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
Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology.
Nature Medicine
Sturm, Dominik D; Capper, David D; Andreiuolo, Felipe F; Gessi, Marco M; Kölsche, Christian C; Reinhardt, Annekathrin A; Sievers, Philipp P; Wefers, Annika K AK; Ebrahimi, Azadeh A; Suwala, Abigail K AK; Gielen, Gerrit H GH; Sill, Martin M; Schrimpf, Daniel D; Stichel, Damian D; Hovestadt, Volker V; Daenekas, Bjarne B; Rode, Agata A; Hamelmann, Stefan S; Previti, Christopher C; Jäger, Natalie N; Buchhalter, Ivo I; Blattner-Johnson, Mirjam M; Jones, Barbara C BC; Warmuth-Metz, Monika M; Bison, Brigitte B; Grund, Kerstin K; Sutter, Christian C; Hirsch, Steffen S; Dikow, Nicola N; Hasselblatt, Martin M; Schüller, Ulrich U; Gerber, Nicolas U NU; White, Christine L CL; Buntine, Molly K MK; Kinross, Kathryn K; Algar, Elizabeth M EM; Hansford, Jordan R JR; Gottardo, Nicholas G NG; Hernáiz Driever, Pablo P; Gnekow, Astrid A; Witt, Olaf O; Müller, Hermann L HL; Calaminus, Gabriele G; Fleischhack, Gudrun G; Kordes, Uwe U; Mynarek, Martin M; Rutkowski, Stefan S; Frühwald, Michael C MC; Kramm, Christof M CM; von Deimling, Andreas A; Pietsch, Torsten T; Sahm, Felix F; Pfister, Stefan M SM; Jones, David T W DTW
Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry.
Cancer Research Communications
White, Jason A JA; Kaninjing, Ernest T ET; Adeniji, Kayode A KA; Jibrin, Paul P; Obafunwa, John O JO; Ogo, Chidiebere N CN; Mohammed, Faruk F; Popoola, Ademola A; Fatiregun, Omolara A OA; Oluwole, Olabode P OP; Karanam, Balasubramanyam B; Elhussin, Isra I; Ambs, Stefan S; Tang, Wei W; Davis, Melissa M; Polak, Paz P; Campbell, Moray J MJ; Brignole, Kathryn R KR; Rotimi, Solomon O SO; Dean-Colomb, Windy W; Odedina, Folake T FT; Martin, Damali N DN; Yates, Clayton C
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: CTNNB1: 98C>T; Ser33Phe
Efficacy and clinicogenomic correlates of response to immune checkpoint inhibitors alone or with chemotherapy in non-small cell lung cancer.
Nature Communications
Hong, Lingzhi L; Aminu, Muhammad M; Li, Shenduo S; Lu, Xuetao X; Petranovic, Milena M; Saad, Maliazurina B MB; Chen, Pingjun P; Qin, Kang K; Varghese, Susan S; Rinsurongkawong, Waree W; Rinsurongkawong, Vadeerat V; Spelman, Amy A; Elamin, Yasir Y YY; Negrao, Marcelo V MV; Skoulidis, Ferdinandos F; Gay, Carl M CM; Cascone, Tina T; Gandhi, Saumil J SJ; Lin, Steven H SH; Lee, Percy P PP; Carter, Brett W BW; Wu, Carol C CC; Antonoff, Mara B MB; Sepesi, Boris B; Lewis, Jeff J; Gibbons, Don L DL; Vaporciyan, Ara A AA; Le, Xiuning X; Jack Lee, J J; Roy-Chowdhuri, Sinchita S; Routbort, Mark J MJ; Gainor, Justin F JF; Heymach, John V JV; Lou, Yanyan Y; Wu, Jia J; Zhang, Jianjun J; Vokes, Natalie I NI
Early detection of colorectal cancer somatic mutations using cfDNA liquid biopsies in a murine carcinogenesis model.
