2025
Assessment of ctDNA somatic homologous recombination deficiency (HRD) in triple-negative breast cancer (TNBC) from SWOG S1416 trial.
Stecklein S, Barlow W, Tsai J, Yablonovitch A, Rodler E, Kuhn P, Hicks J, Pathak H, Hayes D, Rae J, Hortobagyi G, Thompson A, Godwin A, Pusztai L, Sharma P. Assessment of ctDNA somatic homologous recombination deficiency (HRD) in triple-negative breast cancer (TNBC) from SWOG S1416 trial. Journal Of Clinical Oncology 2025, 43: 1012-1012. DOI: 10.1200/jco.2025.43.16_suppl.1012.Peer-Reviewed Original ResearchTriple-negative breast cancerHomologous recombination deficiencyProgression-free survivalMetastatic TNBCWildtype patientsMetastatic triple-negative breast cancerHomologous recombination deficiency phenotypePre-treatment blood samplesDetect somatic alterationsPredictive of benefitDNA-damaging chemotherapyEvaluated pre-treatmentGBRCA mutationRecombination deficiencyPARP inhibitorsSomatic alterationsGBRCABRCABreast cancerGene panelPathway alterationsVeliparibHomologous recombination repairBiomarker panelAssociated with benefitsClinicogenomic characterization of inflammatory breast cancer.
Priedigkeit N, Harrison B, Shue R, Hughes M, Li Y, Lebrón-Torres A, Kirkner G, Spurr L, Remolano M, Strauss S, Files J, Feeney A, Grant L, Mohammed-Abreu A, Garrido-Castro A, Barroso Sousa R, Bychkovsky B, Nakhlis F, Bellon J, King T, Winer E, Lindeman N, Johnson B, Sholl L, Dillon D, Overmoyer B, Tolaney S, Cherniack A, Lin N, Lynce F. Clinicogenomic characterization of inflammatory breast cancer. Clinical Cancer Research 2025, of1-of12. PMID: 40378057, DOI: 10.1158/1078-0432.ccr-24-2081.Peer-Reviewed Original ResearchInflammatory breast cancerTumor mutational burdenNon-IBC casesNon-IBCCopy number variantsSingle nucleotide variantsSomatic alterationsPoor outcomeMetastatic inflammatory breast cancerAssociated with poor outcomesFrequent somatic alterationsHER2+ diseaseHormone receptor-positiveNotch pathway alterationsCohort of patientsClinically distinct formsIBC pathogenesisMultivariate logistic regressionReceptor-positiveHER2+TP53 mutationsRB1 alterationsAggressive diseaseMutational burdenSurvival outcomes
2024
22 Association of a germline single nucleotide polymorphism (SNP) in the interleukin-7 (IL7) gene with immune-related adverse events (irAEs)
Saad E, Mehrabad E, Labaki C, Saliby R, Semaan K, Eid M, Machaalani M, Chehade R, Nawfal R, Sun M, Sharon E, Shah P, Vemula S, Gupta S, Braun D, Van Allen E, Gusev A, Choueiri T. 22 Association of a germline single nucleotide polymorphism (SNP) in the interleukin-7 (IL7) gene with immune-related adverse events (irAEs). The Oncologist 2024, 29: s1-s2. PMCID: PMC11301885, DOI: 10.1093/oncolo/oyae181.003.Peer-Reviewed Original ResearchImmune-related adverse eventsMetastatic non-small cell lung cancerMetastatic renal cell carcinomaImmune checkpoint inhibitorsProgression-free survivalWhole-exome sequencingRecurrent grade 2Overall survivalGrade 2Interleukin-7Single nucleotide polymorphismsNivolumab armPembrolizumab armSomatic alterationsAdverse eventsTreatment armsPrediction of immune-related adverse eventsCumulative rates of adverse eventsTumor whole-exome sequencingRates of grade 2Non-small cell lung cancerGermline single nucleotide polymorphismsClinical trials of patientsAssociated with significantly higher ratesPD-1 inhibitorsCharacterizing genomic alterations in patients with metastatic urothelial carcinoma (mUC) treated with enfortumab-vedotin (EV) with a focus on 1q23.3.
