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 factorsVariantsRisk 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 fractionAneurysm
2023
Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing
Marczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Pusztai L, Hatzis C, Symmans W. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathology 2023, 131: 289-299. PMID: 36650408, PMCID: PMC10614161, DOI: 10.1002/cncy.22679.Peer-Reviewed Original ResearchConceptsCytology smearsBreast cancerConcordance correlation coefficientTumor tissue samplesParaffin-embedded sectionsClinical diagnostic proceduresSurgical resectionRNA sequencingTumor stromaCytologic specimensDiagnostic proceduresLin's concordance correlation coefficientPapanicolaou stainCancerTissue samplesDNA mutation testingSmearsSimilar concordanceTranscriptome RNA-SeqDiagnostic cytologyAllele fractionExpression levelsRNA-seqExpression of genesGene expression levels
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
2019
Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non–Small Cell Lung Cancer
Aggarwal C, Thompson J, Black T, Katz S, Fan R, Yee S, Chien A, Evans T, Bauml J, Alley E, Ciunci C, Berman A, Cohen R, Lieberman D, Majmundar K, Savitch S, Morrissette J, Hwang W, Elenitoba-Johnson K, Langer C, Carpenter E. Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non–Small Cell Lung Cancer. JAMA Oncology 2019, 5: 173-180. PMID: 30325992, PMCID: PMC6396811, DOI: 10.1001/jamaoncol.2018.4305.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorCarcinoma, Non-Small-Cell LungClinical Decision-MakingDNA Mutational AnalysisFemaleGenetic Predisposition to DiseaseHumansLung NeoplasmsMaleMiddle AgedMutationPatient SelectionPhenotypePrecision MedicinePredictive Value of TestsPrognosisProspective StudiesConceptsNon-small cell lung cancerTissue next-generation sequencingMetastatic non-small cell lung cancerCell lung cancerTargetable mutationsNext-generation sequencingLung cancerPlasma testingStage IV non-small cell lung cancerAllele fractionNGS testingClinical implicationsPlasma next-generation sequencingPersonalized therapyReal-world clinical settingProspective cohort studyResponse Evaluation CriteriaRoutine clinical managementNumber of patientsSolid Tumors responseDNA next-generation sequencingStable diseaseMutation allele fractionCohort studyPartial response
2018
Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA
Goldberg SB, Narayan A, Kole AJ, Decker RH, Teysir J, Carriero NJ, Lee A, Nemati R, Nath SK, Mane SM, Deng Y, Sukumar N, Zelterman D, Boffa DJ, Politi K, Gettinger S, Wilson LD, Herbst RS, Patel AA. Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA. Clinical Cancer Research 2018, 24: 1872-1880. PMID: 29330207, PMCID: PMC5899677, DOI: 10.1158/1078-0432.ccr-17-1341.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerImmune checkpoint inhibitorsCtDNA responseCheckpoint inhibitorsCtDNA levelsMetastatic non-small cell lung cancerImmune checkpoint inhibitor therapySuperior progression-free survivalRadiographic tumor sizeCheckpoint inhibitor therapyProgression-free survivalSuperior overall survivalTumor DNA levelsCell lung cancerAllele fractionClin Cancer ResMultigene next-generation sequencingMutant allele fractionTumor cell deathInhibitor therapyOverall survivalRadiographic responseImmunotherapy efficacyImmunotherapy responseMedian time
2017
Feasibility of monitoring advanced melanoma patients using cell‐free DNA from plasma
Gangadhar T, Savitch S, Yee S, Xu W, Huang A, Harmon S, Lieberman D, Soucier D, Fan R, Black T, Morrissette J, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan J, Xu X, Amaravadi R, Schuchter L, Karakousis G, Hwang W, Carpenter E. Feasibility of monitoring advanced melanoma patients using cell‐free DNA from plasma. Pigment Cell & Melanoma Research 2017, 31: 73-81. PMID: 28786531, PMCID: PMC5742050, DOI: 10.1111/pcmr.12623.Peer-Reviewed Original ResearchConceptsCell-free DNAStage III/IV patientsTissue next-generation sequencingAdvanced melanoma patientsMonitoring of patientsPrevious therapyIV patientsAdvanced melanomaMelanoma patientsTumor burdenBlood drawUltra-deep sequencingPatientsPlasma mutationsLiquid biopsyNext-generation sequencingFrequent mutationsAllele fractionTherapyMore mutationsMutationsBiopsyMelanomaBRAFOverexpressed 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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