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
ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC).
Plos Genetics
Ferrando, Lorenzo L; Vingiani, Andrea A; Garuti, Anna A; Vernieri, Claudio C; Belfiore, Antonino A; Agnelli, Luca L; Dagrada, Gianpaolo G; Ivanoiu, Diana D; Bonizzi, Giuseppina G; Munzone, Elisabetta E; Lippolis, Luana L; Dameri, Martina M; Ravera, Francesco F; Colleoni, Marco M; Viale, Giuseppe G; Magnani, Luca L; Ballestrero, Alberto A; Zoppoli, Gabriele G; Pruneri, Giancarlo G
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
Cancer Research
Sjöström, Martin M; Zhao, Shuang G SG; Levy, Samuel S; Zhang, Meng M; Ning, Yuhong Y; Shrestha, Raunak R; Lundberg, Arian A; Herberts, Cameron C; Foye, Adam A; Aggarwal, Rahul R; Hua, Junjie T JT; Li, Haolong H; Bergamaschi, Anna A; Maurice-Dror, Corinne C; Maheshwari, Ashutosh A; Chen, Sujun S; Ng, Sarah W S SWS; Ye, Wenbin W; Petricca, Jessica J; Fraser, Michael M; Chesner, Lisa L; Perry, Marc D MD; Moreno-Rodriguez, Thaidy T; Chen, William S WS; Alumkal, Joshi J JJ; Chou, Jonathan J; Morgans, Alicia K AK; Beer, Tomasz M TM; Thomas, George V GV; Gleave, Martin M; Lloyd, Paul P; Phillips, Tierney T; McCarthy, Erin E; Haffner, Michael C MC; Zoubeidi, Amina A; Annala, Matti M; Reiter, Robert E RE; Rettig, Matthew B MB; Witte, Owen N ON; Fong, Lawrence L; Bose, Rohit R; Huang, Franklin W FW; Luo, Jianhua J; Bjartell, Anders A; Lang, Joshua M JM; Mahajan, Nupam P NP; Lara, Primo N PN; Evans, Christopher P CP; Tran, Phuoc T PT; Posadas, Edwin M EM; He, Chuan C; Cui, Xiao-Long XL; Huang, Jiaoti J; Zwart, Wilbert W; Gilbert, Luke A LA; Maher, Christopher A CA; Boutros, Paul C PC; Chi, Kim N KN; Ashworth, Alan A; Small, Eric J EJ; He, Housheng H HH; Wyatt, Alexander W AW; Quigley, David A DA; Feng, Felix Y FY
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.
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
The genomics and epigenetics of olfactory neuroblastoma: A systematic review.
Laryngoscope Investigative Otolaryngology
Kaur, Raman Preet RP; Izumchenko, Evgeny E; Blakaj, Dukagjin M DM; Mladkova, Nikol N; Lechner, Matt M; Beaumont, Thomas L TL; Floudas, Charalampos S CS; Gallia, Gary L GL; London, Nyall R NR
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
Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus.
Nature Medicine
Jin, Sheng Chih SC; Dong, Weilai W; Kundishora, Adam J AJ; Panchagnula, Shreyas S; Moreno-De-Luca, Andres A; Furey, Charuta G CG; Allocco, August A AA; Walker, Rebecca L RL; Nelson-Williams, Carol C; Smith, Hannah H; Dunbar, Ashley A; Conine, Sierra S; Lu, Qiongshi Q; Zeng, Xue X; Sierant, Michael C MC; Knight, James R JR; Sullivan, William W; Duy, Phan Q PQ; DeSpenza, Tyrone T; Reeves, Benjamin C BC; Karimy, Jason K JK; Marlier, Arnaud A; Castaldi, Christopher C; Tikhonova, Irina R IR; Li, Boyang B; Peña, Helena Perez HP; Broach, James R JR; Kabachelor, Edith M EM; Ssenyonga, Peter P; Hehnly, Christine C; Ge, Li L; Keren, Boris B; Timberlake, Andrew T AT; Goto, June J; Mangano, Francesco T FT; Johnston, James M JM; Butler, William E WE; Warf, Benjamin C BC; Smith, Edward R ER; Schiff, Steven J SJ; Limbrick, David D DD; Heuer, Gregory G; Jackson, Eric M EM; Iskandar, Bermans J BJ; Mane, Shrikant S; Haider, Shozeb S; Guclu, Bulent B; Bayri, Yasar Y; Sahin, Yener Y; Duncan, Charles C CC; Apuzzo, Michael L J MLJ; DiLuna, Michael L ML; Hoffman, Ellen J EJ; Sestan, Nenad N; Ment, Laura R LR; Alper, Seth L SL; Bilguvar, Kaya K; Geschwind, Daniel H DH; Günel, Murat M; Lifton, Richard P RP; Kahle, Kristopher T KT
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
NOTCH and DNA repair pathways are more frequently targeted by genomic alterations in inflammatory than in non-inflammatory breast cancers.
