2025
Pilot study evaluating duplex sequencing of urinary DNA as a biomarker for recurrence in non-muscle invasive bladder cancer.
Ghali F, Blaha O, Lam H, Kennedy S, Wright J. Pilot study evaluating duplex sequencing of urinary DNA as a biomarker for recurrence in non-muscle invasive bladder cancer. Journal Of Clinical Oncology 2025, 43: 865-865. DOI: 10.1200/jco.2025.43.5_suppl.865.Peer-Reviewed Original ResearchNon-muscle invasive bladder cancerInvasive bladder cancerVariant allele fractionUrinary DNAIntravesical therapyBladder cancerPathogenic variantsTransurethral resection of bladder tumorMedian time to recurrenceResection of bladder tumorNext-generation sequencingDetection of recurrenceTime to recurrenceTime to relapseRecurrence of tumorBiomarkers of recurrencePilot studyTransurethral resectionBladder tumorsMedian ageRecurrenceAllele fractionUrine samplesTumorBiomarkers
2024
Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms
Hong Y, Pasca S, Shi W, Puiu D, Lake N, Lek M, Ru M, Grove M, Prizment A, Joshu C, Platz E, Guallar E, Arking D, Gondek L. Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms. Nature Communications 2024, 15: 10133. PMID: 39578475, PMCID: PMC11584845, DOI: 10.1038/s41467-024-54443-3.Peer-Reviewed Original ResearchConceptsClonal hematopoiesis of indeterminate potentialClonal hematopoiesisVariant allele fractionHeteroplasmic variantsIndeterminate potentialMyeloid neoplasmsHeteroplasmyMultiple mutationsAllele fractionMutationsHigh-risk groupPathogenic risk factorsMarkersRisk score modelDeleteriousnessSpliceosomeHematologic malignanciesRisk stratificationNeoplasm developmentNeoplasmsNeoplasm incidenceRisk factorsVariantsMapping extrachromosomal DNA amplifications during cancer progression
Kim H, Kim S, Wade T, Yeo E, Lipsa A, Golebiewska A, Johnson K, An S, Ko J, Nam Y, Lee H, Kang S, Chung H, Niclou S, Moon H, Paek S, Bafna V, Luebeck J, Verhaak R. Mapping extrachromosomal DNA amplifications during cancer progression. Nature Genetics 2024, 56: 2447-2454. PMID: 39402156, PMCID: PMC11549044, DOI: 10.1038/s41588-024-01949-7.Peer-Reviewed Original ResearchConceptsPretreatment tumorsCancer progressionChemotherapy-pretreated patientsNewly diagnosed tumorsVariant allele fractionUntreated metastasesPrimary cancerUntreated cancerTreatment responseFocal amplificationTumor samplesChromosomal amplificationsDiagnosed cancerTumorExtrachromosomal DNA amplificationsAdvanced cancerCancerEcDNATime pointsMetastasisNewlyDNA amplificationProgressionExtrachromosomal DNAPatientsRisk prediction for clonal cytopenia: multicenter real-world evidence
Xie Z, Komrokji R, Al Ali N, Regelson A, Geyer S, Patel A, Saygin C, Zeidan A, Bewersdorf J, Mendez L, Kishtagari A, Zeidner J, Coombs C, Madanat Y, Chung S, Badar T, Foran J, Desai P, Tsai C, Griffiths E, Al Malki M, Amanam I, Lai C, Deeg H, Ades L, Arana Yi C, Osman A, Dinner S, Abaza Y, Taylor J, Chandhok N, Soong D, Brunner A, Carraway H, Singh A, Elena C, Ferrari J, Gallì A, Pozzi S, Padron E, Patnaik M, Malcovati L, Savona M, Al-Kali A. Risk prediction for clonal cytopenia: multicenter real-world evidence. Blood 2024, 144: 2033-2044. PMID: 38996210, PMCID: PMC11561536, DOI: 10.1182/blood.2024024756.Peer-Reviewed Original ResearchMyeloid neoplasmsIncidence of MNClonal cytopeniaCumulative incidencePlatelet count <High-risk mutationsCox proportional hazards modelsVariant allele fractionProportional hazards modelClinical trial designCCUS patientsStratify patientsGray's testC-indexDisease entityRisk groupsCytopeniasAllele fractionSomatic mutationsRisk factorsHigh riskNatural historyRisk scoreHazards modelPatientsSomatic Variants Acquired Later in Life Associated with Thoracic Aortic Aneurysms: JAK2 V617F