Saliby R, Semaan K, Epstein I, Liria S, Dall C, Saad E, Eid M, Canniff J, Kwak L, Berg S, Mantia C, McGregor B, Braun D, CHOUEIRI T, Bellmunt J. Characterizing genomic alterations in patients with metastatic urothelial carcinoma (mUC) treated with enfortumab-vedotin (EV) with a focus on 1q23.3. Journal Of Clinical Oncology 2024, 42: e16570-e16570. DOI: 10.1200/jco.2024.42.16_suppl.e16570.Peer-Reviewed Original ResearchMetastatic urothelial carcinomaToxicity-free survivalProgression-free survivalEnfortumab vedotinOverall survivalProgressive diseaseTwo-copy deletionGenomic alterationsClinical outcomesAssociation of genomic alterationsNumerically longer OSDana-Farber Cancer InstituteLog-rank testFisher's exact testUnivariate Cox regressionAdvanced UCLonger OSUrothelial carcinomaSomatic alterationsDana-FarberExact testCox regressionEV efficacyPatientsImprove outcomesToward 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 management
2022
Glioma progression is shaped by genetic evolution and microenvironment interactions
Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R, Consortium T, Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Alfaro K, Amin S, Ashley D, Bock C, Brodbelt A, Bulsara K, Castro A, Connelly J, Costello J, de Groot J, Finocchiaro G, French P, Golebiewska A, Hau A, Hong C, Horbinski C, Kannan K, Kouwenhoven M, Lasorella A, LaViolette P, Ligon K, Lowman A, Mehta S, Miletic H, Molinaro A, Ng H, Niclou S, Niers J, Phillips J, Rabadan R, Rao G, Reifenberger G, Sanai N, Short S, Smitt P, Sloan A, Smits M, Snyder J, Suzuki H, Tabatabai G, Tanner G, Tomaszewski W, Wells M, Westerman B, Wheeler H, Xie J, Yung W, Zadeh G, Zhao J, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022, 185: 2184-2199.e16. PMID: 35649412, PMCID: PMC9189056, DOI: 10.1016/j.cell.2022.04.038.Peer-Reviewed Original ResearchConceptsSpecific ligand-receptor interactionsMicroenvironment interactionsDNA sequencing dataGlioma progressionLigand-receptor interactionsNeoplastic cellsSignaling programsCell statesSequencing dataGenetic evolutionGenetic changesIDH wild-type tumorsIsocitrate dehydrogenaseMesenchymal transitionSomatic alterationsDistinct mannerActive tumor growthIDH-mutant gliomasPotential targetTherapy resistanceAdult patientsDisease progressionPossible roleCellsTumor growth
2020
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant’ Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon JC, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nature Medicine 2020, 26: 909-918. PMID: 32472114, PMCID: PMC7499153, DOI: 10.1038/s41591-020-0839-y.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAntigen PresentationAntineoplastic Agents, ImmunologicalCarcinoma, Renal CellCD8-Positive T-LymphocytesChromosome DeletionChromosomes, Human, Pair 6Chromosomes, Human, Pair 9Class I Phosphatidylinositol 3-KinasesDNA-Binding ProteinsExome SequencingFemaleFluorescent Antibody TechniqueGene DeletionGenomicsHistocompatibility Antigens Class IIHistone DemethylasesHistone-Lysine N-MethyltransferaseHumansKidney NeoplasmsLymphocytes, Tumor-InfiltratingMaleMiddle AgedMutationNivolumabPrognosisProteasome Endopeptidase ComplexPTEN PhosphohydrolaseSequence Analysis, RNATOR Serine-Threonine KinasesTranscription