2025
5. A rare case of 45X/46XY mosaic Turner syndrome in a neonate
Garg A, Hittelman A, Lepore C, Gujral J, Derar N, Vash-Margita A. 5. A rare case of 45X/46XY mosaic Turner syndrome in a neonate. Journal Of Pediatric And Adolescent Gynecology 2025, 38: 232. DOI: 10.1016/j.jpag.2025.01.038.Peer-Reviewed Original ResearchMosaic Turner syndromeTurner syndromeUrogenital sinusHemi-uterusStreak gonadsMullerian structuresFallopian tubeAmbiguous genitaliaInguinal canalSurgical findingsRare caseLeft inguinal hernia repairLeft inguinal canalRight streak gonadRisk of gonadoblastomaPrenatal cell-free DNAInguinal hernia repairSerum hormone evaluationCell-free DNAWeeks of lifeDysgenetic gonadsInguinal orchiopexySingle cervixDiagnostic laparoscopyUncomplicated pregnancies
2024
FINAL RESULTS OF A MULTICENTER STUDY COMPARING CELL-FREE DNA AND TROPHECTODERM BIOPSIES IN 2539 HUMAN BLASTOCYSTS
Sanchez L, Sakkas D, Frantz N, Soscia D, Venier W, De La Fuente Lucena E, Bisioli C, Teke B, Barroso G, Perilla D, Simon C, Lluesa C. FINAL RESULTS OF A MULTICENTER STUDY COMPARING CELL-FREE DNA AND TROPHECTODERM BIOPSIES IN 2539 HUMAN BLASTOCYSTS. Fertility And Sterility 2024, 122: e327-e328. DOI: 10.1016/j.fertnstert.2024.07.987.Peer-Reviewed Original ResearchCell-free DNATrophectoderm biopsyUltra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction
Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez F, Wang Y, Tang P, Yao Q, Bosenberg M, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. EMBO Molecular Medicine 2024, 16: 2188-2209. PMID: 39164471, PMCID: PMC11393307, DOI: 10.1038/s44321-024-00115-0.Peer-Reviewed Original ResearchMolecular residual diseaseCirculating tumor DNAWhole-genome sequencingCell-free DNAGenome sequenceDetection of molecular residual diseaseCirculating tumor DNA detectionResidual disease detectionConsistent with clinical outcomesVariant allele frequencyResidual diseaseMelanoma patientsMonitoring immunotherapyTumor DNAEsophageal cancerClinical outcomesColorectal cancerWGS technologiesAllele frequenciesCancerDNAAnalytical sensitivitySequenceImmunotherapyRelapseP-543 Multicenter concordance study of embryo cell-free DNA and trophectoderm biopsies: impact on clinical outcomes
Sánchez L, Sakkas D, Frantz N, Soscia D, Venier B, Bisioli C, DiMattina M, Ozturk B, Barroso G, Escudero E, De la Fuente E, Valbuena D, Simon C, Rubio C. P-543 Multicenter concordance study of embryo cell-free DNA and trophectoderm biopsies: impact on clinical outcomes. Human Reproduction 2024, 39: deae108.882. DOI: 10.1093/humrep/deae108.882.Peer-Reviewed Original ResearchSingle embryo transferTE biopsy resultsCell-free DNATrophectoderm biopsyMiscarriage rateBiopsy resultsClinical outcomesChi-square testNon-invasive preimplantation genetic testingFrozen single embryo transferInner cell mass biopsiesStatistical significanceCell-free DNA analysisDecrease miscarriage ratesPGT-A cyclesPreimplantation genetic testingDroplet of culture mediumLocal institutional review boardAssisted reproduction centerBiopsied blastocystsNiPGT-ATE biopsyEuploid embryosBlastocyst biopsyBlastocyst mediumP-533 Impact on clinical outcomes of day-6 extended culture and reduced culture media volume applied to non-invasive PGT-A
