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
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
Genomic complexity predicts resistance to endocrine therapy and CDK4/6 inhibition in hormone receptor-positive (HR+)/HER2-negative metastatic breast cancer.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Davis, Andrew A AA; Luo, Jingqin J; Zheng, Tiantian T; Dai, Chao C; Dong, Xiaoxi X; Tan, Lu L; Suresh, Rama R; Ademuyiwa, Foluso O FO; Rigden, Caron C; Rearden, Timothy P TP; Clifton, Katherine K; Weilbaecher, Katherine K; Frith, Ashley A; Tandra, Pavankumar K PK; Summa, Tracy T; Haas, Brittney B; Thomas, Shana S; Hernandez-Aya, Leonel F LF; Peterson, Lindsay L LL; Wang, Xiaohong X; Luo, Shujun J SJ; Zhou, Kemin K; Du, Pan P; Jia, Shidong S; King, Bonnie L BL; Krishnamurthy, Jairam J; Ma, Cynthia X CX
Publication Date: 2023-01-24
Variant appearance in text: TP53: 839G>C; Arg280Thr
Clinical sequencing identifies potential actionable alterations in a high rate of urachal and primary bladder adenocarcinomas.
Cancer Medicine
Varadi, Melinda M; Nagy, Nikolett N; Reis, Henning H; Hadaschik, Boris B; Niedworok, Christian C; Modos, Orsolya O; Szendroi, Attila A; Ablat, Jason J; Black, Peter C PC; Keresztes, David D; Csizmarik, Anita A; Olah, Csilla C; Gaisa, Nadine T NT; Kiss, Andras A; Timar, Jozsef J; Toth, Erika E; Csernak, Erzsebet E; Gerstner, Arpad A; Mittal, Vinay V; Karkampouna, Sofia S; Kruithof de Julio, Marianna M; Gyorffy, Balazs B; Bedics, Gabor G; Rink, Michael M; Fisch, Margit M; Nyirady, Peter P; Szarvas, Tibor T
Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors.
Cell Reports. Medicine
Álvarez-Prado, Ángel F ÁF; Maas, Roeltje R RR; Soukup, Klara K; Klemm, Florian F; Kornete, Mara M; Krebs, Fanny S FS; Zoete, Vincent V; Berezowska, Sabina S; Brouland, Jean-Philippe JP; Hottinger, Andreas F AF; Daniel, Roy T RT; Hegi, Monika E ME; Joyce, Johanna A JA
Comprehensive clinicopathological and genomic profiling of gallbladder cancer reveals actionable targets in half of patients.
Npj Precision Oncology
de Bitter, Tessa J J TJJ; de Reuver, Philip R PR; de Savornin Lohman, Elise A J EAJ; Kroeze, Leonie I LI; Vink-Börger, Marianne E ME; van Vliet, Shannon S; Simmer, Femke F; von Rhein, Daniel D; Jansen, Erik A M EAM; Verheij, Joanne J; van Herpen, Carla M L CML; Nagtegaal, Iris D ID; Ligtenberg, Marjolijn J L MJL; van der Post, Rachel S RS
Publication Date: 2022-11-05
Variant appearance in text: TP53: 839G>C; Arg280Thr
A transcriptional network of cell cycle dysregulation in noninvasive papillary urothelial carcinoma.
Scientific Reports
Warrick, Joshua I JI; Knowles, Margaret A MA; Hurst, Carolyn D CD; Shuman, Lauren L; Raman, Jay D JD; Walter, Vonn V; Putt, Jeffrey J; Dyrskjøt, Lars L; Groeneveld, Clarice C; Castro, Mauro A A MAA; Robertson, A Gordon AG; DeGraff, David J DJ
New methodology of TMB assessment from tissue and liquid biopsy in NSCLC.