Waldron C, Zafar M, Ma D, Zhang H, Dykas D, Ziganshin B, Popa A, Jha A, Kwan J, Elefteriades J. Somatic Variants Acquired Later in Life Associated with Thoracic Aortic Aneurysms: JAK2 V617F. Genes 2024, 15: 883. PMID: 39062663, PMCID: PMC11276600, DOI: 10.3390/genes15070883.Peer-Reviewed Original ResearchThoracic aortic aneurysmDevelopment of thoracic aortic aneurysmAortic aneurysmJAK2 V617FMyeloproliferative neoplasmsSomatic variantsPrevalence of thoracic aortic aneurysmsDescending thoracic aortic aneurysmJAK2 V617F burdenAortic valve diseaseTarget of therapyDriver of myeloproliferative neoplasmsSurgical aortic replacementVariant allele fractionAscending thoracic aortic aneurysmAortic replacementAneurysm sizeAneurysm patientsValve diseaseVariant carriersIncreased riskJAK2 geneExome sequencing databaseAllele fractionAneurysmCirculating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors
Hu Y, Narayan A, Xu Y, Wolfe J, Vu D, Trinh T, Kantak C, Ivy S, Eder J, Deng Y, LoRusso P, Kim J, Patel A. Circulating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors. JCO Precision Oncology 2024, 8: e2300289. PMID: 38412387, PMCID: PMC10914240, DOI: 10.1200/po.23.00289.Peer-Reviewed Original ResearchConceptsCell-free circulating tumor DNANon-small-cell lung cancerSmall-cell lung cancerTriple-negative breast cancerPancreatic ductal adenocarcinomaAdvanced solid tumorsVariant allele fractionRadiographic responseOverall survivalCombination therapySolid tumorsCtDNA levelsLung cancerPretreated advanced solid tumorsDays of combination therapyMetastatic pancreatic ductal adenocarcinomaResponse to anticancer therapyAssociated with disease progressionProgression-free survivalPlasma samplesLead-InPoly(ADP-riboseInferior OSTumor DNASurvival outcomes
2023
Unlike TET2 and ASXL1, Co-Occurring DNMT3A Mutations Are Not Associated with Increased Age in JAK2-Mutant Myeloproliferative Neoplasms (MPNs)
How J, Marneth A, Kamaz B, Kim C, Neuberg D, Ren S, Wazir M, Weeks L, Stahl M, DeAngelo D, Lindsley R, Luskin M, Hormoz S, Mullally A. Unlike TET2 and ASXL1, Co-Occurring DNMT3A Mutations Are Not Associated with Increased Age in JAK2-Mutant Myeloproliferative Neoplasms (MPNs). Blood 2023, 142: 4521. DOI: 10.1182/blood-2023-179407.Peer-Reviewed Original ResearchJAK2-mutated myeloproliferative neoplasmsJAK2-mutated patientsFraction of patientsVariant allele fractionASXL1 mutationsDNMT3A mutationsMyeloproliferative neoplasmsConcomitant mutationsMyeloproliferative neoplasms diagnosisAssociated with increasing ageEssential thrombocythemiaPolycythemia veraDriver mutationsMyeloproliferative neoplasm driver mutationsNext generation sequencingCo-mutated patientsHomozygous JAK2 mutationPhenotypic driver mutationsClinical next generation sequencingJAK2-mutantMPL mutationsMF patientsClonal hematopoiesisPV patientsJAK2 mutationCardiovascular Risk Factors Are Common in Myeloproliferative Neoplasms and Portend Worse Survival and Thrombotic Outcomes
How J, Leiva O, Marneth A, Kamaz B, Kim C, Weeks L, Wazir M, Stahl M, DeAngelo D, Lindsley R, Luskin M, Hobbs G. Cardiovascular Risk Factors Are Common in Myeloproliferative Neoplasms and Portend Worse Survival and Thrombotic Outcomes. Blood 2023, 142: 4568. DOI: 10.1182/blood-2023-179324.Peer-Reviewed Original ResearchMyeloproliferative neoplasm patientsEssential thrombocythemiaVariant allele fractionMyeloproliferative neoplasmsPolycythemia veraAcute myeloid leukemiaHistory of atherosclerotic diseaseMF patientsCV-RFCardiovascular risk factorsRisk of deathOverall survivalRisk factorsMPN diagnosisLeukemia progressionArterial thrombosisGenomic profilingHazard ratioAssociated with increased risk of deathAssociated with adverse outcomesAssociated with higher risk of deathAtherosclerotic diseaseAssociated with increased riskHigher risk of deathAssociated with higher riskTP53 mutations and Their Impact on Survival in Patients with Myeloproliferative Neoplasms