LLuesa C, Navarro-Sánchez L, Ardestani G, Barroso G, Bisioli C, Boynukalin K, Cimadomo D, Andrade G, Valbuena D, Simon-Valles C, Sakkas D. P-533 Impact on clinical outcomes of day-6 extended culture and reduced culture media volume applied to non-invasive PGT-A. Human Reproduction 2024, 39: deae108.873. DOI: 10.1093/humrep/deae108.873.Peer-Reviewed Original ResearchNon-invasive PGT-ACell-free DNAPGT-ASingle embryo transferClinical outcomesDay 5Pregnancy rateStudy groupNiPGT-AConcordance ratePregnancy outcomesDay 6Control groupCell-free DNA resultsDay 5 blastocystsDay 6 blastocystsClinical pregnancy rateDay of biopsyOverall pregnancy outcomeEmbryo culture protocolsBiopsy stepPGT-A.Euploidy rateBlastocyst viabilityBlastocyst qualityTranslation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology
Tan W, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Current Issues In Molecular Biology 2024, 46: 6533-6565. PMID: 39057032, PMCID: PMC11276574, DOI: 10.3390/cimb46070390.Peer-Reviewed Original ResearchCell-free DNA liquid biopsyCell-free DNALiquid biopsy technologiesLiquid biopsyBiopsy technologyEarly cancer detectionClinical applicationCfDNA-based liquid biopsyMonitoring residual diseaseEarly detection testsCancer detectionPotential of epigeneticsPersonalized cancer treatmentImprove cancer outcomesTissue of originFragmentation pattern analysisResidual diseaseDNA methylationMulti-cancer early detection testTreatment responseBiopsyCancer outcomesCancer preventionEpigeneticsPrecision oncologyLongitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy
Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiotherapy And Oncology 2024, 197: 110364. PMID: 38834154, DOI: 10.1016/j.radonc.2024.110364.Peer-Reviewed Original ResearchCopy number alterationsCell-free DNACancer patientsTumor fractionHead and neck cancer patientsPlasma cell-free DNAAssociated with tumor aggressivenessSCCHN patient samplesSystemic tumor spreadTumor-agnostic approachHigh-dose radiotherapyPlasma cfDNA samplesWhole-genome sequencingHead and neckCell-free DNA sequencing dataDetect viral DNAViral DNAOligometastatic patientsSCCHN patientsRadiotherapy guidelinesTumor spreadTumor aggressivenessImaging findingsCfDNA samplesTreatment strategiesSingle-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA
Cheng J, Swarup N, Morselli M, Huang W, Aziz M, Caggiano C, Kordi M, Patel A, Chia D, Kim Y, Li F, Wei F, Zaitlen N, Krysan K, Dubinett S, Pellegrini M, Wong D. Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA. Nucleic Acids Research 2024, 52: e50-e50. PMID: 38797520, PMCID: PMC11194076, DOI: 10.1093/nar/gkae276.Peer-Reviewed Original ResearchTranscription start siteMethylation profilesCell-free DNAWhole-genome bisulfite sequencingCytosine methylation changesLevels of DNA methylationSingle-base resolutionUpstream transcription start siteBS-seqStart siteBisulfite sequencingCpG islandsDNA fragmentationBisulfite conversionMethylation changesDNA methylationBisulfite treatmentLarge DNAsMethylation analysisDNANon-cancer samplesBisulfiteFragmentsHemopoietic cellsMethylationCulture time to optimize embryo cell-free DNA analysis for frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy
Ardestani G, Banti M, García-Pascual C, Navarro-Sánchez L, Van Zyl E, Castellón J, Simón C, Sakkas D, Rubio C. Culture time to optimize embryo cell-free DNA analysis for frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy. Fertility And Sterility 2024, 122: 465-473. PMID: 38718960, DOI: 10.1016/j.fertnstert.2024.04.037.Peer-Reviewed Original ResearchFrozen-thawed blastocystsCell-free DNANon-invasive preimplantation genetic testingPreimplantation genetic testingNiPGT-ADay 5Concordance rateDay 6Genetic testingExpansion gradeBlastocyst expansion gradeNext generation sequencingSpent mediumWhole genome amplificationBlastocyst DNABlastocyst mediumPGT-ANo significant differenceGrade 3BlastocystSignificant differenceGenome amplificationAneuploidyIdeal timeCompare timeNeural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis
Yasumizu Y, Hagiwara M, Umezu Y, Fuji H, Iwaisako K, Asagiri M, Uemoto S, Nakamura Y, Thul S, Ueyama A, Yokoi K, Tanemura A, Nose Y, Saito T, Wada H, Kakuda M, Kohara M, Nojima S, Morii E, Doki Y, Sakaguchi S, Ohkura N. Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis. NAR Cancer 2024, 6: zcae022. PMID: 38751935, PMCID: PMC11094754, DOI: 10.1093/narcan/zcae022.Peer-Reviewed Original ResearchCell deconvolutionDNA methylation dataCancer prognosisTumor-infiltrating immune cellsFormalin-fixed paraffin-embedded sectionsImmune cell profilesAssociated with cancer prognosisImmune cell statusCell-free DNADNA methylationMethylation dataParaffin-embedded sectionsPeripheral bloodImmune cellsIntrahepatic cholangiocarcinoma samplesCell profilesFlow cytometryCell populationsClinical practiceClinical settingCholangiocarcinoma samplesCellular identityEpigenetic modificationsTumorPrognosisToward Informed Selection and Interpretation of Clinical Genomic Tests in Prostate Cancer
Vandekerkhove G, Giri V, Halabi S, McNair C, Hamade K, Bitting R, Wyatt A. Toward Informed Selection and Interpretation of Clinical Genomic Tests in Prostate Cancer. JCO Precision Oncology 2024, 8: e2300654. PMID: 38547422, PMCID: PMC10994438, DOI: 10.1200/po.23.00654.Peer-Reviewed Original ResearchConceptsClinical genomic testingGenomic testingProstate cancerTumor tissuesPoly (ADP-ribose) polymerase inhibitorsPlasma cell-free DNAHereditary cancer implicationsLow tumor fractionAdvanced prostate cancerDNA damage repair genesHealth care professionalsCell-free DNANonpathogenic variantsPatient's germlineOptimal patient careSomatic alterationsSubclonal alterationsClinical decision makingClonal hematopoiesisCare professionalsGenotyping testPoor prognosisTumor fractionPatient careCancer managementDetection of sarcomatoid renal cell carcinoma using plasma cell-free DNA methylation.
Semaan K, El Zarif T, Seo J, Eid M, Canniff J, Fortunato B, Savignano H, Davidsohn M, Lakshminarayanan G, Saad E, Saliby R, Bakouny Z, Matar S, Nuzzo P, Berchuck J, Signoretti S, Braun D, Freedman M, Baca S, Choueiri T. Detection of sarcomatoid renal cell carcinoma using plasma cell-free DNA methylation. Journal Of Clinical Oncology 2024, 42: 449-449. DOI: 10.1200/jco.2024.42.4_suppl.449.Peer-Reviewed Original ResearchDifferentially methylated regionsRenal cell carcinomaCell-free DNAMeDIP-seqSarcomatoid differentiationDNA methylation signalsArea under the receiver operating characteristicHigh-throughput sequencingCell carcinomaCell-free DNA methylationFalse discovery rateResponse to immune checkpoint blockadeEpigenomic approachesCfMeDIP-seqSarcomatoid renal cell carcinomaMethylation immunoprecipitationDNA methylationHistological subtypes of cancerAssociated with poor survivalImmune checkpoint blockadeSubtypes of cancerDana-Farber Cancer InstituteSpatial heterogeneityArea under the receiver operating characteristic curveWilcoxon rank sum testFragmentstein—facilitating data reuse for cell-free DNA fragment analysis
