Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.
Nature Communications
Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA
Impact of EGFRA289T/V mutation on relapse pattern in glioblastoma.
Esmo Open
Noeuveglise, A A; Sarafan-Vasseur, N N; Beaussire, L L; Marguet, F F; Modzelewski, R R; Hanzen, C C; Alexandru, C C; Magne, N N; Langlois, O O; Di Fiore, F F; Clatot, F F; Thureau, S S; Fontanilles, M M
Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors.
Neuro-Oncology
Kashani, Elham E; Schnidrig, Désirée D; Hashemi Gheinani, Ali A; Ninck, Martina Selina MS; Zens, Philipp P; Maragkou, Theoni T; Baumgartner, Ulrich U; Schucht, Philippe P; Rätsch, Gunnar G; Rubin, Mark A MA; Berezowska, Sabina S; Ng, Charlotte K Y CKY; Vassella, Erik E; ,
Publication Date: 2022-09-17
Variant appearance in text: EGFR: 664C>T; Arg222Cys
Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma.
Nature Communications
Gounder, Mrinal M MM; Agaram, Narasimhan P NP; Trabucco, Sally E SE; Robinson, Victoria V; Ferraro, Richard A RA; Millis, Sherri Z SZ; Krishnan, Anita A; Lee, Jessica J; Attia, Steven S; Abida, Wassim W; Drilon, Alexander A; Chi, Ping P; Angelo, Sandra P D' SP; Dickson, Mark A MA; Keohan, Mary Lou ML; Kelly, Ciara M CM; Agulnik, Mark M; Chawla, Sant P SP; Choy, Edwin E; Chugh, Rashmi R; Meyer, Christian F CF; Myer, Parvathi A PA; Moore, Jessica L JL; Okimoto, Ross A RA; Pollock, Raphael E RE; Ravi, Vinod V; Singh, Arun S AS; Somaiah, Neeta N; Wagner, Andrew J AJ; Healey, John H JH; Frampton, Garrett M GM; Venstrom, Jeffrey M JM; Ross, Jeffrey S JS; Ladanyi, Marc M; Singer, Samuel S; Brennan, Murray F MF; Schwartz, Gary K GK; Lazar, Alexander J AJ; Thomas, David M DM; Maki, Robert G RG; Tap, William D WD; Ali, Siraj M SM; Jin, Dexter X DX
Custom multi‑tumor next‑generation sequencing panel for routine molecular diagnosis of solid tumors: Validation and results from three‑year clinical use.
International Journal Of Molecular Medicine
Chevrier, Sandy S; Brasselet, Astrid A; Carnet, Marion M; Chevriaux, Angélique A; Gibeaud, Anne A; Jourdain, Marine M; Mananet, Hugo H; Truntzer, Caroline C; Beltjens, Françoise F; Charon-Barra, Céline C; Arnould, Laurent L; Albuisson, Juliette J; Comte, Anthony A; Derangère, Valentin V; Goussot, Vincent V; Boidot, Romain R
Publication Date: 2022-05
Variant appearance in text: EGFR: 664C>T; Arg222Cys
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants.
Nature Biotechnology
Sánchez-Rivera, Francisco J FJ; Diaz, Bianca J BJ; Kastenhuber, Edward R ER; Schmidt, Henri H; Katti, Alyna A; Kennedy, Margaret M; Tem, Vincent V; Ho, Yu-Jui YJ; Leibold, Josef J; Paffenholz, Stella V SV; Barriga, Francisco M FM; Chu, Kevan K; Goswami, Sukanya S; Wuest, Alexandra N AN; Simon, Janelle M JM; Tsanov, Kaloyan M KM; Chakravarty, Debyani D; Zhang, Hongxin H; Leslie, Christina S CS; Lowe, Scott W SW; Dow, Lukas E LE
Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas.
Neuro-Oncology Advances
van de Geer, Wesley S WS; Hoogstrate, Youri Y; Draaisma, Kaspar K; Robe, Pierre A PA; Bins, Sander S; Mathijssen, Ron H J RHJ; French, Pim P; van de Werken, Harmen J G HJG; de Vos, Filip Y F FYF
Genomic landscape of gliosarcoma: distinguishing features and targetable alterations.
Scientific Reports
Zaki, Mark M MM; Mashouf, Leila A LA; Woodward, Eleanor E; Langat, Pinky P; Gupta, Saksham S; Dunn, Ian F IF; Wen, Patrick Y PY; Nahed, Brian V BV; Bi, Wenya Linda WL
Nivolumab Plus Ipilimumab vs Nivolumab for Previously Treated Patients With Stage IV Squamous Cell Lung Cancer: The Lung-MAP S1400I Phase 3 Randomized Clinical Trial.