FactorsTuberous Sclerosis Complex 1 ProteinTumor Suppressor ProteinsUbiquitin ThiolesteraseVon Hippel-Lindau Tumor Suppressor ProteinConceptsAdvanced clear cell renal cell carcinomaClear cell renal cell carcinomaPD-1 blockadeCell renal cell carcinomaRenal cell carcinomaCell carcinomaDegree of CD8Numerous chromosomal alterationsProspective clinical trialsSomatic alterationsInfiltrated tumorsClinical responseCell infiltrationTherapeutic responseClinical trialsTherapeutic efficacyBlockadeCcRCC tumorsTumorsPBRM1 mutationsModulates responseCD8Chromosomal alterationsImmunofluorescence analysisCarcinomaComparative Molecular Life History of Spontaneous Canine and Human Gliomas
Amin S, Anderson K, Boudreau C, Martinez-Ledesma E, Kocakavuk E, Johnson K, Barthel F, Varn F, Kassab C, Ling X, Kim H, Barter M, Lau C, Ngan C, Chapman M, Koehler J, Long J, Miller A, Miller C, Porter B, Rissi D, Mazcko C, LeBlanc A, Dickinson P, Packer R, Taylor A, Rossmeisl J, Woolard K, Heimberger A, Levine J, Verhaak R. Comparative Molecular Life History of Spontaneous Canine and Human Gliomas. Cancer Cell 2020, 37: 243-257.e7. PMID: 32049048, PMCID: PMC7132629, DOI: 10.1016/j.ccell.2020.01.004.Peer-Reviewed Original ResearchConceptsComparative genomic analysisDNA methylation patternsReceptor tyrosine kinasesCell cycle pathwayGenomic analysisMethylation sequencingLife historyMutational processesTyrosine kinaseHigh similarityHuman gliomasTumorigenic mechanismsHost environmentMutational rateSomatic alterationsSporadic gliomasIDH1 R132Canine gliomasMolecular profileGlioma etiologyHuman pediatricPediatric gliomasTranscriptomeKinaseUnique insights
2019
Ampullary cancer: Evaluation of somatic and germline genetic alterations and association with clinical outcomes
Wong W, Lowery M, Berger M, Kemel Y, Taylor B, Zehir A, Srinivasan P, Bandlamudi C, Chou J, Capanu M, Varghese A, Yu K, Iacobuzio‐Donahue C, Shia J, Klimstra D, Jarnagin W, Stadler Z, O’Reilly E. Ampullary cancer: Evaluation of somatic and germline genetic alterations and association with clinical outcomes. Cancer 2019, 125: 1441-1448. PMID: 30620386, PMCID: PMC6467723, DOI: 10.1002/cncr.31951.Peer-Reviewed Original ResearchConceptsPathogenic germline alterationsAmpullary carcinomaSomatic alterationsGermline testingSomatic testingMemorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer TargetsMemorial Sloan Kettering Cancer CenterDe-identified fashionMedian overall survivalPartial radiographic responseRare gastrointestinal cancerTargetable somatic alterationsGermline genetic alterationsSubtypes of ACOpt-in strategyRadiographic responseOverall survivalMSK-IMPACTClinicopathological featuresGermline alterationsClinical outcomesPathological subtypesGenetic alterationsClinical correlatesGastrointestinal cancer
2018
