2019
Sequencing and curation strategies for identifying candidate glioblastoma treatments
Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB. Sequencing and curation strategies for identifying candidate glioblastoma treatments. BMC Medical Genomics 2019, 12: 56. PMID: 31023376, PMCID: PMC6485090, DOI: 10.1186/s12920-019-0500-0.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overFemaleGlioblastomaHigh-Throughput Nucleotide SequencingHumansMaleMiddle AgedMolecular Targeted TherapyPloidiesReproducibility of ResultsWhole Genome SequencingConceptsPotential treatment optionClinical research studiesWhole-genome sequencingPharmacologic interventionsCancer patientsTreatment optionsClinical resultsPatientsConclusionThese resultsGlioblastoma treatmentPotential cancer treatmentPanel sequencingActionable variantsCancer treatmentGlioblastoma tumorsSame variantSequencing assaysDrug targetsRNA sequencingRNA-seqTreatmentNew York CitySequencingTumorsCliniciansTumor mutational load predicts survival after immunotherapy across multiple cancer types
Samstein RM, Lee CH, Shoushtari AN, Hellmann MD, Shen R, Janjigian YY, Barron DA, Zehir A, Jordan EJ, Omuro A, Kaley TJ, Kendall SM, Motzer RJ, Hakimi AA, Voss MH, Russo P, Rosenberg J, Iyer G, Bochner BH, Bajorin DF, Al-Ahmadie HA, Chaft JE, Rudin CM, Riely GJ, Baxi S, Ho AL, Wong RJ, Pfister DG, Wolchok JD, Barker CA, Gutin PH, Brennan CW, Tabar V, Mellinghoff IK, DeAngelis LM, Ariyan CE, Lee N, Tap WD, Gounder MM, D’Angelo S, Saltz L, Stadler ZK, Scher HI, Baselga J, Razavi P, Klebanoff CA, Yaeger R, Segal NH, Ku GY, DeMatteo RP, Ladanyi M, Rizvi NA, Berger MF, Riaz N, Solit DB, Chan TA, Morris LGT. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nature Genetics 2019, 51: 202-206. PMID: 30643254, PMCID: PMC6365097, DOI: 10.1038/s41588-018-0312-8.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsHigh-Throughput Nucleotide SequencingHumansImmunotherapyMutationNeoplasmsTumor BurdenConceptsTumor mutational burdenHigh tumor mutational burdenImproved survivalCancer typesImmune checkpoint inhibitor treatmentAdvanced cancer patientsBetter overall survivalCheckpoint inhibitor treatmentMultiple cancer typesClinical responseOverall survivalCancer patientsPredictive biomarkersCancer histologyMetastatic cancerMutational burdenPatientsInhibitor treatmentNext-generation sequencingSurvivalICIMutational loadUniversal definitionAssociationImmunotherapy
2017
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine 2017, 23: 703-713. PMID: 28481359, PMCID: PMC5461196, DOI: 10.1038/nm.4333.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorCohort StudiesData MiningDNA, NeoplasmFeasibility StudiesFemaleGenomicsHigh-Throughput Nucleotide SequencingHumansMaleMutationNeoplasm MetastasisNeoplasmsProspective StudiesSequence Analysis, DNAConceptsMemorial Sloan-Kettering Cancer CenterCancer-related genesProspective clinical sequencingAdvanced solid cancersSequencing platformsStructural variantsGenomic landscapeGenomic mutationsDetailed clinical annotationMutational landscapeSequencing resultsNumber alterationsCancer CenterPatient enrollmentClinical trialsMSK-IMPACTMetastatic cancerSolid cancersNew insightsNormal tissuesClinical sequencingCancer therapyPatientsCancerClinical annotation
2016
Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid
Pentsova EI, Shah RH, Tang J, Boire A, You D, Briggs S, Omuro A, Lin X, Fleisher M, Grommes C, Panageas KS, Meng F, Selcuklu SD, Ogilvie S, Distefano N, Shagabayeva L, Rosenblum M, DeAngelis LM, Viale A, Mellinghoff IK, Berger MF. Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid. Journal Of Clinical Oncology 2016, 34: 2404-2415. PMID: 27161972, PMCID: PMC4981784, DOI: 10.1200/jco.2016.66.6487.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBrain NeoplasmsCell-Free SystemDNA, NeoplasmFemaleHigh-Throughput Nucleotide SequencingHumansMaleMiddle AgedMutationConceptsCentral nervous systemPrimary brain tumorsCerebrospinal fluidCell-free DNACNS involvementBrain tumorsNervous systemCommon malignant primary brain tumorMalignant primary brain tumorRoutine lumbar punctureRelevant genomic alterationsCNS metastasesCNS cancersLumbar punctureCancer-associated genesTumor disseminationHarbored mutationsPatientsTumor evolutionSolid tumorsTumor progressionTumor tissueCancerLiquid biopsyTumors