Jama Oncology
Gettinger, Scott N SN; Redman, Mary W MW; Bazhenova, Lyudmila L; Hirsch, Fred R FR; Mack, Philip C PC; Schwartz, Lawrence H LH; Bradley, Jeffrey D JD; Stinchcombe, Thomas E TE; Leighl, Natasha B NB; Ramalingam, Suresh S SS; Tavernier, Susan S SS; Yu, Hui H; Unger, Joseph M JM; Minichiello, Katherine K; Highleyman, Louise L; Papadimitrakopoulou, Vassiliki A VA; Kelly, Karen K; Gandara, David R DR; Herbst, Roy S RS
FGFR3 overexpression is a useful detection tool for FGFR3 fusions and sequence variations in glioma.
Neuro-Oncology Practice
Schittenhelm, Jens J; Ziegler, Lukas L; Sperveslage, Jan J; Mittelbronn, Michel M; Capper, David D; Burghardt, Isabel I; Poso, Antti A; Biskup, Saskia S; Skardelly, Marco M; Tabatabai, Ghazaleh G
Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors.
Jama Oncology
Cobain, Erin F EF; Wu, Yi-Mi YM; Vats, Pankaj P; Chugh, Rashmi R; Worden, Francis F; Smith, David C DC; Schuetze, Scott M SM; Zalupski, Mark M MM; Sahai, Vaibhav V; Alva, Ajjai A; Schott, Anne F AF; Caram, Megan E V MEV; Hayes, Daniel F DF; Stoffel, Elena M EM; Jacobs, Michelle F MF; Kumar-Sinha, Chandan C; Cao, Xuhong X; Wang, Rui R; Lucas, David D; Ning, Yu Y; Rabban, Erica E; Bell, Janice J; Camelo-Piragua, Sandra S; Udager, Aaron M AM; Cieslik, Marcin M; Lonigro, Robert J RJ; Kunju, Lakshmi P LP; Robinson, Dan R DR; Talpaz, Moshe M; Chinnaiyan, Arul M AM
Correlation of genetic alterations by whole-exome sequencing with clinical outcomes of glioblastoma patients from the Lebanese population.
Plos One
Saadeh, Fadi S FS; Morsi, Rami Z RZ; El-Kurdi, Abdallah A; Nemer, Georges G; Mahfouz, Rami R; Charafeddine, Maya M; Khoury, Jessica J; Najjar, Marwan W MW; Khoueiry, Pierre P; Assi, Hazem I HI
TP53 mutations and CDKN2A mutations/deletions are highly recurrent molecular alterations in the malignant progression of sinonasal papillomas.
Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc
Brown, Noah A NA; Plouffe, Komal R KR; Yilmaz, Osman O; Weindorf, Steven C SC; Betz, Bryan L BL; Carey, Thomas E TE; Seethala, Raja R RR; McHugh, Jonathan B JB; Tomlins, Scott A SA; Udager, Aaron M AM
TP53 mutations and CDKN2A mutations/deletions are highly recurrent molecular alterations in the malignant progression of sinonasal papillomas.
Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc
Brown, Noah A NA; Plouffe, Komal R KR; Yilmaz, Osman O; Weindorf, Steven C SC; Betz, Bryan L BL; Carey, Thomas E TE; Seethala, Raja R RR; McHugh, Jonathan B JB; Tomlins, Scott A SA; Udager, Aaron M AM
A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population.
Breast Cancer Research : Bcr
Kang, Taekyu T; Yau, Christina C; Wong, Christopher K CK; Sanborn, John Z JZ; Newton, Yulia Y; Vaske, Charlie C; Benz, Stephen C SC; Krings, Gregor G; Camarda, Roman R; Henry, Jill E JE; Stuart, Josh J; Powell, Mark M; Benz, Christopher C CC
Identification of relevant genetic alterations in cancer using topological data analysis.
Nature Communications
Rabadán, Raúl R; Mohamedi, Yamina Y; Rubin, Udi U; Chu, Tim T; Alghalith, Adam N AN; Elliott, Oliver O; Arnés, Luis L; Cal, Santiago S; Obaya, Álvaro J ÁJ; Levine, Arnold J AJ; Cámara, Pablo G PG
EGFR mutations are associated with response to depatux-m in combination with temozolomide and result in a receptor that is hypersensitive to ligand.
Neuro-Oncology Advances
Hoogstrate, Youri Y; Vallentgoed, Wies W; Kros, Johan M JM; de Heer, Iris I; de Wit, Maurice M; Eoli, Marica M; Sepulveda, Juan Manuel JM; Walenkamp, Annemiek M E AME; Frenel, Jean-Sebastien JS; Franceschi, Enrico E; Clement, Paul M PM; Weller, Micheal M; van Royen, Martin E ME; Ansell, Peter P; Looman, Jim J; Bain, Earle E; Morfouace, Marie M; Gorlia, Thierry T; Golfinopoulos, Vassilis V; van den Bent, Martin M; French, Pim J PJ
mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.
