A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression.
Cancer Cell
Hutten, Stefan J SJ; de Bruijn, Roebi R; Lutz, Catrin C; Badoux, Madelon M; Eijkman, Timo T; Chao, Xue X; Ciwinska, Marta M; Sheinman, Michael M; Messal, Hendrik H; Herencia-Ropero, Andrea A; Kristel, Petra P; Mulder, Lennart L; van der Waal, Rens R; Sanders, Joyce J; Almekinders, Mathilde M MM; Llop-Guevara, Alba A; Davies, Helen R HR; van Haren, Matthijs J MJ; Martin, Nathaniel I NI; Behbod, Fariba F; Nik-Zainal, Serena S; Serra, Violeta V; van Rheenen, Jacco J; Lips, Esther H EH; Wessels, Lodewyk F A LFA; , ; Wesseling, Jelle J; Scheele, Colinda L G J CLGJ; Jonkers, Jos J
Genetic heterogeneity and tissue-specific patterns of tumors with multiple PIK3CA mutations.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Sivakumar, Smruthy S; Jin, Dexter X DX; Rathod, Ruchita R; Ross, Jeffrey J; Cantley, Lewis C LC; Scaltriti, Maurizio M; Chen, Jessica W JW; Hutchinson, Katherine E KE; Wilson, Timothy R TR; Sokol, Ethan S ES; Vasan, Neil N
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
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
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients.
Genome Medicine
Tsui, Dana W Y DWY; Cheng, Michael L ML; Shady, Maha M; Yang, Julie L JL; Stephens, Dennis D; Won, Helen H; Srinivasan, Preethi P; Huberman, Kety K; Meng, Fanli F; Jing, Xiaohong X; Patel, Juber J; Hasan, Maysun M; Johnson, Ian I; Gedvilaite, Erika E; Houck-Loomis, Brian B; Socci, Nicholas D ND; Selcuklu, S Duygu SD; Seshan, Venkatraman E VE; Zhang, Hongxin H; Chakravarty, Debyani D; Zehir, Ahmet A; Benayed, Ryma R; Arcila, Maria M; Ladanyi, Marc M; Funt, Samuel A SA; Feldman, Darren R DR; Li, Bob T BT; Razavi, Pedram P; Rosenberg, Jonathan J; Bajorin, Dean D; Iyer, Gopa G; Abida, Wassim W; Scher, Howard I HI; Rathkopf, Dana D; Viale, Agnes A; Berger, Michael F MF; Solit, David B DB
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
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
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
Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids.
Cell
Koundouros, Nikos N; Karali, Evdoxia E; Tripp, Aurelien A; Valle, Adamo A; Inglese, Paolo P; Perry, Nicholas J S NJS; Magee, David J DJ; Anjomani Virmouni, Sara S; Elder, George A GA; Tyson, Adam L AL; Dória, Maria Luisa ML; van Weverwijk, Antoinette A; Soares, Renata F RF; Isacke, Clare M CM; Nicholson, Jeremy K JK; Glen, Robert C RC; Takats, Zoltan Z; Poulogiannis, George G
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
Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer.
Cancer Cell
Woolston, Andrew A; Khan, Khurum K; Spain, Georgia G; Barber, Louise J LJ; Griffiths, Beatrice B; Gonzalez-Exposito, Reyes R; Hornsteiner, Lisa L; Punta, Marco M; Patil, Yatish Y; Newey, Alice A; Mansukhani, Sonia S; Davies, Matthew N MN; Furness, Andrew A; Sclafani, Francesco F; Peckitt, Clare C; Jiménez, Mirta M; Kouvelakis, Kyriakos K; Ranftl, Romana R; Begum, Ruwaida R; Rana, Isma I; Thomas, Janet J; Bryant, Annette A; Quezada, Sergio S; Wotherspoon, Andrew A; Khan, Nasir N; Fotiadis, Nikolaos N; Marafioti, Teresa T; Powles, Thomas T; Lise, Stefano S; Calvo, Fernando F; Guettler, Sebastian S; von Loga, Katharina K; Rao, Sheela S; Watkins, David D; Starling, Naureen N; Chau, Ian I; Sadanandam, Anguraj A; Cunningham, David D; Gerlinger, Marco M
DNA methylation changes and somatic mutations as tumorigenic events in Lynch syndrome-associated adenomas retaining mismatch repair protein expression.
Ebiomedicine
Mäki-Nevala, Satu S; Valo, Satu S; Ristimäki, Ari A; Sarhadi, Virinder V; Knuutila, Sakari S; Nyström, Minna M; Renkonen-Sinisalo, Laura L; Lepistö, Anna A; Mecklin, Jukka-Pekka JP; Peltomäki, Päivi P
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
Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery.
