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
A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Jang, H Josh HJ; Hostetter, Galen G; MacFarlane, Alexander W AW; Madaj, Zachary Z; Ross, Eric A EA; Hinoue, Toshinori T; Kulchycki, Justin R JR; Burgos, Ryan S RS; Tafseer, Mahvish M; Alpaugh, R Katherine RK; Schwebel, Candice L CL; Kokate, Rutika R; Geynisman, Daniel M DM; Zibelman, Matthew R MR; Ghatalia, Pooja P; Nichols, Peter W PW; Chung, Woonbok W; Madzo, Jozef J; Hahn, Noah M NM; Quinn, David I DI; Issa, Jean-Pierre J JJ; Topper, Michael J MJ; Baylin, Stephen B SB; Shen, Hui H; Campbell, Kerry S KS; Jones, Peter A PA; Plimack, Elizabeth R ER
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
Publication Date: 2023-01-03
Variant appearance in text: PIK3CA: 3068G>A; R1023Q
Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer.
Nature Communications
Sivakumar, Smruthy S; Jin, Dexter X DX; Tukachinsky, Hanna H; Murugesan, Karthikeyan K; McGregor, Kimberly K; Danziger, Natalie N; Pavlick, Dean D; Gjoerup, Ole O; Ross, Jeffrey S JS; Harmon, Robert R; Chung, Jon J; Decker, Brennan B; Dennis, Lucas L; Frampton, Garrett M GM; Molinero, Luciana L; Oesterreich, Steffi S; Venstrom, Jeffrey M JM; Oxnard, Geoffrey R GR; Hegde, Priti S PS; Sokol, Ethan S ES
Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers.
Nature Communications
Shah, Jennifer B JB; Pueschl, Dana D; Wubbenhorst, Bradley B; Fan, Mengyao M; Pluta, John J; D'Andrea, Kurt K; Hubert, Anna P AP; Shilan, Jake S JS; Zhou, Wenting W; Kraya, Adam A AA; Llop Guevara, Alba A; Ruan, Catherine C; Serra, Violeta V; Balmaña, Judith J; Feldman, Michael M; Morin, Pat J PJ; Nayak, Anupma A; Maxwell, Kara N KN; Domchek, Susan M SM; Nathanson, Katherine L KL
Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution.
Leukemia
Richter-Pechańska, Paulina P; Kunz, Joachim B JB; Rausch, Tobias T; Erarslan-Uysal, Büşra B; Bornhauser, Beat B; Frismantas, Viktoras V; Assenov, Yassen Y; Zimmermann, Martin M; Happich, Margit M; von Knebel-Doeberitz, Caroline C; von Neuhoff, Nils N; Köhler, Rolf R; Stanulla, Martin M; Schrappe, Martin M; Cario, Gunnar G; Escherich, Gabriele G; Kirschner-Schwabe, Renate R; Eckert, Cornelia C; Avigad, Smadar S; Pfister, Stefan M SM; Muckenthaler, Martina U MU; Bourquin, Jean-Pierre JP; Korbel, Jan O JO; Kulozik, Andreas E AE
Molecular Evaluation of Endometrial Dedifferentiated Carcinoma, Endometrioid Carcinoma, Carcinosarcoma, and Serous Carcinoma Using a Custom-Made Small Cancer Panel.
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
Phase Ib Trial of Copanlisib, A Phosphoinositide-3 Kinase (PI3K) Inhibitor, with Trastuzumab in Advanced Pre-Treated HER2-Positive Breast Cancer "PantHER".
Cancers
Keegan, Niamh M NM; Furney, Simon J SJ; Walshe, Janice M JM; Gullo, Giuseppe G; Kennedy, M John MJ; Smith, Diarmuid D; McCaffrey, John J; Kelly, Catherine M CM; Egan, Keith K; Kerr, Jennifer J; Given, Mark M; O'Donovan, Peter P; Hernando, Andres A; Teiserskiene, Ausra A; Parker, Imelda I; Kay, Elaine E; Farrelly, Angela A; Carr, Aoife A; Calzaferri, Giulio G; McDermott, Ray R; Keane, Maccon M MM; Grogan, Liam L; Breathnach, Oscar O; Morris, Patrick G PG; Toomey, Sinead S; Hennessy, Bryan T BT
A next-generation sequencing-based strategy combining microsatellite instability and tumor mutation burden for comprehensive molecular diagnosis of advanced colorectal cancer.
Utility of a custom designed next generation DNA sequencing gene panel to molecularly classify endometrial cancers according to The Cancer Genome Atlas subgroups.
Bmc Medical Genomics
Miller, Eirwen M EM; Patterson, Nicole E NE; Gressel, Gregory M GM; Karabakhtsian, Rouzan G RG; Bejerano-Sagie, Michal M; Ravi, Nivedita N; Maslov, Alexander A; Quispe-Tintaya, Wilber W; Wang, Tao T; Lin, Juan J; Smith, Harriet O HO; Goldberg, Gary L GL; Kuo, Dennis Y S DYS; Montagna, Cristina C
Comprehensive next-generation profiling of clonal hematopoiesis in cancer patients using paired tumor-blood sequencing for guiding personalized therapies.
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
Clinicopathological characteristics and genetic analysis of pulmonary carcinoid tumors: A single-center retrospective cohort study and literature review.
Oncology Letters
Li, Xiongfei X; Hou, Yuelong Y; Shi, Tao T; He, Yue Y; Ren, Dian D; Song, Zuoqing Z; Wei, Sen S; Chen, Gang G; Chen, Jun J; Xu, Song S
PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia.
Embo Molecular Medicine
Richter-Pechańska, Paulina P; Kunz, Joachim B JB; Bornhauser, Beat B; von Knebel Doeberitz, Caroline C; Rausch, Tobias T; Erarslan-Uysal, Büşra B; Assenov, Yassen Y; Frismantas, Viktoras V; Marovca, Blerim B; Waszak, Sebastian M SM; Zimmermann, Martin M; Seemann, Julia J; Happich, Margit M; Stanulla, Martin M; Schrappe, Martin M; Cario, Gunnar G; Escherich, Gabriele G; Bakharevich, Kseniya K; Kirschner-Schwabe, Renate R; Eckert, Cornelia C; Muckenthaler, Martina U MU; Korbel, Jan O JO; Bourquin, Jean-Pierre JP; Kulozik, Andreas E AE
Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.
Plos One
Prentice, Leah M LM; Miller, Ruth R RR; Knaggs, Jeff J; Mazloomian, Alborz A; Aguirre Hernandez, Rosalia R; Franchini, Patrick P; Parsa, Kourosh K; Tessier-Cloutier, Basile B; Lapuk, Anna A; Huntsman, David D; Schaeffer, David F DF; Sheffield, Brandon S BS
Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.
The Journal Of Pathology
Temko, Daniel D; Van Gool, Inge C IC; Rayner, Emily E; Glaire, Mark M; Makino, Seiko S; Brown, Matthew M; Chegwidden, Laura L; Palles, Claire C; Depreeuw, Jeroen J; Beggs, Andrew A; Stathopoulou, Chaido C; Mason, John J; Baker, Ann-Marie AM; Williams, Marc M; Cerundolo, Vincenzo V; Rei, Margarida M; Taylor, Jenny C JC; Schuh, Anna A; Ahmed, Ahmed A; Amant, Frédéric F; Lambrechts, Diether D; Smit, Vincent Thbm VT; Bosse, Tjalling T; Graham, Trevor A TA; Church, David N DN; Tomlinson, Ian I
Publication Date: 2018-07
Variant appearance in text: PIK3CA: 3068G>A; R1023Q
Impact of somatic PI3K pathway and ERBB family mutations on pathological complete response (pCR) in HER2-positive breast cancer patients who received neoadjuvant HER2-targeted therapies.
Breast Cancer Research : Bcr
Toomey, Sinead S; Eustace, Alexander J AJ; Fay, Joanna J; Sheehan, Katherine M KM; Carr, Aoife A; Milewska, Malgorzata M; Madden, Stephen F SF; Teiserskiene, Ausra A; Kay, Elaine W EW; O'Donovan, Norma N; Gallagher, William W; Grogan, Liam L; Breathnach, Oscar O; Walshe, Janice J; Kelly, Catherine C; Moulton, Brian B; Kennedy, M John MJ; Gullo, Guiseppe G; Hill, Arnold D AD; Power, Colm C; Duke, Deirdre D; Hambly, Niamh N; Crown, John J; Hennessy, Bryan T BT
Enrichment of PI3K-AKT-mTOR Pathway Activation in Hepatic Metastases from Breast Cancer.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Pierobon, Mariaelena M; Ramos, Corinne C; Wong, Shukmei S; Hodge, K Alex KA; Aldrich, Jessica J; Byron, Sara S; Anthony, Stephen P SP; Robert, Nicholas J NJ; Northfelt, Donald W DW; Jahanzeb, Mohammad M; Vocila, Linda L; Wulfkuhle, Julia J; Gambara, Guido G; Gallagher, Rosa I RI; Dunetz, Bryant B; Hoke, Nicholas N; Dong, Ting T; Craig, David W DW; Cristofanilli, Massimo M; Leyland-Jones, Brian B; Liotta, Lance A LA; O'Shaughnessy, Joyce A JA; Carpten, John D JD; Petricoin, Emanuel F EF
Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.
Blood Cancer Journal
Richter-Pechańska, P P; Kunz, J B JB; Hof, J J; Zimmermann, M M; Rausch, T T; Bandapalli, O R OR; Orlova, E E; Scapinello, G G; Sagi, J C JC; Stanulla, M M; Schrappe, M M; Cario, G G; Kirschner-Schwabe, R R; Eckert, C C; Benes, V V; Korbel, J O JO; Muckenthaler, M U MU; Kulozik, A E AE
Dual EGFR inhibition in combination with anti-VEGF treatment in colorectal cancer.
Oncoscience
Falchook, Gerald S GS; Naing, Aung A; Wheler, Jennifer J JJ; Tsimberidou, Apostolia M AM; Zinner, Ralph R; Hong, David S DS; Fu, Siqing S; Piha-Paul, Sarina A SA; Janku, Filip F; Hess, Kenneth R KR; Bastida, Christel C; Kurzrock, Razelle R
Target-based therapeutic matching in early-phase clinical trials in patients with advanced colorectal cancer and PIK3CA mutations.
Molecular Cancer Therapeutics
Ganesan, Prasanth P; Janku, Filip F; Naing, Aung A; Hong, David S DS; Tsimberidou, Apostolia M AM; Falchook, Gerald S GS; Wheler, Jennifer J JJ; Piha-Paul, Sarina A SA; Fu, Siqing S; Stepanek, Vanda M VM; Lee, J Jack JJ; Luthra, Rajyalakshmi R; Overman, Michael J MJ; Kopetz, E Scott ES; Wolff, Robert A RA; Kurzrock, Razelle R
PIK3CA mutation H1047R is associated with response to PI3K/AKT/mTOR signaling pathway inhibitors in early-phase clinical trials.
Cancer Research
Janku, Filip F; Wheler, Jennifer J JJ; Naing, Aung A; Falchook, Gerald S GS; Hong, David S DS; Stepanek, Vanda M VM; Fu, Siqing S; Piha-Paul, Sarina A SA; Lee, J Jack JJ; Luthra, Rajyalakshmi R; Tsimberidou, Apostolia M AM; Kurzrock, Razelle R
PTEN gene expression and mutations in the PIK3CA gene as predictors of clinical benefit to anti-epidermal growth factor receptor antibody therapy in patients with KRAS wild-type metastatic colorectal cancer.
Clinical Colorectal Cancer
Sood, Arjun A; McClain, Danielle D; Maitra, Radhashree R; Basu-Mallick, Atrayee A; Seetharam, Raviraja R; Kaubisch, Andreas A; Rajdev, Lakshmi L; Mariadason, John M JM; Tanaka, Kathryn K; Goel, Sanjay S