RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer.
Nature
Jbara, Amina A; Lin, Kuan-Ting KT; Stossel, Chani C; Siegfried, Zahava Z; Shqerat, Haya H; Amar-Schwartz, Adi A; Elyada, Ela E; Mogilevsky, Maxim M; Raitses-Gurevich, Maria M; Johnson, Jared L JL; Yaron, Tomer M TM; Ovadia, Ofek O; Jang, Gun Ho GH; Danan-Gotthold, Miri M; Cantley, Lewis C LC; Levanon, Erez Y EY; Gallinger, Steven S; Krainer, Adrian R AR; Golan, Talia T; Karni, Rotem R
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
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Nature Genetics
Liu, Ilon I; Jiang, Li L; Samuelsson, Erik R ER; Marco Salas, Sergio S; Beck, Alexander A; Hack, Olivia A OA; Jeong, Daeun D; Shaw, McKenzie L ML; Englinger, Bernhard B; LaBelle, Jenna J; Mire, Hafsa M HM; Madlener, Sibylle S; Mayr, Lisa L; Quezada, Michael A MA; Trissal, Maria M; Panditharatna, Eshini E; Ernst, Kati J KJ; Vogelzang, Jayne J; Gatesman, Taylor A TA; Halbert, Matthew E ME; Palova, Hana H; Pokorna, Petra P; Sterba, Jaroslav J; Slaby, Ondrej O; Geyeregger, Rene R; Diaz, Aaron A; Findlay, Izac J IJ; Dun, Matthew D MD; Resnick, Adam A; Suvà, Mario L ML; Jones, David T W DTW; Agnihotri, Sameer S; Svedlund, Jessica J; Koschmann, Carl C; Haberler, Christine C; Czech, Thomas T; Slavc, Irene I; Cotter, Jennifer A JA; Ligon, Keith L KL; Alexandrescu, Sanda S; Yung, W K Alfred WKA; Arrillaga-Romany, Isabel I; Gojo, Johannes J; Monje, Michelle M; Nilsson, Mats M; Filbin, Mariella G MG
Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1.
Acta Neuropathologica
Lucas, Calixto-Hope G CG; Sloan, Emily A EA; Gupta, Rohit R; Wu, Jasper J; Pratt, Drew D; Vasudevan, Harish N HN; Ravindranathan, Ajay A; Barreto, Jairo J; Williams, Erik A EA; Shai, Anny A; Whipple, Nicholas S NS; Bruggers, Carol S CS; Maher, Ossama O; Nabors, Burt B; Rodriguez, Michael M; Samuel, David D; Brown, Melandee M; Carmichael, Jason J; Lu, Rufei R; Mirchia, Kanish K; Sullivan, Daniel V DV; Pekmezci, Melike M; Tihan, Tarik T; Bollen, Andrew W AW; Perry, Arie A; Banerjee, Anuradha A; Mueller, Sabine S; Gupta, Nalin N; Hervey-Jumper, Shawn L SL; Oberheim Bush, Nancy Ann NA; Daras, Mariza M; Taylor, Jennie W JW; Butowski, Nicholas A NA; de Groot, John J; Clarke, Jennifer L JL; Raleigh, David R DR; Costello, Joseph F JF; Phillips, Joanna J JJ; Reddy, Alyssa T AT; Chang, Susan M SM; Berger, Mitchel S MS; Solomon, David A DA
Fragment size and dynamics of EGFR-mutated tumor-derived DNA provide prognostic information regarding EGFR-TKI efficacy in patients with EGFR-mutated NSCLC.
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: 380C>A; Ser127Tyr
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.
Comparative Panel Sequencing of DNA Variants in cf-, ev- and tumorDNA for Pancreatic Ductal Adenocarcinoma Patients.
