeuroendocrine tumorsCDK4/6 inhibitorsSequencing studiesGenomic DNAProtein cyclin D1Pathway genesTumors expressing high amountsSuppressor pathwayGenetic changesCopy numberOverexpression of CDK4Xenograft mouse modelNumber analysisExpressed high levelsGene amplificationGenesSmall molecule activation
2011
Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1. Science 2011, 333: 1154-1157. PMID: 21798897, PMCID: PMC3162986, DOI: 10.1126/science.1206923.Peer-Reviewed Original ResearchMeSH KeywordsCarcinomaCarcinoma, Squamous CellCell Cycle ProteinsCodon, NonsenseExonsF-Box ProteinsF-Box-WD Repeat-Containing Protein 7Gene DosageGenes, p53Genes, Tumor SuppressorHead and Neck NeoplasmsHumansINDEL MutationMutationMutation, MissenseNeoplasms, Squamous CellOligonucleotide Array Sequence AnalysisOncogenesPapillomaviridaePapillomavirus InfectionsReceptor, Notch1Sequence Analysis, DNASmokingSquamous Cell Carcinoma of Head and NeckUbiquitin-Protein LigasesConceptsNeck squamous cell carcinomaSquamous cell carcinomaCell carcinomaHuman papillomavirusHPV-positive tumorsWhole-exome sequencingMore mutationsPrimary tumorCommon cancerMultiple tumorsTobacco useTumor typesTumorsTumor suppressor geneExome sequencingGene copy number analysisNotch1Copy number analysisPatientsCarcinomaInactivating mutationCancerSuppressor geneMutationsGenetic origin
2009
GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer
Scott KL, Kabbarah O, Liang MC, Ivanova E, Anagnostou V, Wu J, Dhakal S, Wu M, Chen S, Feinberg T, Huang J, Saci A, Widlund HR, Fisher DE, Xiao Y, Rimm DL, Protopopov A, Wong KK, Chin L. GOLPH3 modulates mTOR signalling and rapamycin sensitivity in cancer. Nature 2009, 459: 1085-1090. PMID: 19553991, PMCID: PMC2753613, DOI: 10.1038/nature08109.Peer-Reviewed Original ResearchConceptsTarget of rapamycinTrans-Golgi networkHuman cancersGenome-wide copy number analysisCopy number analysisRetromer complexGolgi proteinsHuman cancer cellsRapamycin sensitivityNew oncogeneGOLPH3Integrative analysisPotent oncogeneGenomic profilesBiochemical dataCancer cellsFunction studiesNumber analysisYeastSolid tumor typesCell sizeOncogeneMTORRapamycinMTOR inhibitors
2007
Rapid identification of disease‐causing mutations using copy number analysis within linkage intervals
Bayrakli F, Bilguvar K, Mason CE, DiLuna ML, Bayri Y, Gungor L, Terzi M, Mane SM, Lifton RP, State MW, Gunel M. Rapid identification of disease‐causing mutations using copy number analysis within linkage intervals. Human Mutation 2007, 28: 1236-1240. PMID: 17676595, DOI: 10.1002/humu.20592.Peer-Reviewed Original ResearchConceptsCopy number variationsComparative genome hybridization arraysParametric linkage analysisArray-based detectionCopy number analysisDisease-causing mutationsGenome rearrangementsLinkage intervalRapid identificationAutosomal recessive parkinsonismFunctional mutationsLinkage analysisNumber variationsRecessive parkinsonismHybridization arraysPARK2 gene
2005
Rapid array‐based genomic characterization of a subtle structural abnormality: A patient with psychosis and der(18)t(5;18)(p14.1;p11.23)
Drazinic CM, Ercan‐Sencicek A, Gault LM, Hisama FM, Qumsiyeh MB, Nowak NJ, Cubells JF, State MW. Rapid array‐based genomic characterization of a subtle structural abnormality: A patient with psychosis and der(18)t(5;18)(p14.1;p11.23). American Journal Of Medical Genetics Part A 2005, 134A: 282-289. PMID: 15754353, DOI: 10.1002/ajmg.a.30616.Peer-Reviewed Original ResearchMeSH KeywordsChromosome BandingChromosomes, Artificial, BacterialChromosomes, Human, Pair 18Chromosomes, Human, Pair 5FemaleHumansIn Situ Hybridization, FluorescenceKaryotypingMagnetic Resonance ImagingMiddle AgedNucleic Acid HybridizationPolymorphism, Single NucleotidePsychotic DisordersTranslocation, GeneticConceptsBacterial artificial chromosomeChromosome 18Molecular cytogenetic mappingSingle nucleotide polymorphism arrayArray-based copy number analysisCytogenetic mappingNucleotide polymorphism arrayCopy number analysisArray-based methodsSubtle chromosomal abnormalitiesSNP chipArtificial chromosomesChromosomal intervalChromosomal rearrangementsDerivative chromosome 18Array findingsSNP arrayGenomic characterizationLinkage analysisArray-based experimentsPolymorphism array
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