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
Network expansion of genetic associations defines a pleiotropy map of human cell biology.
Nature Genetics
Barrio-Hernandez, Inigo I; Schwartzentruber, Jeremy J; Shrivastava, Anjali A; Del-Toro, Noemi N; Gonzalez, Asier A; Zhang, Qian Q; Mountjoy, Edward E; Suveges, Daniel D; Ochoa, David D; Ghoussaini, Maya M; Bradley, Glyn G; Hermjakob, Henning H; Orchard, Sandra S; Dunham, Ian I; Anderson, Carl A CA; Porras, Pablo P; Beltrao, Pedro P
Publication Date: 2023-02-23
Variant appearance in text: EGFR: 1793G>T; Gly598Val
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
Improvements in Quality Control and Library Preparation for Targeted Sequencing Allowed Detection of Potentially Pathogenic Alterations in Circulating Cell-Free DNA Derived from Plasma of Brain Tumor Patients.
Cancers
Szadkowska, Paulina P; Roura, Adria-Jaume AJ; Wojtas, Bartosz B; Wojnicki, Kamil K; Licholai, Sabina S; Waller, Tomasz T; Gubala, Tomasz T; Zukowski, Kacper K; Karpeta, Michal M; Wilkus, Kinga K; Kaspera, Wojciech W; Nawrocki, Sergiusz S; Kaminska, Bozena B
Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma.
Nature Communications
Coy, Shannon S; Wang, Shu S; Stopka, Sylwia A SA; Lin, Jia-Ren JR; Yapp, Clarence C; Ritch, Cecily C CC; Salhi, Lisa L; Baker, Gregory J GJ; Rashid, Rumana R; Baquer, Gerard G; Regan, Michael M; Khadka, Prasidda P; Cole, Kristina A KA; Hwang, Jaeho J; Wen, Patrick Y PY; Bandopadhayay, Pratiti P; Santi, Mariarita M; De Raedt, Thomas T; Ligon, Keith L KL; Agar, Nathalie Y R NYR; Sorger, Peter K PK; Touat, Mehdi M; Santagata, Sandro S
Construction and validation of an immunoediting-based optimized neoantigen load (ioTNL) model to predict the response and prognosis of immune checkpoint therapy in various cancers.
Fundamental immune-oncogenicity trade-offs define driver mutation fitness.
Nature
Hoyos, David D; Zappasodi, Roberta R; Schulze, Isabell I; Sethna, Zachary Z; de Andrade, Kelvin César KC; Bajorin, Dean F DF; Bandlamudi, Chaitanya C; Callahan, Margaret K MK; Funt, Samuel A SA; Hadrup, Sine R SR; Holm, Jeppe S JS; Rosenberg, Jonathan E JE; Shah, Sohrab P SP; Vázquez-García, Ignacio I; Weigelt, Britta B; Wu, Michelle M; Zamarin, Dmitriy D; Campitelli, Laura F LF; Osborne, Edward J EJ; Klinger, Mark M; Robins, Harlan S HS; Khincha, Payal P PP; Savage, Sharon A SA; Balachandran, Vinod P VP; Wolchok, Jedd D JD; Hellmann, Matthew D MD; Merghoub, Taha T; Levine, Arnold J AJ; Łuksza, Marta M; Greenbaum, Benjamin D BD
Genomic Analysis of Tumors from Patients with Glioblastoma with Long-Term Response to Afatinib.
Oncotargets And Therapy
Owen, Scott S; Alken, Scheryll S; Alshami, Jad J; Guiot, Marie-Christine MC; Kavan, Petr P; Reardon, David A DA; Muanza, Thierry T; Gibson, Neil N; Pemberton, Karine K; Solca, Flavio F; Cseh, Agnieszka A; Saran, Frank F
Prospective genomically guided identification of "early/evolving" and "undersampled" IDH-wildtype glioblastoma leads to improved clinical outcomes.
Neuro-Oncology
Zhang, Yalan Y; Lucas, Calixto-Hope G CG; Young, Jacob S JS; Morshed, Ramin A RA; McCoy, Lucie L; Oberheim Bush, Nancy Ann NA; Taylor, Jennie W JW; Daras, Mariza M; Butowski, Nicholas A NA; Villanueva-Meyer, Javier E JE; Cha, Soonmee S; Wrensch, Margaret M; Wiencke, John K JK; Lee, Julieann C JC; Pekmezci, Melike M; Phillips, Joanna J JJ; Perry, Arie A; Bollen, Andrew W AW; Aghi, Manish K MK; Theodosopoulos, Philip P; Chang, Edward F EF; Hervey-Jumper, Shawn L SL; Berger, Mitchel S MS; Clarke, Jennifer L JL; Chang, Susan M SM; Molinaro, Annette M AM; Solomon, David A DA
Association of differential expression of immunoregulatory molecules and presence of targetable mutations may inform rational design of clinical trials.
Esmo Open
Szeto, C W CW; Kurzrock, R R; Kato, S S; Goloubev, A A; Veerapaneni, S S; Preble, A A; Reddy, S K SK; Adashek, J J JJ
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
Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis.
Frontiers In Endocrinology
Hescheler, Daniel A DA; Riemann, Burkhard B; Hartmann, Milan J M MJM; Michel, Maximilian M; Faust, Michael M; Bruns, Christiane J CJ; Alakus, Hakan H; Chiapponi, Costanza C
Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis.
