A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes.
Npj Precision Oncology
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Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity.
Nature Communications
Möhrmann, Lino L; Werner, Maximilian M; Oleś, Małgorzata M; Mock, Andreas A; Uhrig, Sebastian S; Jahn, Arne A; Kreutzfeldt, Simon S; Fröhlich, Martina M; Hutter, Barbara B; Paramasivam, Nagarajan N; Richter, Daniela D; Beck, Katja K; Winter, Ulrike U; Pfütze, Katrin K; Heilig, Christoph E CE; Teleanu, Veronica V; Lipka, Daniel B DB; Zapatka, Marc M; Hanf, Dorothea D; List, Catrin C; Allgäuer, Michael M; Penzel, Roland R; Rüter, Gina G; Jelas, Ivan I; Hamacher, Rainer R; Falkenhorst, Johanna J; Wagner, Sebastian S; Brandts, Christian H CH; Boerries, Melanie M; Illert, Anna L AL; Metzeler, Klaus H KH; Westphalen, C Benedikt CB; Desuki, Alexander A; Kindler, Thomas T; Folprecht, Gunnar G; Weichert, Wilko W; Brors, Benedikt B; Stenzinger, Albrecht A; Schröck, Evelin E; Hübschmann, Daniel D; Horak, Peter P; Heining, Christoph C; Fröhling, Stefan S; Glimm, Hanno H
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
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
Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers.
Nature Medicine
Parikh, Aparna R AR; Leshchiner, Ignaty I; Elagina, Liudmila L; Goyal, Lipika L; Levovitz, Chaya C; Siravegna, Giulia G; Livitz, Dimitri D; Rhrissorrakrai, Kahn K; Martin, Elizabeth E EE; Van Seventer, Emily E EE; Hanna, Megan M; Slowik, Kara K; Utro, Filippo F; Pinto, Christopher J CJ; Wong, Alicia A; Danysh, Brian P BP; de la Cruz, Ferran Fece FF; Fetter, Isobel J IJ; Nadres, Brandon B; Shahzade, Heather A HA; Allen, Jill N JN; Blaszkowsky, Lawrence S LS; Clark, Jeffrey W JW; Giantonio, Bruce B; Murphy, Janet E JE; Nipp, Ryan D RD; Roeland, Eric E; Ryan, David P DP; Weekes, Colin D CD; Kwak, Eunice L EL; Faris, Jason E JE; Wo, Jennifer Y JY; Aguet, François F; Dey-Guha, Ipsita I; Hazar-Rethinam, Mehlika M; Dias-Santagata, Dora D; Ting, David T DT; Zhu, Andrew X AX; Hong, Theodore S TS; Golub, Todd R TR; Iafrate, A John AJ; Adalsteinsson, Viktor A VA; Bardelli, Alberto A; Parida, Laxmi L; Juric, Dejan D; Getz, Gad G; Corcoran, Ryan B RB
The evolutionary landscape of colorectal tumorigenesis.
Nature Ecology & Evolution
Cross, William W; Kovac, Michal M; Mustonen, Ville V; Temko, Daniel D; Davis, Hayley H; Baker, Ann-Marie AM; Biswas, Sujata S; Arnold, Roland R; Chegwidden, Laura L; Gatenbee, Chandler C; Anderson, Alexander R AR; Koelzer, Viktor H VH; Martinez, Pierre P; Jiang, Xiaowei X; Domingo, Enric E; Woodcock, Dan J DJ; Feng, Yun Y; Kovacova, Monika M; Maughan, Tim T; , ; Jansen, Marnix M; Rodriguez-Justo, Manuel M; Ashraf, Shazad S; Guy, Richard R; Cunningham, Christopher C; East, James E JE; Wedge, David C DC; Wang, Lai Mun LM; Palles, Claire C; Heinimann, Karl K; Sottoriva, Andrea A; Leedham, Simon J SJ; Graham, Trevor A TA; Tomlinson, Ian P M IPM
Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors.
Nature Communications
Schütte, Moritz M; Risch, Thomas T; Abdavi-Azar, Nilofar N; Boehnke, Karsten K; Schumacher, Dirk D; Keil, Marlen M; Yildiriman, Reha R; Jandrasits, Christine C; Borodina, Tatiana T; Amstislavskiy, Vyacheslav V; Worth, Catherine L CL; Schweiger, Caroline C; Liebs, Sandra S; Lange, Martin M; Warnatz, Hans-Jörg HJ; Butcher, Lee M LM; Barrett, James E JE; Sultan, Marc M; Wierling, Christoph C; Golob-Schwarzl, Nicole N; Lax, Sigurd S; Uranitsch, Stefan S; Becker, Michael M; Welte, Yvonne Y; Regan, Joseph Lewis JL; Silvestrov, Maxine M; Kehler, Inge I; Fusi, Alberto A; Kessler, Thomas T; Herwig, Ralf R; Landegren, Ulf U; Wienke, Dirk D; Nilsson, Mats M; Velasco, Juan A JA; Garin-Chesa, Pilar P; Reinhard, Christoph C; Beck, Stephan S; Schäfer, Reinhold R; Regenbrecht, Christian R A CR; Henderson, David D; Lange, Bodo B; Haybaeck, Johannes J; Keilholz, Ulrich U; Hoffmann, Jens J; Lehrach, Hans H; Yaspo, Marie-Laure ML
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
Cell Reports
Giannakis, Marios M; Mu, Xinmeng Jasmine XJ; Shukla, Sachet A SA; Qian, Zhi Rong ZR; Cohen, Ofir O; Nishihara, Reiko R; Bahl, Samira S; Cao, Yin Y; Amin-Mansour, Ali A; Yamauchi, Mai M; Sukawa, Yasutaka Y; Stewart, Chip C; Rosenberg, Mara M; Mima, Kosuke K; Inamura, Kentaro K; Nosho, Katsuhiko K; Nowak, Jonathan A JA; Lawrence, Michael S MS; Giovannucci, Edward L EL; Chan, Andrew T AT; Ng, Kimmie K; Meyerhardt, Jeffrey A JA; Van Allen, Eliezer M EM; Getz, Gad G; Gabriel, Stacey B SB; Lander, Eric S ES; Wu, Catherine J CJ; Fuchs, Charles S CS; Ogino, Shuji S; Garraway, Levi A LA