2024
Circulating 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
The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring
Batool S, Yekula A, Khanna P, Hsia T, Gamblin A, Ekanayake E, Escobedo A, You D, Castro C, Im H, Kilic T, Garlin M, Skog J, Dinulescu D, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle D, Chia D, Elashoff D, Grognan T, Krysan K, Oh S, Strom C, Tu M, Wei F, Xian R, Skates S, Zhang D, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel S, Yang C, Shen C, Hochberg F, Wong D, Patel A, Papadopoulos N, Bettegowda C, Cote R, Srivastava S, Lee H, Carter B, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Reports Medicine 2023, 4: 101198. PMID: 37716353, PMCID: PMC10591039, DOI: 10.1016/j.xcrm.2023.101198.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
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
Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing
Song P, Chen SX, Yan YH, Pinto A, Cheng LY, Dai P, Patel AA, Zhang DY. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nature Biomedical Engineering 2021, 5: 690-701. PMID: 33941896, PMCID: PMC9631981, DOI: 10.1038/s41551-021-00713-0.Peer-Reviewed Original ResearchTumor 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
2019
Overall survival is improved when DCIS accompanies invasive breast cancer
Kole AJ, Park HS, Johnson SB, Kelly JR, Moran MS, Patel AA. Overall survival is improved when DCIS accompanies invasive breast cancer. Scientific Reports 2019, 9: 9934. PMID: 31289308, PMCID: PMC6616329, DOI: 10.1038/s41598-019-46309-2.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingCarcinoma, LobularCombined Modality TherapyFemaleFollow-Up StudiesHumansMiddle AgedNeoplasm InvasivenessPrognosisReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneRetrospective StudiesSurvival RateConceptsInvasive ductal carcinomaOverall survivalDCIS componentDuctal carcinomaBreast cancerER/PR positivityPure invasive ductal carcinomasMultivariable Cox modelingReceipt of mastectomyNational Cancer DatabaseSuperior overall survivalNode-negative diseaseBetter overall survivalInvasive breast cancerFavorable clinical characteristicsTreatment-related variablesUseful prognostic factorBreast cancer patientsInvasive tumor sizeDifferent biological behaviorPR positivityClinical characteristicsNegative diseaseCox modelingPrognostic factors
2018
Monitoring immunotherapy outcomes with circulating tumor DNA
Goldberg SB, Patel AA. Monitoring immunotherapy outcomes with circulating tumor DNA. Immunotherapy 2018, 10: 1023-1025. PMID: 30185140, DOI: 10.2217/imt-2018-0084.Peer-Reviewed Original ResearchOligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors
Lopez Sambrooks C, Baro M, Quijano A, Narayan A, Cui W, Greninger P, Egan R, Patel A, Benes CH, Saltzman WM, Contessa JN. Oligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors. Cancer Research 2018, 78: canres.0505.2018. PMID: 30026325, PMCID: PMC6125176, DOI: 10.1158/0008-5472.can-18-0505.Peer-Reviewed Original ResearchConceptsMutant NSCLCMutant non-small cell lung cancerNon-small cell lung cancerSignificant tumor growth delayEGFR-TKI treatmentCell lung cancerTyrosine kinase inhibitor resistanceEGFR tyrosine kinase inhibitor resistanceLung cancer cell linesNGI-1Tumor growth delayEffective therapeutic targetCell linesKinase inhibitor resistanceTumor cell viabilityH1975 xenograftsCancer cell linesTKI treatmentComplex transmembrane proteinsEGFR-TKILung cancerTumor responseCell cycle arrestPreclinical modelsTherapeutic strategiesEarly 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 timeA novel multiple biomarker panel for the early detection of high-grade serous ovarian carcinoma