Cell Reports
Triki, Mouna M; Rinaldi, Gianmarco G; Planque, Melanie M; Broekaert, Dorien D; Winkelkotte, Alina M AM; Maier, Carina R CR; Janaki Raman, Sudha S; Vandekeere, Anke A; Van Elsen, Joke J; Orth, Martin F MF; Grünewald, Thomas G P TGP; Schulze, Almut A; Fendt, Sarah-Maria SM
Phase and context shape the function of composite oncogenic mutations.
Nature
Gorelick, Alexander N AN; Sánchez-Rivera, Francisco J FJ; Cai, Yanyan Y; Bielski, Craig M CM; Biederstedt, Evan E; Jonsson, Philip P; Richards, Allison L AL; Vasan, Neil N; Penson, Alexander V AV; Friedman, Noah D ND; Ho, Yu-Jui YJ; Baslan, Timour T; Bandlamudi, Chaitanya C; Scaltriti, Maurizio M; Schultz, Nikolaus N; Lowe, Scott W SW; Reznik, Ed E; Taylor, Barry S BS
A large peptidome dataset improves HLA class I epitope prediction across most of the human population.
Nature Biotechnology
Sarkizova, Siranush S; Klaeger, Susan S; Le, Phuong M PM; Li, Letitia W LW; Oliveira, Giacomo G; Keshishian, Hasmik H; Hartigan, Christina R CR; Zhang, Wandi W; Braun, David A DA; Ligon, Keith L KL; Bachireddy, Pavan P; Zervantonakis, Ioannis K IK; Rosenbluth, Jennifer M JM; Ouspenskaia, Tamara T; Law, Travis T; Justesen, Sune S; Stevens, Jonathan J; Lane, William J WJ; Eisenhaure, Thomas T; Lan Zhang, Guang G; Clauser, Karl R KR; Hacohen, Nir N; Carr, Steven A SA; Wu, Catherine J CJ; Keskin, Derin B DB
Pan-cancer whole-genome analyses of metastatic solid tumours.
Nature
Priestley, Peter P; Baber, Jonathan J; Lolkema, Martijn P MP; Steeghs, Neeltje N; de Bruijn, Ewart E; Shale, Charles C; Duyvesteyn, Korneel K; Haidari, Susan S; van Hoeck, Arne A; Onstenk, Wendy W; Roepman, Paul P; Voda, Mircea M; Bloemendal, Haiko J HJ; Tjan-Heijnen, Vivianne C G VCG; van Herpen, Carla M L CML; Labots, Mariette M; Witteveen, Petronella O PO; Smit, Egbert F EF; Sleijfer, Stefan S; Voest, Emile E EE; Cuppen, Edwin E
Tumor mutational signatures in sebaceous skin lesions from individuals with Lynch syndrome.
Molecular Genetics & Genomic Medicine
Georgeson, Peter P; Walsh, Michael D MD; Clendenning, Mark M; Daneshvar, Simin S; Pope, Bernard J BJ; Mahmood, Khalid K; Joo, Jihoon E JE; Jayasekara, Harindra H; Jenkins, Mark A MA; Winship, Ingrid M IM; Buchanan, Daniel D DD
Sequencing and curation strategies for identifying candidate glioblastoma treatments.
Bmc Medical Genomics
Frank, Mayu O MO; Koyama, Takahiko T; Rhrissorrakrai, Kahn K; Robine, Nicolas N; Utro, Filippo F; Emde, Anne-Katrin AK; Chen, Bo-Juen BJ; Arora, Kanika K; Shah, Minita M; Geiger, Heather H; Felice, Vanessa V; Dikoglu, Esra E; Rahman, Sadia S; Fang, Alice A; Vacic, Vladimir V; Bergmann, Ewa A EA; Vogel, Julia L Moore JLM; Reeves, Catherine C; Khaira, Depinder D; Calabro, Anthony A; Kim, Duyang D; Lamendola-Essel, Michelle F MF; Esteves, Cecilia C; Agius, Phaedra P; Stolte, Christian C; Boockvar, John J; Demopoulos, Alexis A; Placantonakis, Dimitris G DG; Golfinos, John G JG; Brennan, Cameron C; Bruce, Jeffrey J; Lassman, Andrew B AB; Canoll, Peter P; Grommes, Christian C; Daras, Mariza M; Diamond, Eli E; Omuro, Antonio A; Pentsova, Elena E; Orange, Dana E DE; Harvey, Stephen J SJ; Posner, Jerome B JB; Michelini, Vanessa V VV; Jobanputra, Vaidehi V; Zody, Michael C MC; Kelly, John J; Parida, Laxmi L; Wrzeszczynski, Kazimierz O KO; Royyuru, Ajay K AK; Darnell, Robert B RB
Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma.