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Gao Q, Liang W, Foltz S, Mutharasu G, Jayasinghe R, Cao S, Liao W, Reynolds S, Wyczalkowski M, Yao L, Yu L, Sun S, Group T, Network T, Caesar-Johnson S, Demchok J, Felau I, Kasapi M, Ferguson M, Hutter C, Sofia H, Tarnuzzer R, Wang Z, Yang L, Zenklusen J, Zhang J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Cho J, DeFreitas T, Frazer S, Gehlenborg N, Getz G, Heiman D, Kim J, Lawrence M, Lin P, Meier S, Noble M, Saksena G, Voet D, Zhang H, Bernard B, Chambwe N, Dhankani V, Knijnenburg T, Kramer R, Leinonen K, Liu Y, Miller M, Reynolds S, Shmulevich I, Thorsson V, Zhang W, Akbani R, Broom B, Hegde A, Ju Z, Kanchi R, Korkut A, Li J, Liang H, Ling S, Liu W, Lu Y, Mills G, Ng K, Rao A, Ryan M, Wang J, Weinstein J, Zhang J, Abeshouse A, Armenia J, Chakravarty D, Chatila W, de Bruijn I, Gao J, Gross B, Heins Z, Kundra R, La K, Ladanyi M, Luna A, Nissan M, Ochoa A, Phillips S, Reznik E, Sanchez-Vega F, Sander C, Schultz N, Sheridan R, Sumer S, Sun Y, Taylor B, Wang J, Zhang H, Anur P, Peto M, Spellman P, Benz C, Stuart J, Wong C, Yau C, Hayes D, Parker J, Wilkerson M, Ally A, Balasundaram M, Bowlby R, Brooks D, Carlsen R, Chuah E, Dhalla N, Holt R, Jones S, Kasaian K, Lee D, Ma Y, Marra M, Mayo M, Moore R, Mungall A, Mungall K, Robertson A, Sadeghi S, Schein J, Sipahimalani P, Tam A, Thiessen N, Tse K, Wong T, Berger A, Beroukhim R, Cherniack A, Cibulskis C, Gabriel S, Gao G, Ha G, Meyerson M, Schumacher S, Shih J, Kucherlapati M, Kucherlapati R, Baylin S, Cope L, Danilova L, Bootwalla M, Lai P, Maglinte D, Van Den Berg D, Weisenberger D, Auman J, Balu S, Bodenheimer T, Fan C, Hoadley K, Hoyle A, Jefferys S, Jones C, Meng S, Mieczkowski P, Mose L, Perou A, Perou C, Roach J, Shi Y, Simons J, Skelly T, Soloway M, Tan D, Veluvolu U, Fan H, Hinoue T, Laird P, Shen H, Zhou W, Bellair M, Chang K, Covington K, Creighton C, Dinh H, Doddapaneni H, Donehower L, Drummond J, Gibbs R, Glenn R, Hale W, Han Y, Hu J, Korchina V, Lee S, Lewis L, Li W, Liu X, Morgan M, Morton D, Muzny D, Santibanez J, Sheth M, Shinbrot E, Wang L, Wang M, Wheeler D, Xi L, Zhao F, Hess J, Appelbaum E, Bailey M, Cordes M, Ding L, Fronick C, Fulton L, Fulton R, Kandoth C, Mardis E, McLellan M, Miller C, Schmidt H, Wilson R, Crain D, Curley E, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Thompson E, Yena P, Bowen J, Gastier-Foster J, Gerken M, Leraas K, Lichtenberg T, Ramirez N, Wise L, Zmuda E, Corcoran N, Costello T, Hovens C, Carvalho A, de Carvalho A, Fregnani J, Longatto-Filho A, Reis R, Scapulatempo-Neto C, Silveira H, Vidal D, Burnette A, Eschbacher J, Hermes B, Noss A, Singh R, Anderson M, Castro P, Ittmann M, Huntsman D, Kohl B, Le X, Thorp R, Andry C, Duffy E, Lyadov V, Paklina O, Setdikova G, Shabunin A, Tavobilov M, McPherson C, Warnick R, Berkowitz R, Cramer D, Feltmate C, Horowitz N, Kibel A, Muto M, Raut C, Malykh A, Barnholtz-Sloan J, Barrett W, Devine K, Fulop J, Ostrom Q, Shimmel K, Wolinsky Y, Sloan A, De Rose A, Giuliante F, Goodman M, Karlan B, Hagedorn C, Eckman J, Harr J, Myers J, Tucker K, Zach L, Deyarmin B, Hu H, Kvecher L, Larson C, Mural R, Somiari S, Vicha A, Zelinka T, Bennett J, Iacocca M, Rabeno B, Swanson P, Latour M, Lacombe L, Têtu B, Bergeron A, McGraw M, Staugaitis S, Chabot J, Hibshoosh H, Sepulveda A, Su T, Wang T, Potapova O, Voronina O, Desjardins L, Mariani O, Roman-Roman S, Sastre X, Stern M, Cheng F, Signoretti S, Berchuck A, Bigner D, Lipp E, Marks J, McCall S, McLendon R, Secord A, Sharp A, Behera M, Brat D, Chen A, Delman K, Force S, Khuri F, Magliocca K, Maithel S, Olson J, Owonikoko T, Pickens A, Ramalingam S, Shin D, Sica G, Van Meir E, Zhang H, Eijckenboom W, Gillis A, Korpershoek