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
Publication Date: 2023-02-23
Variant appearance in text: RB1: 1666C>T; Arg556Ter
Circulating tumour DNA analysis predicts relapse and improves risk stratification in primary refractory multiple myeloma.
Blood Cancer Journal
Mithraprabhu, Sridurga S; Reynolds, John J; Turner, Rose R; Quach, Hang H; Horvath, Noemi N; Kerridge, Ian I; Kalff, Anna A; Bergin, Krystal K; Hocking, Jay J; Yuen, Flora F; Khong, Tiffany T; Durie, Brian M BM; Spencer, Andrew A
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
Mutant-RB1 circulating tumor DNA in the blood of unilateral retinoblastoma patients: What happens during enucleation surgery: A pilot study.
Plos One
Abramson, David H DH; Mandelker, Diana L DL; Brannon, A Rose AR; Dunkel, Ira J IJ; Benayed, Ryma R; Berger, Michael F MF; Arcila, Maria E ME; Ladanyi, Marc M; Friedman, Danielle Novetsky DN; Jayakumaran, Gowtham G; Diosdado, Monica S MS; Robbins, Melissa A MA; Haggag-Lindgren, Dianna D; Shukla, Neerav N; Walsh, Michael F MF; Kothari, Prachi P; Tsui, Dana W Y DWY; Francis, Jasmine H JH
Retrospective Evaluation of Somatic Alterations in Cell-Free DNA from Blood in Retinoblastoma.
Ophthalmology Science
Abramson, David H DH; Mandelker, Diana D; Francis, Jasmine H JH; Dunkel, Ira J IJ; Brannon, A Rose AR; Benayed, Ryma R; Berger, Michael F MF; Arcila, Maria E ME; Ladanyi, Marc M; Friedman, Danielle Novetsky DN; Jayakumaran, Gowtham G; Diosdado, Monica S MS; Robbins, Melissa A MA; Haggag-Lindgren, Dianna D; Shukla, Neerav N; Walsh, Michael M; Kothari, Prachi P; Tsui, Dana W Y DWY
Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma.
The Journal Of Pathology
Birkeälv, Sofia S; Harland, Mark M; Matsuyama, Larissa Satiko Alcantara Sekimoto LSAS; Rashid, Mamun M; Mehta, Ishan I; Laye, Jonathan P JP; Haase, Kerstin K; Mell, Tracey T; Iyer, Vivek V; Robles-Espinoza, Carla Daniela CD; McDermott, Ultan U; van Loo, Peter P; Kuijjer, Marieke L ML; Possik, Patricia A PA; Maria Engler, Silvya Stuchi SS; Bishop, D Timothy DT; Newton-Bishop, Julia J; Adams, David J DJ
Rb Tumor Suppressor in Small Cell Lung Cancer: Combined Genomic and IHC Analysis with a Description of a Distinct Rb-Proficient Subset.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Febres-Aldana, Christopher A CA; Chang, Jason C JC; Ptashkin, Ryan R; Wang, Yuhan Y; Gedvilaite, Erika E; Baine, Marina K MK; Travis, William D WD; Ventura, Katia K; Bodd, Francis F; Yu, Helena A HA; Quintanal-Villalonga, Alvaro A; Lai, W Victoria WV; Egger, Jacklynn V JV; Offin, Michael M; Ladanyi, Marc M; Rudin, Charles M CM; Rekhtman, Natasha 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
Discordance of PIK3CA and TP53 mutations between breast cancer brain metastases and matched primary tumors.
Scientific Reports
Thulin, Anna A; Andersson, Carola C; Werner Rönnerman, Elisabeth E; De Lara, Shahin S; Chamalidou, Chaido C; Schoenfeld, Arnd A; Kovács, Anikó A; Fagman, Henrik H; Enlund, Fredrik F; Linderholm, Barbro K BK
Discordance of PIK3CA and TP53 mutations between breast cancer brain metastases and matched primary tumors.
Scientific Reports
Thulin, Anna A; Andersson, Carola C; Werner Rönnerman, Elisabeth E; De Lara, Shahin S; Chamalidou, Chaido C; Schoenfeld, Arnd A; Kovács, Anikó A; Fagman, Henrik H; Enlund, Fredrik F; Linderholm, Barbro K BK
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort.