Journal Of Cancer
Martínez-Gregorio, Héctor H; Díaz-Velásquez, Clara Estela CE; Romero-Piña, Mario Esaú ME; Ruiz De La Cruz, Miguel M; Delgado-Buenrostro, Norma Laura NL; De La Cruz-Montoya, Aldo A; Chirino, Yolanda Irasema YI; Terrazas, Luis Ignacio LI; Medina, Luis Alberto LA; Vaca-Paniagua, Felipe F
Uterine lavage identifies cancer mutations and increased TP53 somatic mutation burden in individuals with ovarian cancer.
Cancer Research Communications
Ghezelayagh, Talayeh S TS; Kohrn, Brendan F BF; Fredrickson, Jeanne J; Manhardt, Enna E; Radke, Marc R MR; Katz, Ronit R; Gray, Heidi J HJ; Urban, Renata R RR; Pennington, Kathryn P KP; Liao, John B JB; Doll, Kemi M KM; Simons, Elise J EJ; Burzawa, Jennifer K JK; Goff, Barbara A BA; Speiser, Paul P; Swisher, Elizabeth M EM; Norquist, Barbara M BM; Risques, Rosa Ana RA
Genetic and Methylation Analysis of CTNNB1 in Benign and Malignant Melanocytic Lesions.
Cancers
Zaremba, Anne A; Jansen, Philipp P; Murali, Rajmohan R; Mayakonda, Anand A; Riedel, Anna A; Krahl, Dieter D; Burkhardt, Hans H; John, Stefan S; Géraud, Cyrill C; Philip, Manuel M; Kretz, Julia J; Möller, Inga I; Stadtler, Nadine N; Sucker, Antje A; Paschen, Annette A; Ugurel, Selma S; Zimmer, Lisa L; Livingstone, Elisabeth E; Horn, Susanne S; Plass, Christoph C; Schadendorf, Dirk D; Hadaschik, Eva E; Lutsik, Pavlo P; Griewank, Klaus K
CTNNB1 mutations, TERT polymorphism and CD8+ cell densities in resected hepatocellular carcinoma are associated with longer time to recurrence.
Bmc Cancer
Ambrozkiewicz, Filip F; Trailin, Andriy A; Červenková, Lenka L; Vaclavikova, Radka R; Hanicinec, Vojtech V; Allah, Mohammad Al Obeed MAO; Palek, Richard R; Třeška, Vladislav V; Daum, Ondrej O; Tonar, Zbyněk Z; Liška, Václav V; Hemminki, Kari K
Pugh, Trevor J TJ; Bell, Jonathan L JL; Bruce, Jeff P JP; Doherty, Gary J GJ; Galvin, Matthew M; Green, Michelle F MF; Hunter-Zinck, Haley H; Kumari, Priti P; Lenoue-Newton, Michele L ML; Li, Marilyn M MM; Lindsay, James J; Mazor, Tali T; Ovalle, Andrea A; Sammut, Stephen-John SJ; Schultz, Nikolaus N; Yu, Thomas V TV; Sweeney, Shawn M SM; Bernard, Brady B; ,
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
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
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages.
Nature Communications
Ng, Charlotte K Y CKY; Dazert, Eva E; Boldanova, Tuyana T; Coto-Llerena, Mairene M; Nuciforo, Sandro S; Ercan, Caner C; Suslov, Aleksei A; Meier, Marie-Anne MA; Bock, Thomas T; Schmidt, Alexander A; Ketterer, Sylvia S; Wang, Xueya X; Wieland, Stefan S; Matter, Matthias S MS; Colombi, Marco M; Piscuoglio, Salvatore S; Terracciano, Luigi M LM; Hall, Michael N MN; Heim, Markus H MH
Publication Date: 2022-05-04
Variant appearance in text: CTNNB1: 98C>T; S33F; rs121913400
Plasma Genotyping at the Time of Diagnostic Tissue Biopsy Decreases Time-to-Treatment in Patients With Advanced NSCLC-Results From a Prospective Pilot Study.