Plos One
Křížová, Ľudmila Ľ; Šafaříková, Markéta M; Kalousová, Marta M; Pfeiferová, Lucie L; Kuběna, Aleš Antonín AA; Vočka, Michal M; Ulrych, Jan J; Franková, Věra V; Petruželka, Luboš L; Zima, Tomáš T; Feltl, David D
Publication Date: 2022
Variant appearance in text: TP53: 782+400G>C; Arg280Thr; rs121912660
Shallow WGS of individual CTCs identifies actionable targets for informing treatment decisions in metastatic breast cancer.
British Journal Of Cancer
Fernandez-Garcia, Daniel D; Nteliopoulos, Georgios G; Hastings, Robert K RK; Rushton, Amelia A; Page, Karen K; Allsopp, Rebecca C RC; Ambasager, Bana B; Gleason, Kelly K; Guttery, David S DS; Ali, Simak S; Charles Coombes, R R; Shaw, Jacqueline A JA
High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer.
Nature Communications
Palafox, Marta M; Monserrat, Laia L; Bellet, Meritxell M; Villacampa, Guillermo G; Gonzalez-Perez, Abel A; Oliveira, Mafalda M; Brasó-Maristany, Fara F; Ibrahimi, Nusaibah N; Kannan, Srinivasaraghavan S; Mina, Leonardo L; Herrera-Abreu, Maria Teresa MT; Òdena, Andreu A; Sánchez-Guixé, Mònica M; Capelán, Marta M; Azaro, Analía A; Bruna, Alejandra A; Rodríguez, Olga O; Guzmán, Marta M; Grueso, Judit J; Viaplana, Cristina C; Hernández, Javier J; Su, Faye F; Lin, Kui K; Clarke, Robert B RB; Caldas, Carlos C; Arribas, Joaquín J; Michiels, Stefan S; García-Sanz, Alicia A; Turner, Nicholas C NC; Prat, Aleix A; Nuciforo, Paolo P; Dienstmann, Rodrigo R; Verma, Chandra S CS; Lopez-Bigas, Nuria N; Scaltriti, Maurizio M; Arnedos, Monica M; Saura, Cristina C; Serra, Violeta V
Spatiotemporal assessment of immunogenomic heterogeneity in multiple myeloma.
Blood Advances
Merz, Maximilian M; Hu, Qiang Q; Merz, Almuth Maria Anni AMA; Wang, Jie J; Hutson, Nicholas N; Rondeau, Cherie C; Celotto, Kimberly K; Belal, Ahmed A; Alberico, Ronald R; Block, AnneMarie A; Mohammadpour, Hemn H; Wallace, Paul K PK; Tario, Joseph D JD; Luce, Jesse J; Glenn, Sean T ST; Singh, Prashant K PK; Samur, Mehmet Kemal MK; Munshi, Nikhil C NC; Liu, Song S; McCarthy, Philip L PL; Wei, Lei L; Hillengass, Jens J
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis.
Nature Genetics
Kar, Siddhartha P SP; Quiros, Pedro M PM; Gu, Muxin M; Jiang, Tao T; Mitchell, Jonathan J; Langdon, Ryan R; Iyer, Vivek V; Barcena, Clea C; Vijayabaskar, M S MS; Fabre, Margarete A MA; Carter, Paul P; Petrovski, Slavé S; Burgess, Stephen S; Vassiliou, George S GS
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.
Nature Communications
Havugimana, Pierre C PC; Goel, Raghuveera Kumar RK; Phanse, Sadhna S; Youssef, Ahmed A; Padhorny, Dzmitry D; Kotelnikov, Sergei S; Kozakov, Dima D; Emili, Andrew A
Publication Date: 2022-07-13
Variant appearance in text: TP53: 782+400G>C; R280T; rs121912660
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
Prolonged remission with pembrolizumab and radiation therapy in a patient with multisystem Langerhans cell sarcoma.
Haematologica
Zanwar, Saurabh S; Ravindran, Aishwarya A; Abeykoon, Jithma P JP; Young, Jason R JR; Kozelsky, Timothy F TF; Rech, Karen L KL; Goyal, Gaurav G; Go, Ronald S RS
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.
Analysis of the genomic landscapes of Barbadian and Nigerian women with triple negative breast cancer.