Nature Communications
North, Jeffrey P JP; Golovato, Justin J; Vaske, Charles J CJ; Sanborn, J Zachary JZ; Nguyen, Andrew A; Wu, Wei W; Goode, Benjamin B; Stevers, Meredith M; McMullen, Kevin K; Perez White, Bethany E BE; Collisson, Eric A EA; Bloomer, Michele M; Solomon, David A DA; Benz, Stephen C SC; Cho, Raymond J RJ
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.
Cell Reports
Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS
Characterizing temporal genomic heterogeneity in pediatric high-grade gliomas.
Acta Neuropathologica Communications
Salloum, Ralph R; McConechy, Melissa K MK; Mikael, Leonie G LG; Fuller, Christine C; Drissi, Rachid R; DeWire, Mariko M; Nikbakht, Hamid H; De Jay, Nicolas N; Yang, Xiaodan X; Boue, Daniel D; Chow, Lionel M L LML; Finlay, Jonathan L JL; Gayden, Tenzin T; Karamchandani, Jason J; Hummel, Trent R TR; Olshefski, Randal R; Osorio, Diana S DS; Stevenson, Charles C; Kleinman, Claudia L CL; Majewski, Jacek J; Fouladi, Maryam M; Jabado, Nada N
Comprehensive Genomic Profiling of 282 Pediatric Low- and High-Grade Gliomas Reveals Genomic Drivers, Tumor Mutational Burden, and Hypermutation Signatures.
The Oncologist
Johnson, Adrienne A; Severson, Eric E; Gay, Laurie L; Vergilio, Jo-Anne JA; Elvin, Julia J; Suh, James J; Daniel, Sugganth S; Covert, Mandy M; Frampton, Garrett M GM; Hsu, Sigmund S; Lesser, Glenn J GJ; Stogner-Underwood, Kimberly K; Mott, Ryan T RT; Rush, Sarah Z SZ; Stanke, Jennifer J JJ; Dahiya, Sonika S; Sun, James J; Reddy, Prasanth P; Chalmers, Zachary R ZR; Erlich, Rachel R; Chudnovsky, Yakov Y; Fabrizio, David D; Schrock, Alexa B AB; Ali, Siraj S; Miller, Vincent V; Stephens, Philip J PJ; Ross, Jeffrey J; Crawford, John R JR; Ramkissoon, Shakti H SH
Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas.
Neuro-Oncology
Granberg, Kirsi J KJ; Annala, Matti M; Lehtinen, Birgitta B; Kesseli, Juha J; Haapasalo, Joonas J; Ruusuvuori, Pekka P; Yli-Harja, Olli O; Visakorpi, Tapio T; Haapasalo, Hannu H; Nykter, Matti M; Zhang, Wei W
EGFRvIII mutations can emerge as late and heterogenous events in glioblastoma development and promote angiogenesis through Src activation.
Neuro-Oncology
Eskilsson, Eskil E; Rosland, Gro V GV; Talasila, Krishna M KM; Knappskog, Stian S; Keunen, Olivier O; Sottoriva, Andrea A; Foerster, Sarah S; Solecki, Gergely G; Taxt, Torfinn T; Jirik, Radovan R; Fritah, Sabrina S; Harter, Patrick N PN; Välk, Kristjan K; Al Hossain, Jubayer J; Joseph, Justin V JV; Jahedi, Roza R; Saed, Halala S HS; Piccirillo, Sara G SG; Spiteri, Inma I; Leiss, Lina L; Euskirchen, Philipp P; Graziani, Grazia G; Daubon, Thomas T; Lund-Johansen, Morten M; Enger, Per Øyvind PØ; Winkler, Frank F; Ritter, Christoph A CA; Niclou, Simone P SP; Watts, Colin C; Bjerkvig, Rolf R; Miletic, Hrvoje H
Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF.
Molecular Cancer Research : Mcr
Hechtman, Jaclyn F JF; Zehir, Ahmet A; Yaeger, Rona R; Wang, Lu L; Middha, Sumit S; Zheng, Tao T; Hyman, David M DM; Solit, David D; Arcila, Maria E ME; Borsu, Laetitia L; Shia, Jinru J; Vakiani, Efsevia E; Saltz, Leonard L; Ladanyi, Marc M
Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.
Cell
Creixell, Pau P; Schoof, Erwin M EM; Simpson, Craig D CD; Longden, James J; Miller, Chad J CJ; Lou, Hua Jane HJ; Perryman, Lara L; Cox, Thomas R TR; Zivanovic, Nevena N; Palmeri, Antonio A; Wesolowska-Andersen, Agata A; Helmer-Citterich, Manuela M; Ferkinghoff-Borg, Jesper J; Itamochi, Hiroaki H; Bodenmiller, Bernd B; Erler, Janine T JT; Turk, Benjamin E BE; Linding, Rune R