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
ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC).
Plos Genetics
Ferrando, Lorenzo L; Vingiani, Andrea A; Garuti, Anna A; Vernieri, Claudio C; Belfiore, Antonino A; Agnelli, Luca L; Dagrada, Gianpaolo G; Ivanoiu, Diana D; Bonizzi, Giuseppina G; Munzone, Elisabetta E; Lippolis, Luana L; Dameri, Martina M; Ravera, Francesco F; Colleoni, Marco M; Viale, Giuseppe G; Magnani, Luca L; Ballestrero, Alberto A; Zoppoli, Gabriele G; Pruneri, Giancarlo G
GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA.
Blood
Thomas, Nicole N; Dreval, Kostiantyn K; Gerhard, Daniela S DS; Hilton, Laura K LK; Abramson, Jeremy S JS; Barta, Stefan K SK; Bartlett, Nancy L NL; Bethony, Jeffrey J; Bhatia, Kishor K; Bowen, Jay J; Bryan, Anthony C AC; Cesarman, Ethel E; Casper, Corey C; Cruz, Manuela M; Dyer, Maureen M; Farinha, Pedro P; Gastier-Foster, Julie J; Gerrie, Alina S AS; Grande, Bruno B; Greiner, Timothy C TC; Griner, Nicholas N; Gross, Thomas G TG; Harris, Nancy Lee NL; Irvin, John D JD; Jaffe, Elaine S ES; Henry, David D; Huppi, Rebecca Liddell RL; Leal, Fabio E FE; Lee, Michael M; Martin, Jean Paul JP; Martin, Marie-Reine MR; Mbulaiteye, Sam M SM; Mitsuyasu, Ronald R; Morris, Vivian V; Mullighan, Charles G CG; Mungall, Andrew J AJ; Mungall, Karen K; Mutyaba, Innocent I; Nokta, Mostafa M; Namirembe, Constance C; Noy, Ariela A; Ogwang, Martin David MD; Omoding, Abrahams A; Orem, Jackson J; Ott, German G; Petrello, Hilary H; Pittaluga, Stefania S; Phelan, James D JD; Ramos, Juan Carlos JC; Ratner, Lee L; Reynolds, Steven J SJ; Rubinstein, Paul G PG; Sissolak, Gerhard G; Slack, Graham W GW; Soudi, Shaghayegh S; Swerdlow, Steven Howard SH; Traverse-Glehen, Alexandra A; Wilson, Wyndham W; Wong, Jasper Chun Hei JCH; Yarchoan, Robert R; ZenKlusen, Jean C JC; Marra, Marco A MA; Staudt, Louis M LM; Scott, David W DW; Morin, Ryan D RD
Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma.
The Journal Of Clinical Investigation
Lee, Patrick C PC; Klaeger, Susan S; Le, Phuong M PM; Korthauer, Keegan K; Cheng, Jingwei J; Ananthapadmanabhan, Varsha V; Frost, Thomas C TC; Stevens, Jonathan D JD; Wong, Alan Yl AY; Iorgulescu, J Bryan JB; Tarren, Anna Y AY; Chea, Vipheaviny A VA; Carulli, Isabel P IP; Lemvigh, Camilla K CK; Pedersen, Christina B CB; Gartin, Ashley K AK; Sarkizova, Siranush S; Wright, Kyle T KT; Li, Letitia W LW; Nomburg, Jason J; Li, Shuqiang S; Huang, Teddy T; Liu, Xiaoxi X; Pomerance, Lucas L; Doherty, Laura M LM; Apffel, Annie M AM; Wallace, Luke J LJ; Rachimi, Suzanna S; Felt, Kristen D KD; Wolff, Jacquelyn O JO; Witten, Elizabeth E; Zhang, Wandi W; Neuberg, Donna D; Lane, William J WJ; Zhang, Guanglan G; Olsen, Lars R LR; Thakuria, Manisha M; Rodig, Scott J SJ; Clauser, Karl R KR; Starrett, Gabriel J GJ; Doench, John G JG; Buhrlage, Sara J SJ; Carr, Steven A SA; DeCaprio, James A JA; Wu, Catherine J CJ; Keskin, Derin B DB
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
Paired primary and metastatic lesions of patients with ipilimumab-treated melanoma: high variation in lymphocyte infiltration and HLA-ABC expression whereas tumor mutational load is similar and correlates with clinical outcome.
Journal For Immunotherapy Of Cancer
Gorris, Mark A J MAJ; van der Woude, Lieke L LL; Kroeze, Leonie I LI; Bol, Kalijn K; Verrijp, Kiek K; Amir, Avital L AL; Meek, Jelena J; Textor, Johannes J; Figdor, Carl G CG; de Vries, I Jolanda M IJM
Publication Date: 2022-05
Variant appearance in text: TP53: 643A>C; Ser215Arg
Estrogen Receptor-Beta2 (ERβ2)-Mutant p53-FOXM1 Axis: A Novel Driver of Proliferation, Chemoresistance, and Disease Progression in High Grade Serous Ovarian Cancer (HGSOC).