Oncotarget
Bryce, Alan H AH; Egan, Jan B JB; Borad, Mitesh J MJ; Stewart, A Keith AK; Nowakowski, Grzegorz S GS; Chanan-Khan, Asher A; Patnaik, Mrinal M MM; Ansell, Stephen M SM; Banck, Michaela S MS; Robinson, Steven I SI; Mansfield, Aaron S AS; Klee, Eric W EW; Oliver, Gavin R GR; McCormick, Jennifer B JB; Huneke, Norine E NE; Tagtow, Colleen M CM; Jenkins, Robert B RB; Rumilla, Kandelaria M KM; Kerr, Sarah E SE; Kocher, Jean-Pierre A JA; Beck, Scott A SA; Fernandez-Zapico, Martin E ME; Farrugia, Gianrico G; Lazaridis, Konstantinos N KN; McWilliams, Robert R RR
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Genome Medicine
Chalmers, Zachary R ZR; Connelly, Caitlin F CF; Fabrizio, David D; Gay, Laurie L; Ali, Siraj M SM; Ennis, Riley R; Schrock, Alexa A; Campbell, Brittany B; Shlien, Adam A; Chmielecki, Juliann J; Huang, Franklin F; He, Yuting Y; Sun, James J; Tabori, Uri U; Kennedy, Mark M; Lieber, Daniel S DS; Roels, Steven S; White, Jared J; Otto, Geoffrey A GA; Ross, Jeffrey S JS; Garraway, Levi L; Miller, Vincent A VA; Stephens, Phillip J PJ; Frampton, Garrett M GM
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Oncotarget
Fertig, Elana J EJ; Ozawa, Hiroyuki H; Thakar, Manjusha M; Howard, Jason D JD; Kagohara, Luciane T LT; Krigsfeld, Gabriel G; Ranaweera, Ruchira S RS; Hughes, Robert M RM; Perez, Jimena J; Jones, Siân S; Favorov, Alexander V AV; Carey, Jacob J; Stein-O'Brien, Genevieve G; Gaykalova, Daria A DA; Ochs, Michael F MF; Chung, Christine H CH
Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers.
Nature Communications
Miller, Christopher A CA; Gindin, Yevgeniy Y; Lu, Charles C; Griffith, Obi L OL; Griffith, Malachi M; Shen, Dong D; Hoog, Jeremy J; Li, Tiandao T; Larson, David E DE; Watson, Mark M; Davies, Sherri R SR; Hunt, Kelly K; Suman, Vera J VJ; Snider, Jacqueline J; Walsh, Thomas T; Colditz, Graham A GA; DeSchryver, Katherine K; Wilson, Richard K RK; Mardis, Elaine R ER; Ellis, Matthew J MJ
Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B
Age-related mutations associated with clonal hematopoietic expansion and malignancies.
Nature Medicine
Xie, Mingchao M; Lu, Charles C; Wang, Jiayin J; McLellan, Michael D MD; Johnson, Kimberly J KJ; Wendl, Michael C MC; McMichael, Joshua F JF; Schmidt, Heather K HK; Yellapantula, Venkata V; Miller, Christopher A CA; Ozenberger, Bradley A BA; Welch, John S JS; Link, Daniel C DC; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Chen, Feng F; Wilson, Richard K RK; Ley, Timothy J TJ; Ding, Li L
De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes.
Nature Genetics
Rivière, Jean-Baptiste JB; Mirzaa, Ghayda M GM; O'Roak, Brian J BJ; Beddaoui, Margaret M; Alcantara, Diana D; Conway, Robert L RL; St-Onge, Judith J; Schwartzentruber, Jeremy A JA; Gripp, Karen W KW; Nikkel, Sarah M SM; Worthylake, Thea T; Sullivan, Christopher T CT; Ward, Thomas R TR; Butler, Hailly E HE; Kramer, Nancy A NA; Albrecht, Beate B; Armour, Christine M CM; Armstrong, Linlea L; Caluseriu, Oana O; Cytrynbaum, Cheryl C; Drolet, Beth A BA; Innes, A Micheil AM; Lauzon, Julie L JL; Lin, Angela E AE; Mancini, Grazia M S GM; Meschino, Wendy S WS; Reggin, James D JD; Saggar, Anand K AK; Lerman-Sagie, Tally T; Uyanik, Gökhan G; Weksberg, Rosanna R; Zirn, Birgit B; Beaulieu, Chandree L CL; , ; Majewski, Jacek J; Bulman, Dennis E DE; O'Driscoll, Mark M; Shendure, Jay J; Graham, John M JM; Boycott, Kym M KM; Dobyns, William B WB