E, Looijenga L, Oosterhuis W, Stoop H, van Kessel K, Zwarthoff E, Calatozzolo C, Cuppini L, Cuzzubbo S, DiMeco F, Finocchiaro G, Mattei L, Perin A, Pollo B, Chen C, Houck J, Lohavanichbutr P, Hartmann A, Stoehr C, Stoehr R, Taubert H, Wach S, Wullich B, Kycler W, Murawa D, Wiznerowicz M, Chung K, Edenfield W, Martin J, Baudin E, Bubley G, Bueno R, De Rienzo A, Richards W, Kalkanis S, Mikkelsen T, Noushmehr H, Scarpace L, Girard N, Aymerich M, Campo E, Giné E, Guillermo A, Van Bang N, Hanh P, Phu B, Tang Y, Colman H, Evason K, Dottino P, Martignetti J, Gabra H, Juhl H, Akeredolu T, Stepa S, Hoon D, Ahn K, Kang K, Beuschlein F, Breggia A, Birrer M, Bell D, Borad M, Bryce A, Castle E, Chandan V, Cheville J, Copland J, Farnell M, Flotte T, Giama N, Ho T, Kendrick M, Kocher J, Kopp K, Moser C, Nagorney D, O’Brien D, O’Neill B, Patel T, Petersen G, Que F, Rivera M, Roberts L, Smallridge R, Smyrk T, Stanton M, Thompson R, Torbenson M, Yang J, Zhang L, Brimo F, Ajani J, Gonzalez A, Behrens C, Bondaruk J, Broaddus R, Czerniak B, Esmaeli B, Fujimoto J, Gershenwald J, Guo C, Lazar A, Logothetis C, Meric-Bernstam F, Moran C, Ramondetta L, Rice D, Sood A, Tamboli P, Thompson T, Troncoso P, Tsao A, Wistuba I, Carter C, Haydu L, Hersey P, Jakrot V, Kakavand H, Kefford R, Lee K, Long G, Mann G, Quinn M, Saw R, Scolyer R, Shannon K, Spillane A, Stretch J, Synott M, Thompson J, Wilmott J, Al-Ahmadie H, Chan T, Ghossein R, Gopalan A, Levine D, Reuter V, Singer S, Singh B, Tien N, Broudy T, Mirsaidi C, Nair P, Drwiega P, Miller J, Smith J, Zaren H, Park J, Hung N, Kebebew E, Linehan W, Metwalli A, Pacak K, Pinto P, Schiffman M, Schmidt L, Vocke C, Wentzensen N, Worrell R, Yang H, Moncrieff M, Goparaju C, Melamed J, Pass H, Botnariuc N, Caraman I, Cernat M, Chemencedji I, Clipca A, Doruc S, Gorincioi G, Mura S, Pirtac M, Stancul I, Tcaciuc D, Albert M, Alexopoulou I, Arnaout A, Bartlett J, Engel J, Gilbert S, Parfitt J, Sekhon H, Thomas G, Rassl D, Rintoul R, Bifulco C, Tamakawa R, Urba W, Hayward N, Timmers H, Antenucci A, Facciolo F, Grazi G, Marino M, Merola R, de Krijger R, Gimenez-Roqueplo A, Piché A, Chevalier S, McKercher G, Birsoy K, Barnett G, Brewer C, Farver C, Naska T, Pennell N, Raymond D, Schilero C, Smolenski K, Williams F, Morrison C, Borgia J, Liptay M, Pool M, Seder C, Junker K, Omberg L, Dinkin M, Manikhas G, Alvaro D, Bragazzi M, Cardinale V, Carpino G, Gaudio E, Chesla D, Cottingham S, Dubina M, Moiseenko F, Dhanasekaran R, Becker K, Janssen K, Slotta-Huspenina J, Abdel-Rahman M, Aziz D, Bell S, Cebulla C, Davis A, Duell R, Elder J, Hilty J, Kumar B, Lang J, Lehman N, Mandt R, Nguyen P, Pilarski R, Rai K, Schoenfield L, Senecal K, Wakely P, Hansen P, Lechan R, Powers J, Tischler A, Grizzle W, Sexton K, Kastl A, Henderson J, Porten S, Waldmann J, Fassnacht M, L. S, Schadendorf D, Couce M, Graefen M, Huland H, Sauter G, Schlomm T, Simon R, Tennstedt P, Olabode O, Nelson M, Bathe O, Carroll P, Chan J, Disaia P, Glenn P, Kelley R, Landen C, Phillips J, Prados M, Simko J, Smith-McCune K, VandenBerg S, Roggin K, Fehrenbach A, Kendler A, Sifri S, Steele R, Jimeno A, Carey F, Forgie I, Mannelli M, Carney M, Hernandez B, Campos B, Herold-Mende C, Jungk C, Unterberg A, von Deimling A, Bossler A, Galbraith