Cancer Causes & Control : Ccc
Hercules, Shawn M SM; Liu, Xiyu X; Bassey-Archibong, Blessing B I BBI; Skeete, Desiree H A DHA; Smith Connell, Suzanne S; Daramola, Adetola A; Banjo, Adekunbiola A AA; Ebughe, Godwin G; Agan, Thomas T; Ekanem, Ima-Obong IO; Udosen, Joe J; Obiorah, Christopher C; Ojule, Aaron C AC; Misauno, Michael A MA; Dauda, Ayuba M AM; Egbujo, Ejike C EC; Hercules, Jevon C JC; Ansari, Amna A; Brain, Ian I; MacColl, Christine C; Xu, Yili Y; Jin, Yuxin Y; Chang, Sharon S; Carpten, John D JD; Bédard, André A; Pond, Greg R GR; Blenman, Kim R M KRM; Manojlovic, Zarko Z; Daniel, Juliet M JM
Publication Date: 2022-06
Variant appearance in text: TP53: 839G>C; Arg280Thr; rs121912660
Evaluation of the Clinical Utility of Genomic Profiling to Inform Selection of Clinical Trial Therapy in Salivary Gland Cancer.
Cancers
Rack, Samuel S; Feeney, Laura L; Hapuarachi, Brindley B; Adderley, Helen H; Woodhouse, Laura L; Betts, Guy G; Burghel, George J GJ; Harrington, Kevin J KJ; Metcalf, Robert R
Publication Date: 2022-02-23
Variant appearance in text: TP53: 839G>C; Arg280Thr
Somatic and Germline Genomic Alterations in Very Young Women with Breast Cancer.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Waks, Adrienne G AG; Kim, Dewey D; Jain, Esha E; Snow, Craig C; Kirkner, Gregory J GJ; Rosenberg, Shoshana M SM; Oh, Coyin C; Poorvu, Philip D PD; Ruddy, Kathryn J KJ; Tamimi, Rulla M RM; Peppercorn, Jeffrey J; Schapira, Lidia L; Borges, Virginia F VF; Come, Steven E SE; Brachtel, Elena F EF; Warner, Ellen E; Collins, Laura C LC; Partridge, Ann H AH; Wagle, Nikhil N
ATR inhibition reverses the resistance of homologous recombination deficient MGMTlow/MMRproficient cancer cells to temozolomide.
Oncotarget
El Touny, Lara H LH; Hose, Curtis C; Connelly, John J; Harris, Erik E; Monks, Anne A; Dull, Angie B AB; Wilsker, Deborah F DF; Hollingshead, Melinda G MG; Gottholm-Ahalt, Michelle M; Alcoser, Sergio Y SY; Mullendore, Michael E ME; Parchment, Ralph E RE; Doroshow, James H JH; Teicher, Beverly A BA; Rapisarda, Annamaria A
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
FDG positron emission tomography imaging and ctDNA detection as an early dynamic biomarker of everolimus efficacy in advanced luminal breast cancer.
Npj Breast Cancer
Gombos, Andrea A; Venet, David D; Ameye, Lieveke L; Vuylsteke, Peter P; Neven, Patrick P; Richard, Vincent V; Duhoux, Francois P FP; Laes, Jean-Francois JF; Rothe, Françoise F; Sotiriou, Christos C; Paesmans, Marianne M; Awada, Ahmad A; Guiot, Thomas T; Flamen, Patrick P; Piccart-Gebhart, Martine M; Ignatiadis, Michail M; Gebhart, Géraldine G
Woods, Andrew D AD; Purohit, Reshma R; Mitchell, Laura Crocker LC; Collier, John R JR; Collier, Katherine A KA; Lathara, Melvin M; Learned, Katrina K; Vaske, Olena O; Geiger, Heather H; Wrzeszczynski, Kazimierz O KO; Jobanputra, Vaidehi V; Srinivasa, Ganapati G; Rudzinski, Erin R ER; Whelan, Kimberly K; Beierle, Elizabeth E; Spunt, Sheri L SL; Keller, Charles C; Wadhwa, Aman A