Jto Clinical And Research Reports
Thompson, Jeffrey C JC; Aggarwal, Charu C; Wong, Janeline J; Nimgaonkar, Vivek V; Hwang, Wei-Ting WT; Andronov, Michelle M; Dibardino, David M DM; Hutchinson, Christoph T CT; Ma, Kevin C KC; Lanfranco, Anthony A; Moon, Edmund E; Haas, Andrew R AR; Singh, Aditi P AP; Ciunci, Christine A CA; Marmarelis, Melina M; D'Avella, Christopher C; Cohen, Justine V JV; Bauml, Joshua M JM; Cohen, Roger B RB; Langer, Corey J CJ; Vachani, Anil A; Carpenter, Erica L EL
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
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial.
Genome Medicine
Hong, Jung Yong JY; Cho, Hee Jin HJ; Sa, Jason K JK; Liu, Xiaoqiao X; Ha, Sang Yun SY; Lee, Taehyang T; Kim, Hajung H; Kang, Wonseok W; Sinn, Dong Hyun DH; Gwak, Geum-Youn GY; Choi, Moon Seok MS; Lee, Joon Hyeok JH; Koh, Kwang Cheol KC; Paik, Seung Woon SW; Park, Hee Chul HC; Kang, Tae Wook TW; Rhim, Hyunchul H; Lee, Su Jin SJ; Cristescu, Razvan R; Lee, Jeeyun J; Paik, Yong Han YH; Lim, Ho Yeong HY
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial.
Genome Medicine
Hong, Jung Yong JY; Cho, Hee Jin HJ; Sa, Jason K JK; Liu, Xiaoqiao X; Ha, Sang Yun SY; Lee, Taehyang T; Kim, Hajung H; Kang, Wonseok W; Sinn, Dong Hyun DH; Gwak, Geum-Youn GY; Choi, Moon Seok MS; Lee, Joon Hyeok JH; Koh, Kwang Cheol KC; Paik, Seung Woon SW; Park, Hee Chul HC; Kang, Tae Wook TW; Rhim, Hyunchul H; Lee, Su Jin SJ; Cristescu, Razvan R; Lee, Jeeyun J; Paik, Yong Han YH; Lim, Ho Yeong HY
Rearrangement-mediated cis-regulatory alterations in advanced patient tumors reveal interactions with therapy.
Cell Reports
Zhang, Yiqun Y; Chen, Fengju F; Pleasance, Erin E; Williamson, Laura L; Grisdale, Cameron J CJ; Titmuss, Emma E; Laskin, Janessa J; Jones, Steven J M SJM; Cortes-Ciriano, Isidro I; Marra, Marco A MA; Creighton, Chad J CJ
Publication Date: 2021-11-16
Variant appearance in text: CTNNB1: 98C>T; Ser33Phe
Pyrvinium pamoate regulates MGMT expression through suppressing the Wnt/β-catenin signaling pathway to enhance the glioblastoma sensitivity to temozolomide.
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
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study.
Genome Medicine
Sicklick, Jason K JK; Kato, Shumei S; Okamura, Ryosuke R; Patel, Hitendra H; Nikanjam, Mina M; Fanta, Paul T PT; Hahn, Michael E ME; De, Pradip P; Williams, Casey C; Guido, Jessica J; Solomon, Benjamin M BM; McKay, Rana R RR; Krie, Amy A; Boles, Sarah G SG; Ross, Jeffrey S JS; Lee, J Jack JJ; Leyland-Jones, Brian B; Lippman, Scott M SM; Kurzrock, Razelle R
Digital Display Precision Predictor: the prototype of a global biomarker model to guide treatments with targeted therapy and predict progression-free survival.
Npj Precision Oncology
Lazar, Vladimir V; Magidi, Shai S; Girard, Nicolas N; Savignoni, Alexia A; Martini, Jean-François JF; Massimini, Giorgio G; Bresson, Catherine C; Berger, Raanan R; Onn, Amir A; Raynaud, Jacques J; Wunder, Fanny F; Berindan-Neagoe, Ioana I; Sekacheva, Marina M; Braña, Irene I; Tabernero, Josep J; Felip, Enriqueta E; Porgador, Angel A; Kleinman, Claudia C; Batist, Gerald G; Solomon, Benjamin B; Tsimberidou, Apostolia Maria AM; Soria, Jean-Charles JC; Rubin, Eitan E; Kurzrock, Razelle R; Schilsky, Richard L RL
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
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