Balázs Z, Gitchev T, Ivanković I, Krauthammer M. Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics 2024, 40: btae017. PMID: 38224549, PMCID: PMC10805340, DOI: 10.1093/bioinformatics/btae017.Peer-Reviewed Original ResearchConceptsCopy number variantsNucleotide-level informationCell-free DNA sequencing dataDNA fragmentation analysisCell-free DNASensitive genomic dataFragment length analysisNucleosome occupancyBAM filesCommand-line toolSequence dataGenomic dataAnalysis of cell-free DNASequence informationGNU GPLv3Bioinformatics softwareFragment analysisFunctional analysisAlignment mapData sharingLength analysisFragmentsSimplified formatLimited data sharingGenome989 Maternal and ultrasound characteristics associated with persistence of cell-free DNA from a vanishing twin pregnancy
Dugoff L, Kohari K, Adams T, Scholl J, Roman A, Berkin J, Hurt J, Chueh J, Wolf S, Gorman K, Palomares K, Wick M, Al-Khan A, Savasan Z, Wapner R, Livingston J, Prigmore B, Ahmed E, Butskova A, Egbert M, Vourthis S, Rochon M, Souter V. 989 Maternal and ultrasound characteristics associated with persistence of cell-free DNA from a vanishing twin pregnancy. American Journal Of Obstetrics And Gynecology 2024, 230: s521-s522. DOI: 10.1016/j.ajog.2023.11.1016.Peer-Reviewed Original Research
2023
Abstract A123: Circulating tumor DNA (ctDNA) genomic and epigenomic profiling (GuardantINFINITY) for diagnosis of DNA damage repair (DDR) loss of function (LOF) and response monitoring in the TRESR and ATTACC trials
Rosen E, Schonhoft J, Silverman I, Yablonovitch A, Sethuraman S, Nejad P, Ulanet D, Yang J, Kim I, Fei K, Xu Y, Lagow E, Zhang S, Cai M, Koehler M, Carneiro B, Lheureux S, Cecchini M, Herzberg B, Reis-Filho J, Rimkunas V, Yap T. Abstract A123: Circulating tumor DNA (ctDNA) genomic and epigenomic profiling (GuardantINFINITY) for diagnosis of DNA damage repair (DDR) loss of function (LOF) and response monitoring in the TRESR and ATTACC trials. Molecular Cancer Therapeutics 2023, 22: a123-a123. DOI: 10.1158/1535-7163.targ-23-a123.Peer-Reviewed Original ResearchCirculating tumor DNAVariant allele frequencyDNA damage repairEpigenomic profilingTumor DNADamage repairResponse monitoringCirculating tumor DNA sequencingLow variant allele frequencyTreated with PARPiPhase 1 studyCell-free DNAMolecular responseIntragenic deletionsEpigenetic analysisAllele frequenciesRad3-relatedCH variantsGenomic alterationsOn-treatmentClinical outcomesPancreatic cancerAtaxia telangiectasiaPathogenic alterationsEvaluable ptsA Highly Sensitive and Specific Non‐Invasive Test through Genome‐Wide 5‐Hydroxymethylation Mapping for Early Detection of Lung Cancer
Ren Y, Zhang Z, She Y, He Y, Li D, Shi Y, He C, Yang Y, Zhang W, Chen C. A Highly Sensitive and Specific Non‐Invasive Test through Genome‐Wide 5‐Hydroxymethylation Mapping for Early Detection of Lung Cancer. Small Methods 2023, 8: e2300747. PMID: 37990399, DOI: 10.1002/smtd.202300747.Peer-Reviewed Original ResearchConceptsNon-small-cell lung cancerArea under the curveCell-free DNACell lung cancerBlood-based testLung cancerNon-small cell lung cancerLow-dose computed tomography screeningSmall cell lung cancerComputed tomography screeningCell-free DNA samplesEarly detection of lung cancerNon-invasive testsDetect cell-free DNADetection of lung cancerDetect lung cancerPulmonary nodulesSerum biomarkersDiagnostic accuracyHealthy controlsCancerTissue originLungEarly detectionPatientsctDNA and Lung Cancer