J, Jacobus L, Knudson M, Knutson T, Ma D, Milhem M, Sigmund R, Godwin A, Madan R, Rosenthal H, Adebamowo C, Adebamowo S, Boussioutas A, Beer D, Giordano T, Mes-Masson A, Saad F, Bocklage T, Landrum L, Mannel R, Moore K, Moxley K, Postier R, Walker J, Zuna R, Feldman M, Valdivieso F, Dhir R, Luketich J, Pinero E, Quintero-Aguilo M, Carlotti C, Dos Santos J, Kemp R, Sankarankuty A, Tirapelli D, Catto J, Agnew K, Swisher E, Creaney J, Robinson B, Shelley C, Godwin E, Kendall S, Shipman C, Bradford C, Carey T, Haddad A, Moyer J, Peterson L, Prince M, Rozek L, Wolf G, Bowman R, Fong K, Yang I, Korst R, Rathmell W, Fantacone-Campbell J, Hooke J, Kovatich A, Shriver C, DiPersio J, Drake B, Govindan R, Heath S, Ley T, Van Tine B, Westervelt P, Rubin M, Lee J, Aredes N, Mariamidze A, Chen K, Lazar A, Fields R, Wendl M, Van Tine B, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Reports 2018, 23: 227-238.e3. PMID: 29617662, PMCID: PMC5916809, DOI: 10.1016/j.celrep.2018.03.050.Peer-Reviewed Original ResearchGlioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium
Aldape K, Amin SB, Ashley DM, Barnholtz-Sloan JS, Bates AJ, Beroukhim R, Bock C, Brat DJ, Claus EB, Costello JF, de Groot JF, Finocchiaro G, French PJ, Gan HK, Griffith B, Herold-Mende CC, Horbinski C, Iavarone A, Kalkanis SN, Karabatsou K, Kim H, Kouwenhoven MCM, McDonald KL, Miletic H, Nam DH, Ng HK, Niclou SP, Noushmehr H, Ormond D, Poisson LM, Reifenberger G, Roncaroli F, K J, Smitt P, Smits M, Souza CF, Tabatabai G, Van Meir EG, Verhaak RGW, Watts C, Wesseling P, Woehrer A, Yung WKA, Jungk C, Hau AC, van Dyck E, Westerman BA, Yin J, Abiola O, Zeps N, Grimmond S, Buckland M, Khasraw M, Sulman EP, Muscat AM, Stead L. Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro-Oncology 2018, 20: 873-884. PMID: 29432615, PMCID: PMC6280138, DOI: 10.1093/neuonc/noy020.Peer-Reviewed Original ResearchConceptsGlioma Longitudinal Analysis ConsortiumMolecular evolutionAnalysis ConsortiumEvolution of gliomasLethal phenotypeCancer Genome AtlasEpigenetic abnormalitiesTargetable vulnerabilitiesGenome AtlasSomatic alterationsDiverse groupCurrent knowledgeAdult diffuse gliomasComprehensive understandingDiffuse gliomasKnowledge gapsEssential insightsEvolutionMolecular subtypesConsortiumPhenotypeProspective analysis of somatic and germline genetic alterations in patients with ampullary carcinomas.
Wong W, O'Reilly E, Varghese A, Yu K, Iacobuzio-Donahue C, Shia J, Klimstra D, Allen P, Lowery M. Prospective analysis of somatic and germline genetic alterations in patients with ampullary carcinomas. Journal Of Clinical Oncology 2018, 36: 308-308. DOI: 10.1200/jco.2018.36.4_suppl.308.Peer-Reviewed Original ResearchSomatic genetic testingAmpullary carcinomaGermline alterationsSomatic alterationsMSK-IMPACTFamily history of cancerRare gastrointestinal cancerTargetable somatic alterationsGermline genetic alterationsHistory of cancerOpt-in strategyMedian ageClinicopathological featuresClinical historyGenetic alterationsFamily historySubgroup analysisGastrointestinal cancerMultiple genesGenetic testingProspective analysisScreening implicationsTreatment historyPatientsGenes
2017
A prospective analysis of germline alterations (GA) in biliary tract cancer (BTC).