Cancers
Waldenmaier, Mareike M; Schulte, Lucas L; Schönfelder, Jonathan J; Fürstberger, Axel A; Kraus, Johann M JM; Daiss, Nora N; Seibold, Tanja T; Morawe, Mareen M; Ettrich, Thomas J TJ; Kestler, Hans A HA; Kahlert, Christoph C; Seufferlein, Thomas T; Eiseler, Tim T
Marazioti, Antonia A; Krontira, Anthi C AC; Behrend, Sabine J SJ; Giotopoulou, Georgia A GA; Ntaliarda, Giannoula G; Blanquart, Christophe C; Bayram, Hasan H; Iliopoulou, Marianthi M; Vreka, Malamati M; Trassl, Lilith L; Pepe, Mario A A MAA; Hackl, Caroline M CM; Klotz, Laura V LV; Weiss, Stefanie A I SAI; Koch, Ina I; Lindner, Michael M; Hatz, Rudolph A RA; Behr, Juergen J; Wagner, Darcy E DE; Papadaki, Helen H; Antimisiaris, Sophia G SG; Jean, Didier D; Deshayes, Sophie S; Grégoire, Marc M; Kayalar, Özgecan Ö; Mortazavi, Deniz D; Dilege, Şükrü Ş; Tanju, Serhan S; Erus, Suat S; Yavuz, Ömer Ö; Bulutay, Pınar P; Fırat, Pınar P; Psallidas, Ioannis I; Spella, Magda M; Giopanou, Ioanna I; Lilis, Ioannis I; Lamort, Anne-Sophie AS; Stathopoulos, Georgios T GT
Marazioti, Antonia A; Krontira, Anthi C AC; Behrend, Sabine J SJ; Giotopoulou, Georgia A GA; Ntaliarda, Giannoula G; Blanquart, Christophe C; Bayram, Hasan H; Iliopoulou, Marianthi M; Vreka, Malamati M; Trassl, Lilith L; Pepe, Mario A A MAA; Hackl, Caroline M CM; Klotz, Laura V LV; Weiss, Stefanie A I SAI; Koch, Ina I; Lindner, Michael M; Hatz, Rudolph A RA; Behr, Juergen J; Wagner, Darcy E DE; Papadaki, Helen H; Antimisiaris, Sophia G SG; Jean, Didier D; Deshayes, Sophie S; Grégoire, Marc M; Kayalar, Özgecan Ö; Mortazavi, Deniz D; Dilege, Şükrü Ş; Tanju, Serhan S; Erus, Suat S; Yavuz, Ömer Ö; Bulutay, Pınar P; Fırat, Pınar P; Psallidas, Ioannis I; Spella, Magda M; Giopanou, Ioanna I; Lilis, Ioannis I; Lamort, Anne-Sophie AS; Stathopoulos, Georgios T GT
Multi-omic machine learning predictor of breast cancer therapy response.
Nature
Sammut, Stephen-John SJ; Crispin-Ortuzar, Mireia M; Chin, Suet-Feung SF; Provenzano, Elena E; Bardwell, Helen A HA; Ma, Wenxin W; Cope, Wei W; Dariush, Ali A; Dawson, Sarah-Jane SJ; Abraham, Jean E JE; Dunn, Janet J; Hiller, Louise L; Thomas, Jeremy J; Cameron, David A DA; Bartlett, John M S JMS; Hayward, Larry L; Pharoah, Paul D PD; Markowetz, Florian F; Rueda, Oscar M OM; Earl, Helena M HM; Caldas, Carlos C
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
Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival.
Journal Of Experimental & Clinical Cancer Research : Cr
Cho, Eun Jeong EJ; Kim, Minsuh M; Jo, Daum D; Kim, Jihye J; Oh, Ji-Hye JH; Chung, Hee Chul HC; Lee, Sun-Hye SH; Kim, Deokhoon D; Chun, Sung-Min SM; Kim, Jihun J; Lee, Hyeonjin H; Kim, Tae Won TW; Yu, Chang Sik CS; Sung, Chang Ohk CO; Jang, Se Jin SJ
Glioblastoma multiforme: a multi-omics analysis of driver genes and tumour heterogeneity.