Cancer Discovery
Schaettler, Maximilian O MO; Richters, Megan M MM; Wang, Anthony Z AZ; Skidmore, Zachary L ZL; Fisk, Bryan B; Miller, Katherine E KE; Vickery, Tammi L TL; Kim, Albert H AH; Chicoine, Michael R MR; Osbun, Joshua W JW; Leuthardt, Eric C EC; Dowling, Joshua L JL; Zipfel, Gregory J GJ; Dacey, Ralph G RG; Lu, Hsiang-Chih HC; Johanns, Tanner M TM; Griffith, Obi L OL; Mardis, Elaine R ER; Griffith, Malachi M; Dunn, Gavin P GP
Publication Date: 2022-01
Variant appearance in text: EGFR: 1793G>T; Gly598Val
High-Affinity Chimeric Antigen Receptor With Cross-Reactive scFv to Clinically Relevant EGFR Oncogenic Isoforms.
Frontiers In Oncology
Thokala, Radhika R; Binder, Zev A ZA; Yin, Yibo Y; Zhang, Logan L; Zhang, Jiasi Vicky JV; Zhang, Daniel Y DY; Milone, Michael C MC; Ming, Guo-Li GL; Song, Hongjun H; O'Rourke, Donald M DM
Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients.
Embo Molecular Medicine
Mouliere, Florent F; Smith, Christopher G CG; Heider, Katrin K; Su, Jing J; van der Pol, Ymke Y; Thompson, Mareike M; Morris, James J; Wan, Jonathan C M JCM; Chandrananda, Dineika D; Hadfield, James J; Grzelak, Marta M; Hudecova, Irena I; Couturier, Dominique-Laurent DL; Cooper, Wendy W; Zhao, Hui H; Gale, Davina D; Eldridge, Matthew M; Watts, Colin C; Brindle, Kevin K; Rosenfeld, Nitzan N; Mair, Richard R
Publication Date: 2021-08-09
Variant appearance in text: EGFR: 1793G>T; Gly598Val; rs139236063
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
Systematic Review on the Association of Radiomics with Tumor Biological Endpoints.
Cancers
La Greca Saint-Esteven, Agustina A; Vuong, Diem D; Tschanz, Fabienne F; van Timmeren, Janita E JE; Dal Bello, Riccardo R; Waller, Verena V; Pruschy, Martin M; Guckenberger, Matthias M; Tanadini-Lang, Stephanie S
Predictive Biomarkers for Immune Checkpoint Inhibitors in Metastatic Breast Cancer.
Cancer Medicine
Sivapiragasam, Abirami A; Ashok Kumar, Prashanth P; Sokol, Ethan S ES; Albacker, Lee A LA; Killian, Jonathan K JK; Ramkissoon, Shakti H SH; Huang, Richard S P RSP; Severson, Eric A EA; Brown, Charlotte A CA; Danziger, Natalie N; McGregor, Kimberly K; Ross, Jeffrey S JS
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
Esteban-Villarrubia, Jorge J; Soto-Castillo, Juan José JJ; Pozas, Javier J; San Román-Gil, María M; Orejana-Martín, Inmaculada I; Torres-Jiménez, Javier J; Carrato, Alfredo A; Alonso-Gordoa, Teresa T; Molina-Cerrillo, Javier J
A subset of pediatric-type thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of EGFR.
Neuro-Oncology
Sievers, Philipp P; Sill, Martin M; Schrimpf, Daniel D; Stichel, Damian D; Reuss, David E DE; Sturm, Dominik D; Hench, Jürgen J; Frank, Stephan S; Krskova, Lenka L; Vicha, Ales A; Zapotocky, Michal M; Bison, Brigitte B; Castel, David D; Grill, Jacques J; Debily, Marie-Anne MA; Harter, Patrick N PN; Snuderl, Matija M; Kramm, Christof M CM; Reifenberger, Guido G; Korshunov, Andrey A; Jabado, Nada N; Wesseling, Pieter P; Wick, Wolfgang W; Solomon, David A DA; Perry, Arie A; Jacques, Thomas S TS; Jones, Chris C; Witt, Olaf O; Pfister, Stefan M SM; von Deimling, Andreas A; Jones, David T W DTW; Sahm, Felix F
Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology.
Acta Neuropathologica
Golebiewska, Anna A; Hau, Ann-Christin AC; Oudin, Anaïs A; Stieber, Daniel D; Yabo, Yahaya A YA; Baus, Virginie V; Barthelemy, Vanessa V; Klein, Eliane E; Bougnaud, Sébastien S; Keunen, Olivier O; Wantz, May M; Michelucci, Alessandro A; Neirinckx, Virginie V; Muller, Arnaud A; Kaoma, Tony T; Nazarov, Petr V PV; Azuaje, Francisco F; De Falco, Alfonso A; Flies, Ben B; Richart, Lorraine L; Poovathingal, Suresh S; Arns, Thais T; Grzyb, Kamil K; Mock, Andreas A; Herold-Mende, Christel C; Steino, Anne A; Brown, Dennis D; May, Patrick P; Miletic, Hrvoje H; Malta, Tathiane M TM; Noushmehr, Houtan H; Kwon, Yong-Jun YJ; Jahn, Winnie W; Klink, Barbara B; Tanner, Georgette G; Stead, Lucy F LF; Mittelbronn, Michel M; Skupin, Alexander A; Hertel, Frank F; Bjerkvig, Rolf R; Niclou, Simone P SP