Molecular Oncology
Bertucci, François F; Rypens, Charlotte C; Finetti, Pascal P; Guille, Arnaud A; Adélaïde, José J; Monneur, Audrey A; Carbuccia, Nadine N; Garnier, Séverine S; Dirix, Piet P; Gonçalves, Anthony A; Vermeulen, Peter P; Debeb, Bisrat G BG; Wang, Xiaoping X; Dirix, Luc L; Ueno, Naoto T NT; Viens, Patrice P; Cristofanilli, Massimo M; Chaffanet, Max M; Birnbaum, Daniel D; Van Laere, Steven S
Molecular Neuropathology in Practice: Clinical Profiling and Integrative Analysis of Molecular Alterations in Glioblastoma.
Academic Pathology
Nasrallah, MacLean P MP; Binder, Zev A ZA; Oldridge, Derek A DA; Zhao, Jianhua J; Lieberman, David B DB; Roth, Jacquelyn J JJ; Watt, Christopher D CD; Sukhadia, Shrey S; Klinman, Eva E; Daber, Robert D RD; Desai, Arati A; Brem, Steven S; O'Rourke, Donald M DM; Morrissette, Jennifer J D JJD
Sequencing and curation strategies for identifying candidate glioblastoma treatments.
Bmc Medical Genomics
Frank, Mayu O MO; Koyama, Takahiko T; Rhrissorrakrai, Kahn K; Robine, Nicolas N; Utro, Filippo F; Emde, Anne-Katrin AK; Chen, Bo-Juen BJ; Arora, Kanika K; Shah, Minita M; Geiger, Heather H; Felice, Vanessa V; Dikoglu, Esra E; Rahman, Sadia S; Fang, Alice A; Vacic, Vladimir V; Bergmann, Ewa A EA; Vogel, Julia L Moore JLM; Reeves, Catherine C; Khaira, Depinder D; Calabro, Anthony A; Kim, Duyang D; Lamendola-Essel, Michelle F MF; Esteves, Cecilia C; Agius, Phaedra P; Stolte, Christian C; Boockvar, John J; Demopoulos, Alexis A; Placantonakis, Dimitris G DG; Golfinos, John G JG; Brennan, Cameron C; Bruce, Jeffrey J; Lassman, Andrew B AB; Canoll, Peter P; Grommes, Christian C; Daras, Mariza M; Diamond, Eli E; Omuro, Antonio A; Pentsova, Elena E; Orange, Dana E DE; Harvey, Stephen J SJ; Posner, Jerome B JB; Michelini, Vanessa V VV; Jobanputra, Vaidehi V; Zody, Michael C MC; Kelly, John J; Parida, Laxmi L; Wrzeszczynski, Kazimierz O KO; Royyuru, Ajay K AK; Darnell, Robert B RB
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
Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.
The Journal Of Pathology
Temko, Daniel D; Van Gool, Inge C IC; Rayner, Emily E; Glaire, Mark M; Makino, Seiko S; Brown, Matthew M; Chegwidden, Laura L; Palles, Claire C; Depreeuw, Jeroen J; Beggs, Andrew A; Stathopoulou, Chaido C; Mason, John J; Baker, Ann-Marie AM; Williams, Marc M; Cerundolo, Vincenzo V; Rei, Margarida M; Taylor, Jenny C JC; Schuh, Anna A; Ahmed, Ahmed A; Amant, Frédéric F; Lambrechts, Diether D; Smit, Vincent Thbm VT; Bosse, Tjalling T; Graham, Trevor A TA; Church, David N DN; Tomlinson, Ian I
Genomic Evolution of Breast Cancer Metastasis and Relapse.
Cancer Cell
Yates, Lucy R LR; Knappskog, Stian S; Wedge, David D; Farmery, James H R JHR; Gonzalez, Santiago S; Martincorena, Inigo I; Alexandrov, Ludmil B LB; Van Loo, Peter P; Haugland, Hans Kristian HK; Lilleng, Peer Kaare PK; Gundem, Gunes G; Gerstung, Moritz M; Pappaemmanuil, Elli E; Gazinska, Patrycja P; Bhosle, Shriram G SG; Jones, David D; Raine, Keiran K; Mudie, Laura L; Latimer, Calli C; Sawyer, Elinor E; Desmedt, Christine C; Sotiriou, Christos C; Stratton, Michael R MR; Sieuwerts, Anieta M AM; Lynch, Andy G AG; Martens, John W JW; Richardson, Andrea L AL; Tutt, Andrew A; Lønning, Per Eystein PE; Campbell, Peter J PJ
Pan-urologic cancer genomic subtypes that transcend tissue of origin.