Interface Focus
Herrera-Oropeza, Gabriel Emilio GE; Angulo-Rojo, Carla C; Gástelum-López, Santos Alberto SA; Varela-Echavarría, Alfredo A; Hernández-Rosales, Maribel M; Aviña-Padilla, Katia K
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
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
Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer.
Nature Communications
Vandekerkhove, Gillian G; Lavoie, Jean-Michel JM; Annala, Matti M; Murtha, Andrew J AJ; Sundahl, Nora N; Walz, Simon S; Sano, Takeshi T; Taavitsainen, Sinja S; Ritch, Elie E; Fazli, Ladan L; Hurtado-Coll, Antonio A; Wang, Gang G; Nykter, Matti M; Black, Peter C PC; Todenhöfer, Tilman T; Ost, Piet P; Gibb, Ewan A EA; Chi, Kim N KN; Eigl, Bernhard J BJ; Wyatt, Alexander W AW
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
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
A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population.
Breast Cancer Research : Bcr
Kang, Taekyu T; Yau, Christina C; Wong, Christopher K CK; Sanborn, John Z JZ; Newton, Yulia Y; Vaske, Charlie C; Benz, Stephen C SC; Krings, Gregor G; Camarda, Roman R; Henry, Jill E JE; Stuart, Josh J; Powell, Mark M; Benz, Christopher C CC
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
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
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
Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study.
Nature Medicine
Sicklick, Jason K JK; Kato, Shumei S; Okamura, Ryosuke R; Schwaederle, Maria M; Hahn, Michael E ME; Williams, Casey B CB; De, Pradip P; Krie, Amy A; Piccioni, David E DE; Miller, Vincent A VA; Ross, Jeffrey S JS; Benson, Adam A; Webster, Jennifer J; Stephens, Philip J PJ; Lee, J Jack JJ; Fanta, Paul T PT; Lippman, Scott M SM; Leyland-Jones, Brian B; Kurzrock, Razelle R
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
Scientific Reports
Collord, Grace G; Tarpey, Patrick P; Kurbatova, Natalja N; Martincorena, Inigo I; Moran, Sebastian S; Castro, Manuel M; Nagy, Tibor T; Bignell, Graham G; Maura, Francesco F; Young, Matthew D MD; Berna, Jorge J; Tubio, Jose M C JMC; McMurran, Chris E CE; Young, Adam M H AMH; Sanders, Mathijs M; Noorani, Imran I; Price, Stephen J SJ; Watts, Colin C; Leipnitz, Elke E; Kirsch, Matthias M; Schackert, Gabriele G; Pearson, Danita D; Devadass, Abel A; Ram, Zvi Z; Collins, V Peter VP; Allinson, Kieren K; Jenkinson, Michael D MD; Zakaria, Rasheed R; Syed, Khaja K; Hanemann, C Oliver CO; Dunn, Jemma J; McDermott, Michael W MW; Kirollos, Ramez W RW; Vassiliou, George S GS; Esteller, Manel M; Behjati, Sam S; Brazma, Alvis A; Santarius, Thomas T; McDermott, Ultan U
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
appreci8: a pipeline for precise variant calling integrating 8 tools.
Bioinformatics (Oxford, England)
Sandmann, Sarah S; Karimi, Mohsen M; de Graaf, Aniek O AO; Rohde, Christian C; Göllner, Stefanie S; Varghese, Julian J; Ernsting, Jan J; Walldin, Gunilla G; van der Reijden, Bert A BA; Müller-Tidow, Carsten C; Malcovati, Luca L; Hellström-Lindberg, Eva E; Jansen, Joop H JH; Dugas, Martin M
Publication Date: 2018-12-15
Variant appearance in text: TP53: 380C>A; Ser127Tyr