Han C, Bellone S, Siegel ER, Altwerger G, Menderes G, Bonazzoli E, Egawa-Takata T, Pettinella F, Bianchi A, Riccio F, Zammataro L, Yadav G, Marto JA, Penet MF, Levine DA, Drapkin R, Patel A, Litkouhi B, Ratner E, Silasi DA, Huang GS, Azodi M, Schwartz PE, Santin AD. A novel multiple biomarker panel for the early detection of high-grade serous ovarian carcinoma. Gynecologic Oncology 2018, 149: 585-591. PMID: 29572027, PMCID: PMC5986604, DOI: 10.1016/j.ygyno.2018.03.050.Peer-Reviewed Original ResearchConceptsHigh-grade serous ovarian carcinomaSerous ovarian carcinomaIL-6Ovarian cancerOvarian carcinomaE-cadHigh-grade serous ovarian adenocarcinomaEarly-stage ovarian cancerROC analysisEarly detectionMajority of patientsLethal gynecologic malignancyStage ovarian cancerOvarian cancer patientsBenign gynecologic pathologyNon-cancer controlsSerous ovarian adenocarcinomaEffective cancer screeningSerous ovarian cancerMultiple biomarker panelsFour-marker panelHigh differential gene expressionGynecologic malignanciesCA 125IL-1ra
2015
High-throughput RNA profiling via up-front sample parallelization
Narayan A, Bommakanti A, Patel AA. High-throughput RNA profiling via up-front sample parallelization. Nature Methods 2015, 12: 343-346. PMID: 25730493, PMCID: PMC4451056, DOI: 10.1038/nmeth.3311.Peer-Reviewed Original Research
2012
Ultrasensitive Measurement of Hotspot Mutations in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep Sequencing
Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA. Ultrasensitive Measurement of Hotspot Mutations in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep Sequencing. Cancer Research 2012, 72: 3492-3498. PMID: 22581825, PMCID: PMC3426449, DOI: 10.1158/0008-5472.can-11-4037.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerTumor DNATumor DNA levelsCell lung cancerCell-free tumor DNATreatment-associated changesDNA levelsTumor-specific mutationsPractical diagnostic testLung cancerPractical clinical implementationPatient samplesDiagnostic testsHotspot mutationsClinical implementationNext-generation sequencingBloodCancer biomarkersSuccessful useNormal DNAMutationsPatientsDeep sequencing
2009
Implications of Respiratory Motion as Measured by Four-Dimensional Computed Tomography for Radiation Treatment Planning of Esophageal Cancer
Patel AA, Wolfgang JA, Niemierko A, Hong TS, Yock T, Choi NC. Implications of Respiratory Motion as Measured by Four-Dimensional Computed Tomography for Radiation Treatment Planning of Esophageal Cancer. International Journal Of Radiation Oncology • Biology • Physics 2009, 74: 290-296. PMID: 19362248, DOI: 10.1016/j.ijrobp.2008.12.060.Peer-Reviewed Original ResearchConceptsLymph nodesFour-dimensional computed tomographyPrimary tumorEsophageal cancerCT scanComputed tomographyRespiratory tumor motionDistal esophageal tumorsDistal thoracic esophagusEsophageal primary tumorsPrimary esophageal cancerMassachusetts General HospitalTumor motionRespiratory motionDistal tumorsCurative treatmentThoracic esophagusEsophageal tumorsGeneral HospitalLeft-right directionsAnatomic locationRadiation treatment planningLR dimensionAP motionTumors
2006
Estimation of the delivered patient dose in lung IMRT treatment based on deformable registration of 4D-CT data and Monte Carlo simulations
Flampouri S, Jiang SB, Sharp GC, Wolfgang J, Patel AA, Choi NC. Estimation of the delivered patient dose in lung IMRT treatment based on deformable registration of 4D-CT data and Monte Carlo simulations. Physics In Medicine And Biology 2006, 51: 2763-2779. PMID: 16723765, DOI: 10.1088/0031-9155/51/11/006.Peer-Reviewed Original ResearchConceptsHelical CTWhole breathing cycleFree-breathing CTBreathing phasesClinical outcomesRetrospective studyCT scanPrescribed dosePTV expansionCTV volumePatientsDoseEUD valuesIMRT plansGTVComposite dose distributionCTHealthy tissuePatient doseCT setsTumor motionBreathing cycleTreatment planning systemDosesIMRT treatment
2003
Splicing double: insights from the second spliceosome
Patel AA, Steitz JA. Splicing double: insights from the second spliceosome. Nature Reviews Molecular Cell Biology 2003, 4: 960-970. PMID: 14685174, DOI: 10.1038/nrm1259.Peer-Reviewed Original ResearchConceptsMinor class intronsPhylogenetic analysisU12-type intronsMost multicellular organismsSmall nuclear RNASmall nuclear ribonucleoproteinParticular functional classNon-homologous positionsMessenger RNA interactionsMost metazoan taxaParalogous genesMulticellular organismsSpliceosomal factorsHomologous genesEvolutionary historyMetazoan taxaU5 snRNPSplicing machineryAcceptor splice siteAlternative splicingRNA interactionsU6 snRNPsNuclear RNANuclear ribonucleoproteinSplicing reaction