Lowery M, Jordan E, Kemel Y, Mukherjee S, Cercek A, Kemeny N, Varghese A, Rusek M, Boucher T, Mandelker D, Berger M, Ptashkin R, Hyman D, Klimstra D, Saltz L, O'Reilly E, Robson M, Stadler Z, Offit K, Abou-Alfa G. A prospective analysis of germline alterations (GA) in biliary tract cancer (BTC). Journal Of Clinical Oncology 2017, 35: 4085-4085. DOI: 10.1200/jco.2017.35.15_suppl.4085.Peer-Reviewed Original ResearchBiliary tract cancerHistory of cancerGermline alterationsPositive family history of cancerProspective analysisFamily history of cancerHereditary cancer predisposition syndromesMatched tumor samplesPersonal history of cancerPositive family historyCancer predisposition syndromeHereditary cancer predispositionIRB-approved protocolMedian ageMSK-IMPACTPredisposition syndromeSomatic alterationsGermline mutationsTumor samplesMismatch repair genesGermline variantsClinical dataFamily historyCancer predispositionDegree relativesSystematic analysis of telomere length and somatic alterations in 31 cancer types
Barthel F, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin S, Akdemir K, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak R. Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nature Genetics 2017, 49: 349-357. PMID: 28135248, PMCID: PMC5571729, DOI: 10.1038/ng.3781.Peer-Reviewed Original Research
2016
CSN1 Somatic Mutations in Penile Squamous Cell Carcinoma
Feber A, Worth D, Chakravarthy A, de Winter P, Shah K, Arya M, Saqib M, Nigam R, Malone P, Tan W, Rodney S, Freeman A, Jameson C, Wilson G, Powles T, Beck S, Fenton T, Sharp T, Muneer A, Kelly J. CSN1 Somatic Mutations in Penile Squamous Cell Carcinoma. Cancer Research 2016, 76: 4720-4727. PMID: 27325650, PMCID: PMC5302160, DOI: 10.1158/0008-5472.can-15-3134.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingResequencing of candidate genesPenile cancerMiRNA-mediated gene silencingCytoplasmic P-bodiesCopy-number informationAnalysis of somatic alterationsSomatic mutation landscapeDevelopment of penile cancerPenile squamous cell carcinomaTargeted resequencingCandidate genesDNA methylationGene silencingHPV-negative diseaseP-bodiesRecurrent mutationsLandscape of alterationsAPOBEC mutational signaturesSquamous cell carcinomaGermline DNASomatic alterationsMutation dataMutational signaturesGenetic alterationsGermline Variants in Targeted Tumor Sequencing Using Matched Normal DNA
Schrader K, Cheng D, Joseph V, Prasad M, Walsh M, Zehir A, Ni A, Thomas T, Benayed R, Ashraf A, Lincoln A, Arcila M, Stadler Z, Solit D, Hyman D, Zhang L, Klimstra D, Ladanyi M, Offit K, Berger M, Robson M. Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA. JAMA Oncology 2016, 2: 1-8. PMID: 26556299, PMCID: PMC5477989, DOI: 10.1001/jamaoncol.2015.5208.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorDNA Mutational AnalysisFemaleGene Expression ProfilingGenetic Predisposition to DiseaseGerm-Line MutationHumansMaleMiddle AgedModels, GeneticNeoplasmsNew York CityPhenotypePrecision MedicinePredictive Value of TestsPrognosisRisk AssessmentRisk FactorsConceptsTumor-normal sequencingPathogenic germline variantsGermline variantsAdvanced cancer diagnosisClinical tumor sequencingCancer susceptibility genesTumor sequencingMemorial Sloan Kettering Cancer CenterStudies of targeted agentsIndividual cancer typesTumor genetic sequencingGermline findingsProportion of individualsTumor-specific variantsMendelian disease genesTargetable genetic alterationsCancer susceptibilityMatched normal DNACancer diagnosisTargeted tumor sequencingSingle-gene disordersCancer CenterMSK-IMPACTTumor profilingSomatic alterations
2014
Integrative post-genome-wide association analysis of CDKN2A and TP53 SNPs and risk of esophageal adenocarcinoma
Buas MF, Levine DM, Makar KW, Utsugi H, Onstad L, Li X, Galipeau PC, Shaheen NJ, Hardie LJ, Romero Y, Bernstein L, Gammon MD, Casson AG, Bird NC, Risch HA, Ye W, Liu G, Corley DA, Blount PL, Fitzgerald RC, Whiteman DC, Wu AH, Reid BJ, Vaughan TL. Integrative post-genome-wide association analysis of CDKN2A and TP53 SNPs and risk of esophageal adenocarcinoma. Carcinogenesis 2014, 35: 2740-2747. PMID: 25280564, PMCID: PMC4247522, DOI: 10.1093/carcin/bgu207.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAgedBarrett EsophagusCase-Control StudiesCyclin-Dependent Kinase Inhibitor p16Disease ProgressionEsophageal NeoplasmsFemaleFollow-Up StudiesGenome-Wide Association StudyHumansMaleMiddle AgedNeoplasm StagingPolymorphism, Single NucleotidePrognosisRisk FactorsTumor Suppressor Protein p53ConceptsEsophageal adenocarcinomaBarrett's esophagusSingle nucleotide polymorphismsRisk of EACPredictors of progressionGermline single nucleotide polymorphismsTP53 single nucleotide polymorphismsNucleotide polymorphismsCDKN2A polymorphismsEA tumorsFrequent somatic mutationsProspective cohortCDKN2A variantsMale genderRisk factorsReduced riskTumor suppressor gene CDKN2ACaucasian raceMiR-663bEA casesSomatic alterationsGermline variationAdenocarcinomaGenes CDKN2AEsophagus
2012
Next-generation sequencing of FFPE solid tumor specimens for clinical use.