Cancers
Oturkar, Chetan C CC; Gandhi, Nishant N; Rao, Pramod P; Eng, Kevin H KH; Miller, Austin A; Singh, Prashant K PK; Zsiros, Emese E; Odunsi, Kunle O KO; Das, Gokul M GM
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
Acquisition of aneuploidy drives mutant p53-associated gain-of-function phenotypes.
Nature Communications
Redman-Rivera, Lindsay N LN; Shaver, Timothy M TM; Jin, Hailing H; Marshall, Clayton B CB; Schafer, Johanna M JM; Sheng, Quanhu Q; Hongo, Rachel A RA; Beckermann, Kathryn E KE; Wheeler, Ferrin C FC; Lehmann, Brian D BD; Pietenpol, Jennifer A JA
Multiple Resistance Mechanisms to Tyrosine Kinase Inhibitors in EGFR Mutated Lung Adenocarcinoma: A Case Report Harboring EGFR Mutations, MET Amplification, and Squamous Cell Transformation.
Frontiers In Oncology
Bruno, Rossella R; Del Re, Marzia M; Cucchiara, Federico F; Petrini, Iacopo I; Alì, Greta G; Crucitta, Stefania S; Proietti, Agnese A; Valleggi, Simona S; Chella, Antonio A; Danesi, Romano R; Fontanini, Gabriella G
Spatially interacting phosphorylation sites and mutations in cancer.
Nature Communications
Huang, Kuan-Lin KL; Scott, Adam D AD; Zhou, Daniel Cui DC; Wang, Liang-Bo LB; Weerasinghe, Amila A; Elmas, Abdulkadir A; Liu, Ruiyang R; Wu, Yige Y; Wendl, Michael C MC; Wyczalkowski, Matthew A MA; Baral, Jessika J; Sengupta, Sohini S; Lai, Chin-Wen CW; Ruggles, Kelly K; Payne, Samuel H SH; Raphael, Benjamin B; Fenyö, David D; Chen, Ken K; Mills, Gordon G; Ding, Li L
Comprehensive omic characterization of breast cancer in Mexican-Hispanic women.
Nature Communications
Romero-Cordoba, Sandra L SL; Salido-Guadarrama, Ivan I; Rebollar-Vega, Rosa R; Bautista-Piña, Veronica V; Dominguez-Reyes, Carlos C; Tenorio-Torres, Alberto A; Villegas-Carlos, Felipe F; Fernández-López, Juan C JC; Uribe-Figueroa, Laura L; Alfaro-Ruiz, Luis L; Hidalgo-Miranda, Alfredo A
High prevalence of clonal hematopoiesis-type genomic abnormalities in cell-free DNA in invasive gliomas after treatment.
International Journal Of Cancer
Okamura, Ryosuke R; Piccioni, David E DE; Boichard, Amélie A; Lee, Suzanna S; Jimenez, Rebecca E RE; Sicklick, Jason K JK; Kato, Shumei S; Kurzrock, Razelle R
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
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
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
Identification of targeted therapy options for gastric adenocarcinoma by comprehensive analysis of genomic data.
Gastric Cancer : Official Journal Of The International Gastric Cancer Association And The Japanese Gastric Cancer Association
Hescheler, Daniel A DA; Plum, Patrick S PS; Zander, Thomas T; Quaas, Alexander A; Korenkov, Michael M; Gassa, Asmae A; Michel, Maximilian M; Bruns, Christiane J CJ; Alakus, Hakan H
Clinical significance of TP53, BIRC3, ATM and MAPK-ERK genes in chronic lymphocytic leukaemia: data from the randomised UK LRF CLL4 trial.
Leukemia
Blakemore, Stuart J SJ; Clifford, Ruth R; Parker, Helen H; Antoniou, Pavlos P; Stec-Dziedzic, Ewa E; Larrayoz, Marta M; Davis, Zadie Z; Kadalyayil, Latha L; Colins, Andrew A; Robbe, Pauline P; Vavoulis, Dimitris D; Forster, Jade J; Carr, Louise L; Morilla, Ricardo R; Else, Monica M; Bryant, Dean D; McCarthy, Helen H; Walewska, Renata J RJ; Steele, Andrew J AJ; Chan, Jacqueline J; Speight, Graham G; Stankovic, Tanja T; Cragg, Mark S MS; Catovsky, Daniel D; Oscier, David G DG; Rose-Zerilli, Matthew J J MJJ; Schuh, Anna A; Strefford, Jonathan C JC
Microscaled proteogenomic methods for precision oncology.
Nature Communications
Satpathy, Shankha S; Jaehnig, Eric J EJ; Krug, Karsten K; Kim, Beom-Jun BJ; Saltzman, Alexander B AB; Chan, Doug W DW; Holloway, Kimberly R KR; Anurag, Meenakshi M; Huang, Chen C; Singh, Purba P; Gao, Ari A; Namai, Noel N; Dou, Yongchao Y; Wen, Bo B; Vasaikar, Suhas V SV; Mutch, David D; Watson, Mark A MA; Ma, Cynthia C; Ademuyiwa, Foluso O FO; Rimawi, Mothaffar F MF; Schiff, Rachel R; Hoog, Jeremy J; Jacobs, Samuel S; Malovannaya, Anna A; Hyslop, Terry T; Clauser, Karl R KR; Mani, D R DR; Perou, Charles M CM; Miles, George G; Zhang, Bing B; Gillette, Michael A MA; Carr, Steven A SA; Ellis, Matthew J MJ
Novel ovarian cancer maintenance therapy targeted at mortalin and mutant p53.
International Journal Of Cancer
Ramraj, Satish K SK; Elayapillai, Sugantha P SP; Pelikan, Richard C RC; Zhao, Yan D YD; Isingizwe, Zitha R ZR; Kennedy, Amy L AL; Lightfoot, Stanley A SA; Benbrook, Doris M DM
New Chondrosarcoma Cell Lines with Preserved Stem Cell Properties to Study the Genomic Drift During In Vitro/In Vivo Growth.
Journal Of Clinical Medicine
Rey, Veronica V; Menendez, Sofia T ST; Estupiñan, Oscar O; Rodriguez, Aida A; Santos, Laura L; Tornin, Juan J; Martinez-Cruzado, Lucia L; Castillo, David D; Ordoñez, Gonzalo R GR; Costilla, Serafin S; Alvarez-Fernandez, Carlos C; Astudillo, Aurora A; Braña, Alejandro A; Rodriguez, Rene R
Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.
Nature Communications
López, Cristina C; Kleinheinz, Kortine K; Aukema, Sietse M SM; Rohde, Marius M; Bernhart, Stephan H SH; Hübschmann, Daniel D; Wagener, Rabea R; Toprak, Umut H UH; Raimondi, Francesco F; Kreuz, Markus M; Waszak, Sebastian M SM; Huang, Zhiqin Z; Sieverling, Lina L; Paramasivam, Nagarajan N; Seufert, Julian J; Sungalee, Stephanie S; Russell, Robert B RB; Bausinger, Julia J; Kretzmer, Helene H; Ammerpohl, Ole O; Bergmann, Anke K AK; Binder, Hans H; Borkhardt, Arndt A; Brors, Benedikt B; Claviez, Alexander A; Doose, Gero G; Feuerbach, Lars L; Haake, Andrea A; Hansmann, Martin-Leo ML; Hoell, Jessica J; Hummel, Michael M; Korbel, Jan O JO; Lawerenz, Chris C; Lenze, Dido D; Radlwimmer, Bernhard B; Richter, Julia J; Rosenstiel, Philip P; Rosenwald, Andreas A; Schilhabel, Markus B MB; Stein, Harald H; Stilgenbauer, Stephan S; Stadler, Peter F PF; Szczepanowski, Monika M; Weniger, Marc A MA; Zapatka, Marc M; Eils, Roland R; Lichter, Peter P; Loeffler, Markus M; Möller, Peter P; Trümper, Lorenz L; Klapper, Wolfram W; , ; Hoffmann, Steve S; Küppers, Ralf R; Burkhardt, Birgit B; Schlesner, Matthias M; Siebert, Reiner R
From uncertainty to pathogenicity: clinical and functional interrogation of a rare TP53 in-frame deletion.
Cold Spring Harbor Molecular Case Studies
Quinn, Emily A EA; Maciaszek, Jamie L JL; Pinto, Emilia M EM; Phillips, Aaron H AH; Berdy, David D; Khandwala, Mohammad M; Upadhyaya, Santhosh A SA; Zambetti, Gerard P GP; Kriwacki, Richard W RW; Ellison, David W DW; Nichols, Kim E KE; Kesserwan, Chimene C
Publication Date: 2019-08
Variant appearance in text: TP53: 643A>C; Ser215Arg
Targeted mutation detection in breast cancer using MammaSeq™.
Breast Cancer Research : Bcr
Smith, Nicholas G NG; Gyanchandani, Rekha R; Shah, Osama S OS; Gurda, Grzegorz T GT; Lucas, Peter C PC; Hartmaier, Ryan J RJ; Brufsky, Adam M AM; Puhalla, Shannon S; Bahreini, Amir A; Kota, Karthik K; Wald, Abigail I AI; Nikiforov, Yuri E YE; Nikiforova, Marina N MN; Oesterreich, Steffi S; Lee, Adrian V AV
Combined assessment of the TNM stage and BRAF mutational status at diagnosis in sporadic colorectal cancer patients.
Oncotarget
Sayagués, José María JM; Del Carmen, Sofía S; Del Mar Abad, María M; Corchete, Luís Antonio LA; Bengoechea, Oscar O; Anduaga, María Fernanda MF; Baldeón, María Jesús MJ; Cruz, Juan Jesús JJ; Alcazar, Jose Antonio JA; Angoso, María M; González, Marcos M; García, Jacinto J; Muñoz-Bellvis, Luís L; Orfao, Alberto A; Sarasquete, María Eugenia ME