Rolles B, De Oliveira Filho C, Keating J, Luskin M, DeAngelo D, Lindsley C, Kim A, Hem J, Kim C, Weeks L, Wazir M, How J, Marneth A, Liu Y, Aryee M, Tsai H, Stahl M, Mullally A. TP53 mutations and Their Impact on Survival in Patients with Myeloproliferative Neoplasms. Blood 2023, 142: 3160. DOI: 10.1182/blood-2023-185024.Peer-Reviewed Original ResearchMyeloproliferative neoplasms diagnosisLoss of heterozygosityVariant allele fractionTP53 mutation detectionSecondary AMLTP53 mutationsMyeloproliferative neoplasm subtypeMyeloproliferative neoplasm patientsMyeloproliferative neoplasmsOverall survivalEssential thrombocythemiaCourse of diseasePolycythemia veraDriver mutationsBlast phase myeloproliferative neoplasmsChronic phase myeloproliferative neoplasmsContext of myeloproliferative neoplasmsMyeloproliferative neoplasm driver mutationsNext-generation sequencingDetect TP53 mutationsDiagnosis to detectionPost-ET/PV myelofibrosisTP53-mutant patientsTP53-mutated patientsMutation detectionUltrasensitive Circulating Tumor DNA Pilot Study Distinguishes Complete Response and Partial Response With Immunotherapy in Patients With Metastatic Renal Cell Carcinoma
Chehrazi-Raffle A, Muddasani R, Dizman N, Hsu J, Meza L, Zengin Z, Malhotra J, Chawla N, Dorff T, Contente-Cuomo T, Dinwiddie D, McDonald B, McDaniel T, Trent J, Baehner F, Murtaza M, Pal S. Ultrasensitive Circulating Tumor DNA Pilot Study Distinguishes Complete Response and Partial Response With Immunotherapy in Patients With Metastatic Renal Cell Carcinoma. JCO Precision Oncology 2023, 7: e2200543. PMID: 37027813, PMCID: PMC10309555, DOI: 10.1200/po.22.00543.Peer-Reviewed Original ResearchConceptsMetastatic renal cell carcinomaPartial responseComplete responseVariant allele fractionRenal cell carcinomaCell carcinomaCtDNA analysisImmune checkpoint inhibitor therapyCheckpoint inhibitor therapyDiscontinuation of immunotherapyDepth of responseICI therapyNivolumab monotherapyEligible patientsRadiographic progressionInhibitor therapyPeripheral bloodDisease progressionCtDNA assessmentSubsequent progressionPatientsMultiple indicationsSingle time pointPatient-specific mutationsSecondary objective
2021
SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Prashant N, Alomran N, Chen Y, Liu H, Bousounis P, Movassagh M, Edwards N, Horvath A. SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data. BMC Genomics 2021, 22: 689. PMID: 34551708, PMCID: PMC8459565, DOI: 10.1186/s12864-021-07974-8.Peer-Reviewed Original ResearchConceptsSomatic mutationsNovel somatic mutationsBackgroundRecent studiesVariant allele fractionIntra-tumoral heterogeneityVariant allelesNeuroblastoma samplesCell-level expressionCancer studiesExpression signaturesAllele fractionRegions of KRASNormal cellsType of studySmall proportionCellsExpression
2020
EM-mosaic detects mosaic point mutations that contribute to congenital heart disease
Hsieh A, Morton SU, Willcox JAL, Gorham JM, Tai AC, Qi H, DePalma S, McKean D, Griffin E, Manheimer KB, Bernstein D, Kim RW, Newburger JW, Porter GA, Srivastava D, Tristani-Firouzi M, Brueckner M, Lifton RP, Goldmuntz E, Gelb BD, Chung WK, Seidman CE, Seidman JG, Shen Y. EM-mosaic detects mosaic point mutations that contribute to congenital heart disease. Genome Medicine 2020, 12: 42. PMID: 32349777, PMCID: PMC7189690, DOI: 10.1186/s13073-020-00738-1.Peer-Reviewed Original ResearchConceptsCongenital heart diseaseHigher allele fractionHeart diseaseCardiac tissueMosaic variantsAllele fractionBlood DNAHigh variant allele fractionSomatic mosaic variantsVariant allele fractionProband-parent triosCardiac malformationsOocyte fertilizationBloodHeart tissueBenign variantsMosaic mutationsExome sequencesTissue DNACardiovascular tissuesGenetic mutationsCHD probandsTrue frequencyCohortTissue
2017
Overexpressed somatic alleles are enriched in functional elements in Breast Cancer
Restrepo P, Movassagh M, Alomran N, Miller C, Li M, Trenkov C, Manchev Y, Bahl S, Warnken S, Spurr L, Apanasovich T, Crandall K, Edwards N, Horvath A. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. Scientific Reports 2017, 7: 8287. PMID: 28811643, PMCID: PMC5557904, DOI: 10.1038/s41598-017-08416-w.Peer-Reviewed Original ResearchConceptsCancer Gene CensusDNA sequence dataCancer-implicated genesSomatic allelesCancer Genome AtlasGenome regionsSequence dataCancer transcriptomeCGC genesAllele contentAllele expressionFunctional variantsGenesGenetic variantsGenome AtlasTranscriptomeFunctional elementsAllelesExpressionVariantsVariant allele fractionRNAAllele fractionOverexpressionInformation content
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