2024
Single-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 cellsMethylation
2023
ctDNA 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 detection
2022
Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics
Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nature Biomedical Engineering 2022, 6: 232-245. PMID: 35102279, PMCID: PMC9336539, DOI: 10.1038/s41551-021-00837-3.Peer-Reviewed Original Research
2021
Tumor DNA Mutations From Intraparenchymal Brain Metastases Are Detectable in CSF
Cheok SK, Narayan A, Arnal-Estape A, Gettinger S, Goldberg SB, Kluger HM, Nguyen D, Patel A, Chiang V. Tumor DNA Mutations From Intraparenchymal Brain Metastases Are Detectable in CSF. JCO Precision Oncology 2021, 5: 163-172. PMID: 34250381, PMCID: PMC8232069, DOI: 10.1200/po.20.00292.Peer-Reviewed Original ResearchConceptsIntraparenchymal brain metastasesBrain metastasesCell-free DNAExtracranial tumorsBrain metastasis tissuesProgressive brain metastasesThird of patientsNormal pressure hydrocephalusTumor DNA mutationsPrimary cancer typeAnalysis of CSFSamples of CSFLeptomeningeal diseaseEffective surrogate markerBrain biopsyPressure hydrocephalusLumbar punctureSurrogate markerCancer-associated genesMetastasis tissuesPatientsMetastasisDiscordant responsesRenal cellsGenomic profiling
2020
35. EVALUATING CSF CIRCULATING TUMOR DNA IN INTRAPARENCHYMAL BRAIN METASTASIS
Cheok S, Narayan A, Arnal-Estape A, Patel A, Nguyen D, Chiang V. 35. EVALUATING CSF CIRCULATING TUMOR DNA IN INTRAPARENCHYMAL BRAIN METASTASIS. Neuro-Oncology Advances 2020, 2: ii6-ii6. PMCID: PMC7401400, DOI: 10.1093/noajnl/vdaa073.023.Peer-Reviewed Original ResearchIntraparenchymal brain metastasesBrain metastasis tissuesNormal pressure hydrocephalusBrain metastasesCerebrospinal fluidLeptomeningeal diseaseCell-free DNACSF ctDNAMetastasis tissuesTumor DNASamples of CSFStudy 12 patientsPrimary cancer typeAnalysis of CSFIntraparenchymal diseaseFurther therapySystemic metastasesPlasma ctDNASixteen patientsIntraparenchymal tumorsPressure hydrocephalusColorectal cancerLumbar punctureDetection of novelCancer-associated genes