Cheng J, Hu Y, Wong D, Patel A. ctDNA and Lung Cancer. Current Cancer Research 2023, 511-537. DOI: 10.1007/978-3-031-22903-9_20.ChaptersCell-free DNALung cancerNon-small cell lung cancerCell lung cancerMinimal residual diseaseResidual diseasePleural fluidImportant clinical applicationsClinical utilityTreatment selectionEarly cancer detectionPhysiologic underpinningsClinical modelTherapy monitoringClinical applicationCancerCancer detectionImpact of Steroid Withdrawal on Gene Expression Profiling, Donor Derived Cell-Free DNA, and Clinical Outcomes in the SHORE Registry
Bellumkonda L, Uriel N, Fu Y, Shen L, Qu K, Baran D. Impact of Steroid Withdrawal on Gene Expression Profiling, Donor Derived Cell-Free DNA, and Clinical Outcomes in the SHORE Registry. The Journal Of Heart And Lung Transplantation 2023, 42: s494. DOI: 10.1016/j.healun.2023.02.1362.Peer-Reviewed Original ResearchDe novo donor-specific antibodiesDd-cfDNA levelsCardiac allograft vasculopathySteroid withdrawalGraft dysfunctionCell-free DNAGEP scoreGene expression profilingMulti-organ transplant recipientsNovo donor-specific antibodiesDe novo DSAPost-heart transplantSteroid withdrawal groupDonor-specific antibodiesAllograft vasculopathySteroid doseCause mortalityTransplant recipientsMethods PatientsSteroid treatmentComplete discontinuationPropensity matchingClinical outcomesOutcomes RegistryWithdrawal groupA generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes
Ritch E, Herberts C, Warner E, Ng S, Kwan E, Bacon J, Bernales C, Schönlau E, Fonseca N, Giri V, Maurice-Dror C, Vandekerkhove G, Jones S, Chi K, Wyatt A. A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes. Npj Precision Oncology 2023, 7: 27. PMID: 36914848, PMCID: PMC10011564, DOI: 10.1038/s41698-023-00366-z.Peer-Reviewed Original ResearchMetastatic prostate cancerDDR gene alterationsProstate cancerGene alterationsDDR deficiencyOngoing clinical trialsPlasma cell-free DNADNA damage repair defectsLiquid biopsy specimensMismatch repair deficiencyLeukocyte DNA samplesBladder cancer samplesCell-free DNABiopsy specimensBladder cancerClinical trialsTreatment benefitMetastatic prostateGenome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer
Budhraja K, McDonald B, Stephens M, Contente-Cuomo T, Markus H, Farooq M, Favaro P, Connor S, Byron S, Egan J, Ernst B, McDaniel T, Sekulic A, Tran N, Prados M, Borad M, Berens M, Pockaj B, LoRusso P, Bryce A, Trent J, Murtaza M. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer. Science Translational Medicine 2023, 15: eabm6863. PMID: 36630480, PMCID: PMC10080578, DOI: 10.1126/scitranslmed.abm6863.Peer-Reviewed Original ResearchConceptsGenome-wide analysisNucleotide frequenciesDNA fragmentsGenome-wide differencesFragment endsNovel cancer diagnosticsCopy number amplificationChromatin accessibilityGenomic regionsGenomic positionsGC contentDNA sequencesSequencing dataDifferent cancer typesNumber amplificationCell typesCellular originSomatic mutationsCancer cellsFragment lengthCell-free DNADNACancer typesFragmentsSequence
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