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort.
Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing.
Cancer Discovery
Newman, Scott S; Nakitandwe, Joy J; Kesserwan, Chimene A CA; Azzato, Elizabeth M EM; Wheeler, David A DA; Rusch, Michael M; Shurtleff, Sheila S; Hedges, Dale J DJ; Hamilton, Kayla V KV; Foy, Scott G SG; Edmonson, Michael N MN; Thrasher, Andrew A; Bahrami, Armita A; Orr, Brent A BA; Klco, Jeffery M JM; Gu, Jiali J; Harrison, Lynn W LW; Wang, Lu L; Clay, Michael R MR; Ouma, Annastasia A; Silkov, Antonina A; Liu, Yanling Y; Zhang, Zhaojie Z; Liu, Yu Y; Brady, Samuel W SW; Zhou, Xin X; Chang, Ti-Cheng TC; Pande, Manjusha M; Davis, Eric E; Becksfort, Jared J; Patel, Aman A; Wilkinson, Mark R MR; Rahbarinia, Delaram D; Kubal, Manish M; Maciaszek, Jamie L JL; Pastor, Victor V; Knight, Jay J; Gout, Alexander M AM; Wang, Jian J; Gu, Zhaohui Z; Mullighan, Charles G CG; McGee, Rose B RB; Quinn, Emily A EA; Nuccio, Regina R; Mostafavi, Roya R; Gerhardt, Elsie L EL; Taylor, Leslie M LM; Valdez, Jessica M JM; Hines-Dowell, Stacy J SJ; Pappo, Alberto S AS; Robinson, Giles G; Johnson, Liza-Marie LM; Pui, Ching-Hon CH; Ellison, David W DW; Downing, James R JR; Zhang, Jinghui J; Nichols, Kim E KE
Establishing the Clinical Utility of ctDNA Analysis for Diagnosis, Prognosis, and Treatment Monitoring of Retinoblastoma: The Aqueous Humor Liquid Biopsy.
Cancers
Xu, Liya L; Kim, Mary E ME; Polski, Ashley A; Prabakar, Rishvanth K RK; Shen, Lishuang L; Peng, Chen-Ching CC; Reid, Mark W MW; Chévez-Barrios, Patricia P; Kim, Jonathan W JW; Shah, Rachana R; Jubran, Rima R; Kuhn, Peter P; Cobrinik, David D; Biegel, Jaclyn A JA; Gai, Xiaowu X; Hicks, James J; Berry, Jesse L JL
Integrated molecular drivers coordinate biological and clinical states in melanoma.
Nature Genetics
Conway, Jake R JR; Dietlein, Felix F; Taylor-Weiner, Amaro A; AlDubayan, Saud S; Vokes, Natalie N; Keenan, Tanya T; Reardon, Brendan B; He, Meng Xiao MX; Margolis, Claire A CA; Weirather, Jason L JL; Haq, Rizwan R; Schilling, Bastian B; Stephen Hodi, F F; Schadendorf, Dirk D; Liu, David D; Van Allen, Eliezer M EM
Simultaneous identification of clinically relevant RB1 mutations and copy number alterations in aqueous humor of retinoblastoma eyes.
Ophthalmic Genetics
Xu, Liya L; Shen, Lishuang L; Polski, Ashley A; Prabakar, Rishvanth K RK; Shah, Rachana R; Jubran, Rima R; Kim, Jonathan W JW; Biegel, Jacklyn J; Kuhn, Peter P; Cobrinik, David D; Hicks, James J; Gai, Xiaowu X; Berry, Jesse L JL
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
Cell-free DNA profiling in retinoblastoma patients with advanced intraocular disease: An MSKCC experience.
Cancer Medicine
Kothari, Prachi P; Marass, Francesco F; Yang, Julie L JL; Stewart, Caitlin M CM; Stephens, Dennis D; Patel, Juber J; Hasan, Maysun M; Jing, Xiaohong X; Meng, Fanli F; Enriquez, Jeanette J; Huberman, Kety K; Viale, Agnes A; Francis, Jasmine H JH; Berger, Michael F MF; Shukla, Neerav N; Abramson, David H DH; Dunkel, Ira J IJ; Tsui, Dana W Y DWY
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
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.