Yelensky R, Wang K, Dogan S, Borsu L, Frampton G, Lipson D, Stephens P, Bastian B, Klimstra D, Ladanyi M, Cronin M, Hedvat C, Berger M. Next-generation sequencing of FFPE solid tumor specimens for clinical use. Journal Of Clinical Oncology 2012, 30: 10524-10524. DOI: 10.1200/jco.2012.30.15_suppl.10524.Peer-Reviewed Original ResearchNext-generation sequencingCopy changesNext-generation sequencing approachGenomic alterationsLoss-of-function variantsMutant allele frequencyIndividual base pairsConcordant callsFFPE specimensSequence dataGene characterizationLibrary constructionCancer genesBase pairsSolid tumor specimensAllele frequenciesSomatic alterationsDetect mutationsPotential clinical roleInfluence treatment decisionsFusion geneExonMutationsAverage coverageHybridization capture
2011
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Galante P, Parmigiani R, Zhao Q, Caballero O, de Souza J, Navarro F, Gerber A, Nicolás M, Salim A, Silva A, Edsall L, Devalle S, Almeida L, Ye Z, Kuan S, Pinheiro D, Tojal I, Pedigoni R, de Sousa R, Oliveira T, de Paula M, Ohno-Machado L, Kirkness E, Levy S, da Silva W, Vasconcelos A, Ren B, Zago M, Strausberg R, Simpson A, de Souza S, Camargo A. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research 2011, 39: 6056-6068. PMID: 21493686, PMCID: PMC3152357, DOI: 10.1093/nar/gkr221.Peer-Reviewed Original ResearchConceptsTumor genomesSomatic alterationsProtein-protein interaction analysisSynonymous substitutionsKEGG analysisEndogenous mutagensGenomeTumorigenic transformationNucleotide substitutionsBreast tumor cell linesReplication errorsTumor cell linesGenetic alterationsFrequency of mutationsCell linesTumorigenesisMutationsSynergistic functionDistinct patternsInteraction analysisLymphoblastoidAlterationsGenesSame individualPathway
2002
Genetic and Immunohistochemical Analysis of Pancreatic Acinar Cell Carcinoma Frequent Allelic Loss on Chromosome 11p and Alterations in the APC/β-Catenin Pathway
Abraham S, Wu T, Hruban R, Lee J, Yeo C, Conlon K, Brennan M, Cameron J, Klimstra D. Genetic and Immunohistochemical Analysis of Pancreatic Acinar Cell Carcinoma Frequent Allelic Loss on Chromosome 11p and Alterations in the APC/β-Catenin Pathway. American Journal Of Pathology 2002, 160: 953-962. PMID: 11891193, PMCID: PMC1867188, DOI: 10.1016/s0002-9440(10)64917-6.Peer-Reviewed Original ResearchMeSH KeywordsAdenomatous Polyposis Coli ProteinAdolescentAdultAgedbeta CateninCarcinoma, Acinar CellChild, PreschoolChromosomes, Human, Pair 11Chromosomes, Human, Pair 5Cytoskeletal ProteinsFemaleGenes, Tumor SuppressorHumansImmunohistochemistryLoss of HeterozygosityMaleMiddle AgedMutationPancreatic NeoplasmsSignal TransductionTrans-ActivatorsConceptsAllelic lossChromosome 11pAcinar cell carcinomaAPC/beta-catenin pathwayAllelic shiftsAPC/beta-cateninFrequency of allelic lossChromosome arm 11pPancreatic ductal adenocarcinomaFrequent allelic lossDpc4 protein expressionBeta-catenin oncogeneMicrosatellite markersDuctal adenocarcinomaPolymerase chain amplificationMolecular alterationsMicrosatellite instabilityTruncating APC mutationsSomatic alterationsChromosomeRare pancreatic neoplasmP53 accumulationGenetic alterationsBeta-CateninMicrosatellite
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply