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
Pirtobrutinib Targets BTK C481S in Ibrutinib-Resistant CLL but Second-Site BTK Mutations Lead to Resistance.
Blood Advances
Naeem, Aishath A; Utro, Filippo F; Wang, Qing Q; Cha, Justin J; Vihinen, Mauno M; Martindale, Stephen P SP; Zhou, Yinglu Y; Ren, Yue Y; Tyekucheva, Svitlana S; Kim, Annette S AS; Fernandes, Stacey M SM; Saksena, Gordon G; Rhrissorrakrai, Kahn K; Levovitz, Chaya C; Danysh, Brian P BP; Slowik, Kara K; Jacobs, Raquel A RA; Davids, Matthew S MS; Lederer, James A JA; Zain, Rula R; Smith, C I Edvard CIE; Leshchiner, Ignaty I; Parida, Laxmi L; Getz, Gad G; Brown, Jennifer R JR
Phase I trial of the TNF-α inhibitor certolizumab plus chemotherapy in stage IV lung adenocarcinomas.
Nature Communications
Paik, Paul K PK; Luo, Jia J; Ai, Ni N; Kim, Rachel R; Ahn, Linda L; Biswas, Anup A; Coker, Courtney C; Ma, Wanchao W; Wong, Phillip P; Buonocore, Darren J DJ; Lai, W Victoria WV; Chaft, Jamie E JE; Acharyya, Swarnali S; Massagué, Joan J; Kris, Mark G MG
Genomic Alterations Identification and Resistance Mechanisms Exploration of NSCLC With Central Nervous System Metastases Using Liquid Biopsy of Cerebrospinal Fluid: A Real-World Study.
Frontiers In Oncology
Shen, Fangfang F; Liang, Naixin N; Fan, Zaiwen Z; Zhao, Min M; Kang, Jing J; Wang, Xifang X; Hu, Qun Q; Mu, Yongping Y; Wang, Kai K; Yuan, Mingming M; Chen, Rongrong R; Guo, Wei W; Dong, Guilan G; Zhao, Jun J; Bai, Jun J
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
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.
Molecular landscape of TP53 mutations in breast cancer and their utility for predicting the response to HER-targeted therapy in HER2 amplification-positive and HER2 mutation-positive amplification-negative patients.
Comparison of acute myeloid leukemia and myelodysplastic syndromes with TP53 aberrations.
Annals Of Hematology
Dutta, Sayantanee S; Moritz, Jennifer J; Pregartner, Gudrun G; Thallinger, Gerhard G GG; Brandstätter, Ilona I; Lind, Karin K; Rezania, Simin S; Lyssy, Freya F; Reinisch, Andreas A; Zebisch, Armin A; Berghold, Andrea A; Wölfler, Albert A; Sill, Heinz H
Germline Sequencing Improves Tumor-Only Sequencing Interpretation in a Precision Genomic Study of Patients With Pediatric Solid Tumor.
Jco Precision Oncology
Schienda, Jaclyn J; Church, Alanna J AJ; Corson, Laura B LB; Decker, Brennan B; Clinton, Catherine M CM; Manning, Danielle K DK; Imamovic-Tuco, Alma A; Reidy, Deirdre D; Strand, Gianna R GR; Applebaum, Mark A MA; Bagatell, Rochelle R; DuBois, Steven G SG; Glade-Bender, Julia L JL; Kang, Wenjun W; Kim, AeRang A; Laetsch, Theodore W TW; Macy, Margaret E ME; Maese, Luke L; Pinto, Navin N; Sabnis, Amit J AJ; Schiffman, Joshua D JD; Colace, Susan I SI; Volchenboum, Samuel L SL; Weiser, Daniel A DA; Nowak, Jonathan A JA; Lindeman, Neal I NI; Janeway, Katherine A KA; Crompton, Brian D BD; Kamihara, Junne J
Diverse 'just-right' levels of chromosomal instability and their clinical implications in neoadjuvant treated gastric cancer.
British Journal Of Cancer
Kohlruss, Meike M; Krenauer, Marie M; Grosser, Bianca B; Pfarr, Nicole N; Jesinghaus, Moritz M; Slotta-Huspenina, Julia J; Novotny, Alexander A; Hapfelmeier, Alexander A; Schmidt, Thomas T; Steiger, Katja K; Gaida, Matthias M MM; Reiche, Magdalena M; Bauer, Lukas L; Ott, Katja K; Weichert, Wilko W; Keller, Gisela G
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
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
A genetically defined signature of responsiveness to erlotinib in early-stage pancreatic cancer patients: Results from the CONKO-005 trial.
Ebiomedicine
Hoyer, K K; Hablesreiter, R R; Inoue, Y Y; Yoshida, K K; Briest, F F; Christen, F F; Kakiuchi, N N; Yoshizato, T T; Shiozawa, Y Y; Shiraishi, Y Y; Striefler, J K JK; Bischoff, S S; Lohneis, P P; Putter, H H; Blau, O O; Keilholz, U U; Bullinger, L L; Pelzer, U U; Hummel, M M; Riess, H H; Ogawa, S S; Sinn, M M; Damm, F F
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
Tumor genomic, transcriptomic, and immune profiling characterizes differential response to first-line platinum chemotherapy in high grade serous ovarian cancer.
Cancer Medicine
Weberpals, Johanne I JI; Pugh, Trevor J TJ; Marco-Casanova, Paola P; Goss, Glenwood D GD; Andrews Wright, Natalie N; Rath, Prisni P; Torchia, Jonathon J; Fortuna, Alexander A; Jones, Gemma N GN; Roudier, Martine P MP; Bernard, Laurence L; Lo, Bryan B; Torti, Dax D; Leon, Alberto A; Marsh, Kayla K; Hodgson, Darren D; Duciaume, Marc M; Howat, William J WJ; Lukashchuk, Natalia N; Lazic, Stanley E SE; Whelan, Doreen D; Sekhon, Harmanjatinder S HS
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
Networking for advanced molecular diagnosis in acute myeloid leukemia patients is possible: the PETHEMA NGS-AML project
Haematologica
Sargas, Claudia C; Ayala, Rosa R; Chillón, María Carmen MC; Larráyoz, María J MJ; Carrillo-Cruz, Estrella E; Bilbao, Cristina C; Yébenes-Ramírez, Manuel M; Llop, Marta M; Rapado, Inmaculada I; García-Sanz, Ramón R; Vázquez, Iria I; Soria, Elena E; Florido-Ortega, Yanira Y; Janusz, Kamila K; Botella, Carmen C; Serrano, Josefina J; Martínez-Cuadrón, David D; Bergua, Juan J; Amigo, Mari Luz ML; Martínez-Sánchez, Pilar P; Tormo, Mar M; Bernal, Teresa T; Herrera-Puente, Pilar P; García, Raimundo R; Algarra, Lorenzo L; Sayas, María J MJ; Costilla-Barriga, Lisette L; Pérez-Santolalla, Esther E; Marchante, Inmaculada I; Lavilla-Rubira, Esperanza E; Noriega, Víctor V; Alonso-Domínguez, Juan M JM; Sanz, Miguel Á MÁ; Sánchez-Garcia, Joaquín J; Gómez-Casares, María T MT; Pérez-Simón, José A JA; Calasanz, María J MJ; González-Díaz, Marcos M; Martínez-López, Joaquín J; Barragán, Eva E; Montesinos, Pau P
Networking for advanced molecular diagnosis in acute myeloid leukemia patients is possible: the PETHEMA NGS-AML project
Haematologica
Sargas, Claudia C; Ayala, Rosa R; Chillón, María Carmen MC; Larráyoz, María J MJ; Carrillo-Cruz, Estrella E; Bilbao, Cristina C; Yébenes-Ramírez, Manuel M; Llop, Marta M; Rapado, Inmaculada I; García-Sanz, Ramón R; Vázquez, Iria I; Soria, Elena E; Florido-Ortega, Yanira Y; Janusz, Kamila K; Botella, Carmen C; Serrano, Josefina J; Martínez-Cuadrón, David D; Bergua, Juan J; Amigo, Mari Luz ML; Martínez-Sánchez, Pilar P; Tormo, Mar M; Bernal, Teresa T; Herrera-Puente, Pilar P; García, Raimundo R; Algarra, Lorenzo L; Sayas, María J MJ; Costilla-Barriga, Lisette L; Pérez-Santolalla, Esther E; Marchante, Inmaculada I; Lavilla-Rubira, Esperanza E; Noriega, Víctor V; Alonso-Domínguez, Juan M JM; Sanz, Miguel Á MÁ; Sánchez-Garcia, Joaquín J; Gómez-Casares, María T MT; Pérez-Simón, José A JA; Calasanz, María J MJ; González-Díaz, Marcos M; Martínez-López, Joaquín J; Barragán, Eva E; Montesinos, Pau P
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
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
Integrating next-generation sequencing to endoscopic retrograde cholangiopancreatography (ERCP)-obtained biliary specimens improves the detection and management of patients with malignant bile duct strictures.
Gut
Singhi, Aatur D AD; Nikiforova, Marina N MN; Chennat, Jennifer J; Papachristou, Georgios I GI; Khalid, Asif A; Rabinovitz, Mordechai M; Das, Rohit R; Sarkaria, Savreet S; Ayasso, M Samir MS; Wald, Abigail I AI; Monaco, Sara E SE; Nalesnik, Michael M; Ohori, N Paul NP; Geller, David D; Tsung, Allan A; Zureikat, Amer H AH; Zeh, Herbert H; Marsh, J Wallis JW; Hogg, Melissa M; Lee, Kenneth K; Bartlett, David L DL; Pingpank, James F JF; Humar, Abhinav A; Bahary, Nathan N; Dasyam, Anil K AK; Brand, Randall R; Fasanella, Kenneth E KE; McGrath, Kevin K; Slivka, Adam A
Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures.
Plos Genetics
Schumacher, Dirk D; Andrieux, Geoffroy G; Boehnke, Karsten K; Keil, Marlen M; Silvestri, Alessandra A; Silvestrov, Maxine M; Keilholz, Ulrich U; Haybaeck, Johannes J; Erdmann, Gerrit G; Sachse, Christoph C; Templin, Markus M; Hoffmann, Jens J; Boerries, Melanie M; Schäfer, Reinhold R; Regenbrecht, Christian R A CRA
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: 392A>T; Asn131Ile
Influence of TP53 Mutation on Survival in Patients With Advanced EGFR-Mutant Non-Small-Cell Lung Cancer.
Jco Precision Oncology
Aggarwal, Charu C; Davis, Christiana W CW; Mick, Rosemarie R; Thompson, Jeffrey C JC; Ahmed, Saman S; Jeffries, Seth S; Bagley, Stephen S; Gabriel, Peter P; Evans, Tracey L TL; Bauml, Joshua M JM; Ciunci, Christine C; Alley, Evan E; Morrissette, Jennifer J D JJD; Cohen, Roger B RB; Carpenter, Erica L EL; Langer, Corey J CJ
The prognostic effects of somatic mutations in ER-positive breast cancer.
Nature Communications
Griffith, Obi L OL; Spies, Nicholas C NC; Anurag, Meenakshi M; Griffith, Malachi M; Luo, Jingqin J; Tu, Dongsheng D; Yeo, Belinda B; Kunisaki, Jason J; Miller, Christopher A CA; Krysiak, Kilannin K; Hundal, Jasreet J; Ainscough, Benjamin J BJ; Skidmore, Zachary L ZL; Campbell, Katie K; Kumar, Runjun R; Fronick, Catrina C; Cook, Lisa L; Snider, Jacqueline E JE; Davies, Sherri S; Kavuri, Shyam M SM; Chang, Eric C EC; Magrini, Vincent V; Larson, David E DE; Fulton, Robert S RS; Liu, Shuzhen S; Leung, Samuel S; Voduc, David D; Bose, Ron R; Dowsett, Mitch M; Wilson, Richard K RK; Nielsen, Torsten O TO; Mardis, Elaine R ER; Ellis, Matthew J MJ
Copy number signatures and mutational processes in ovarian carcinoma.
Nature Genetics
Macintyre, Geoff G; Goranova, Teodora E TE; De Silva, Dilrini D; Ennis, Darren D; Piskorz, Anna M AM; Eldridge, Matthew M; Sie, Daoud D; Lewsley, Liz-Anne LA; Hanif, Aishah A; Wilson, Cheryl C; Dowson, Suzanne S; Glasspool, Rosalind M RM; Lockley, Michelle M; Brockbank, Elly E; Montes, Ana A; Walther, Axel A; Sundar, Sudha S; Edmondson, Richard R; Hall, Geoff D GD; Clamp, Andrew A; Gourley, Charlie C; Hall, Marcia M; Fotopoulou, Christina C; Gabra, Hani H; Paul, James J; Supernat, Anna A; Millan, David D; Hoyle, Aoisha A; Bryson, Gareth G; Nourse, Craig C; Mincarelli, Laura L; Sanchez, Luis Navarro LN; Ylstra, Bauke B; Jimenez-Linan, Mercedes M; Moore, Luiza L; Hofmann, Oliver O; Markowetz, Florian F; McNeish, Iain A IA; Brenton, James D JD