Nature Communications
Chen, Fengju F; Zhang, Yiqun Y; Bossé, Dominick D; Lalani, Aly-Khan A AA; Hakimi, A Ari AA; Hsieh, James J JJ; Choueiri, Toni K TK; Gibbons, Don L DL; Ittmann, Michael M; Creighton, Chad J CJ
Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study.
Plos Medicine
Nair, Navya N; Camacho-Vanegas, Olga O; Rykunov, Dmitry D; Dashkoff, Matthew M; Camacho, Sandra Catalina SC; Schumacher, Cassie A CA; Irish, Jonathan C JC; Harkins, Timothy T TT; Freeman, Elijah E; Garcia, Isaac I; Pereira, Elena E; Kendall, Sviatoslav S; Belfer, Rachel R; Kalir, Tamara T; Sebra, Robert R; Reva, Boris B; Dottino, Peter P; Martignetti, John A JA
Clinical Genotyping of Non-Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes.
Neoplasia (New York, N.Y.)
Tafe, Laura J LJ; Pierce, Kirsten J KJ; Peterson, Jason D JD; de Abreu, Francine F; Memoli, Vincent A VA; Black, Candice C CC; Pettus, Jason R JR; Marotti, Jonathan D JD; Gutmann, Edward J EJ; Liu, Xiaoying X; Shirai, Keisuke K; Dragnev, Konstantin H KH; Amos, Christopher I CI; Tsongalis, Gregory J GJ
A Landscape of Pharmacogenomic Interactions in Cancer.
Cell
Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ
Pharmacokinetic, pharmacodynamic and biomarker evaluation of transforming growth factor-β receptor I kinase inhibitor, galunisertib, in phase 1 study in patients with advanced cancer.
Investigational New Drugs
Rodón, Jordi J; Carducci, Michael M; Sepulveda-Sánchez, Juan M JM; Azaro, Analía A; Calvo, Emiliano E; Seoane, Joan J; Braña, Irene I; Sicart, Elisabet E; Gueorguieva, Ivelina I; Cleverly, Ann A; Pillay, N Sokalingum NS; Desaiah, Durisala D; Estrem, Shawn T ST; Paz-Ares, Luis L; Holdhoff, Matthias M; Blakeley, Jaishri J; Lahn, Michael M MM; Baselga, Jose J
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.
Proceedings Of The National Academy Of Sciences Of The United States Of America
Perry, Jennifer A JA; Kiezun, Adam A; Tonzi, Peter P; Van Allen, Eliezer M EM; Carter, Scott L SL; Baca, Sylvan C SC; Cowley, Glenn S GS; Bhatt, Ami S AS; Rheinbay, Esther E; Pedamallu, Chandra Sekhar CS; Helman, Elena E; Taylor-Weiner, Amaro A; McKenna, Aaron A; DeLuca, David S DS; Lawrence, Michael S MS; Ambrogio, Lauren L; Sougnez, Carrie C; Sivachenko, Andrey A; Walensky, Loren D LD; Wagle, Nikhil N; Mora, Jaume J; de Torres, Carmen C; Lavarino, Cinzia C; Dos Santos Aguiar, Simone S; Yunes, Jose Andres JA; Brandalise, Silvia Regina SR; Mercado-Celis, Gabriela Elisa GE; Melendez-Zajgla, Jorge J; Cárdenas-Cardós, Rocío R; Velasco-Hidalgo, Liliana L; Roberts, Charles W M CW; Garraway, Levi A LA; Rodriguez-Galindo, Carlos C; Gabriel, Stacey B SB; Lander, Eric S ES; Golub, Todd R TR; Orkin, Stuart H SH; Getz, Gad G; Janeway, Katherine A KA
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
High frequency of PTEN mutations in nevi and melanomas from xeroderma pigmentosum patients.
Pigment Cell & Melanoma Research
Masaki, Taro T; Wang, Yun Y; DiGiovanna, John J JJ; Khan, Sikandar G SG; Raffeld, Mark M; Beltaifa, Senda S; Hornyak, Thomas J TJ; Darling, Thomas N TN; Lee, Chyi-Chia R CC; Kraemer, Kenneth H KH
Evidence of ultraviolet type mutations in xeroderma pigmentosum melanomas.
Proceedings Of The National Academy Of Sciences Of The United States Of America
Wang, Yun Y; Digiovanna, John J JJ; Stern, Jere B JB; Hornyak, Thomas J TJ; Raffeld, Mark M; Khan, Sikandar G SG; Oh, Kyu-Seon KS; Hollander, M Christine MC; Dennis, Philip A PA; Kraemer, Kenneth H KH