Nature Medicine
Razavi, Pedram P; Li, Bob T BT; Brown, David N DN; Jung, Byoungsok B; Hubbell, Earl E; Shen, Ronglai R; Abida, Wassim W; Juluru, Krishna K; De Bruijn, Ino I; Hou, Chenlu C; Venn, Oliver O; Lim, Raymond R; Anand, Aseem A; Maddala, Tara T; Gnerre, Sante S; Vijaya Satya, Ravi R; Liu, Qinwen Q; Shen, Ling L; Eattock, Nicholas N; Yue, Jeanne J; Blocker, Alexander W AW; Lee, Mark M; Sehnert, Amy A; Xu, Hui H; Hall, Megan P MP; Santiago-Zayas, Angie A; Novotny, William F WF; Isbell, James M JM; Rusch, Valerie W VW; Plitas, George G; Heerdt, Alexandra S AS; Ladanyi, Marc M; Hyman, David M DM; Jones, David R DR; Morrow, Monica M; Riely, Gregory J GJ; Scher, Howard I HI; Rudin, Charles M CM; Robson, Mark E ME; Diaz, Luis A LA; Solit, David B DB; Aravanis, Alexander M AM; Reis-Filho, Jorge S JS
Development and validation of a targeted gene sequencing panel for application to disparate cancers.
Scientific Reports
McCabe, Mark J MJ; Gauthier, Marie-Emilie A MA; Chan, Chia-Ling CL; Thompson, Tanya J TJ; De Sousa, Sunita M C SMC; Puttick, Clare C; Grady, John P JP; Gayevskiy, Velimir V; Tao, Jiang J; Ying, Kevin K; Cipponi, Arcadi A; Deng, Niantao N; Swarbrick, Alex A; Thomas, Melissa L ML; Lord, Reginald V RV; Johns, Amber L AL; Kohonen-Corish, Maija M; O'Toole, Sandra A SA; Clark, Jonathan J; Mueller, Simon A SA; Gupta, Ruta R; McCormack, Ann I AI; Dinger, Marcel E ME; Cowley, Mark J MJ; ,
Tumor mutational signatures in sebaceous skin lesions from individuals with Lynch syndrome.
Molecular Genetics & Genomic Medicine
Georgeson, Peter P; Walsh, Michael D MD; Clendenning, Mark M; Daneshvar, Simin S; Pope, Bernard J BJ; Mahmood, Khalid K; Joo, Jihoon E JE; Jayasekara, Harindra H; Jenkins, Mark A MA; Winship, Ingrid M IM; Buchanan, Daniel D DD
A combination of the PI3K pathway inhibitor plus cell cycle pathway inhibitor to combat endocrine resistance in hormone receptor-positive breast cancer: a genomic algorithm-based treatment approach.
American Journal Of Cancer Research
Gul, Anita A; Leyland-Jones, Brain B; Dey, Nandini N; De, Pradip 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
Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer.
Cancer Cell
Hellmann, Matthew D MD; Nathanson, Tavi T; Rizvi, Hira H; Creelan, Benjamin C BC; Sanchez-Vega, Francisco F; Ahuja, Arun A; Ni, Ai A; Novik, Jacki B JB; Mangarin, Levi M B LMB; Abu-Akeel, Mohsen M; Liu, Cailian C; Sauter, Jennifer L JL; Rekhtman, Natasha N; Chang, Eliza E; Callahan, Margaret K MK; Chaft, Jamie E JE; Voss, Martin H MH; Tenet, Megan M; Li, Xue-Mei XM; Covello, Kelly K; Renninger, Andrea A; Vitazka, Patrik P; Geese, William J WJ; Borghaei, Hossein H; Rudin, Charles M CM; Antonia, Scott J SJ; Swanton, Charles C; Hammerbacher, Jeff J; Merghoub, Taha T; McGranahan, Nicholas N; Snyder, Alexandra A; Wolchok, Jedd D JD
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