Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors.
Cell Reports. Medicine
Álvarez-Prado, Ángel F ÁF; Maas, Roeltje R RR; Soukup, Klara K; Klemm, Florian F; Kornete, Mara M; Krebs, Fanny S FS; Zoete, Vincent V; Berezowska, Sabina S; Brouland, Jean-Philippe JP; Hottinger, Andreas F AF; Daniel, Roy T RT; Hegi, Monika E ME; Joyce, Johanna A JA
Comprehensive clinicopathological and genomic profiling of gallbladder cancer reveals actionable targets in half of patients.
Npj Precision Oncology
de Bitter, Tessa J J TJJ; de Reuver, Philip R PR; de Savornin Lohman, Elise A J EAJ; Kroeze, Leonie I LI; Vink-Börger, Marianne E ME; van Vliet, Shannon S; Simmer, Femke F; von Rhein, Daniel D; Jansen, Erik A M EAM; Verheij, Joanne J; van Herpen, Carla M L CML; Nagtegaal, Iris D ID; Ligtenberg, Marjolijn J L MJL; van der Post, Rachel S RS
Publication Date: 2022-11-05
Variant appearance in text: TP53: 112C>T; Gln38Ter
GENETIC SUBGROUPS INFORM ON PATHOBIOLOGY IN ADULT AND PEDIATRIC BURKITT LYMPHOMA.
Blood
Thomas, Nicole N; Dreval, Kostiantyn K; Gerhard, Daniela S DS; Hilton, Laura K LK; Abramson, Jeremy S JS; Barta, Stefan K SK; Bartlett, Nancy L NL; Bethony, Jeffrey J; Bhatia, Kishor K; Bowen, Jay J; Bryan, Anthony C AC; Cesarman, Ethel E; Casper, Corey C; Cruz, Manuela M; Dyer, Maureen M; Farinha, Pedro P; Gastier-Foster, Julie J; Gerrie, Alina S AS; Grande, Bruno B; Greiner, Timothy C TC; Griner, Nicholas N; Gross, Thomas G TG; Harris, Nancy Lee NL; Irvin, John D JD; Jaffe, Elaine S ES; Henry, David D; Huppi, Rebecca Liddell RL; Leal, Fabio E FE; Lee, Michael M; Martin, Jean Paul JP; Martin, Marie-Reine MR; Mbulaiteye, Sam M SM; Mitsuyasu, Ronald R; Morris, Vivian V; Mullighan, Charles G CG; Mungall, Andrew J AJ; Mungall, Karen K; Mutyaba, Innocent I; Nokta, Mostafa M; Namirembe, Constance C; Noy, Ariela A; Ogwang, Martin David MD; Omoding, Abrahams A; Orem, Jackson J; Ott, German G; Petrello, Hilary H; Pittaluga, Stefania S; Phelan, James D JD; Ramos, Juan Carlos JC; Ratner, Lee L; Reynolds, Steven J SJ; Rubinstein, Paul G PG; Sissolak, Gerhard G; Slack, Graham W GW; Soudi, Shaghayegh S; Swerdlow, Steven Howard SH; Traverse-Glehen, Alexandra A; Wilson, Wyndham W; Wong, Jasper Chun Hei JCH; Yarchoan, Robert R; ZenKlusen, Jean C JC; Marra, Marco A MA; Staudt, Louis M LM; Scott, David W DW; Morin, Ryan D RD
Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma.
Frontiers In Oncology
Thind, Amarinder Singh AS; Ashford, Bruce B; Strbenac, Dario D; Mitchell, Jenny J; Lee, Jenny J; Mueller, Simon A SA; Minaei, Elahe E; Perry, Jay R JR; Ch'ng, Sydney S; Iyer, N Gopalakrishna NG; Clark, Jonathan R JR; Gupta, Ruta R; Ranson, Marie M
Publication Date: 2022
Variant appearance in text: TP53: 112C>T; Gln38Ter
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
The Impact of Comprehensive Genomic Profiling (CGP) on the Decision-Making Process in the Treatment of ALK-Rearranged Advanced Non-Small Cell Lung Cancer (aNSCLC) After Failure of 2nd/3rd-Generation ALK Tyrosine Kinase Inhibitors (TKIs).
Frontiers In Oncology
Raphael, Ari A; Onn, Amir A; Holtzman, Liran L; Dudnik, Julia J; Urban, Damien D; Kian, Waleed W; Cohen, Aharon Y AY; Moskovitz, Mor M; Zer, Alona A; Bar, Jair J; Rabinovich, Natalie Maimon NM; Grynberg, Shirly S; Oedegaard, Cecilie C; Agbarya, Abed A; Peled, Nir N; Shochat, Tzippy T; Dudnik, Elizabeth E
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
Utilizing phenotypic characteristics of metastatic brain tumors to improve the probability of detecting circulating tumor DNA from cerebrospinal fluid in non-small-cell lung cancer patients: development and validation of a prediction model in a prospective cohort study.
Esmo Open
Li, M M; Hou, X X; Zheng, L L; Ma, Y Y; Li, D D; Lv, Y Y; Chen, J J; Zheng, W W; Shao, Y Y; Mou, Y Y; Chen, L L
Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study.
Genome Medicine
Sicklick, Jason K JK; Kato, Shumei S; Okamura, Ryosuke R; Patel, Hitendra H; Nikanjam, Mina M; Fanta, Paul T PT; Hahn, Michael E ME; De, Pradip P; Williams, Casey C; Guido, Jessica J; Solomon, Benjamin M BM; McKay, Rana R RR; Krie, Amy A; Boles, Sarah G SG; Ross, Jeffrey S JS; Lee, J Jack JJ; Leyland-Jones, Brian B; Lippman, Scott M SM; Kurzrock, Razelle R
Genomic evidence suggests that cutaneous neuroendocrine carcinomas can arise from squamous dysplastic precursors.
Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc
Harms, Paul W PW; Verhaegen, Monique E ME; Hu, Kevin K; Hrycaj, Steven M SM; Chan, May P MP; Liu, Chia-Jen CJ; Grachtchouk, Marina M; Patel, Rajiv M RM; Udager, Aaron M AM; Dlugosz, Andrzej A AA
Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line.
Scientific Reports
Longo, Jody Fromm JF; Brosius, Stephanie N SN; Znoyko, Iya I; Alers, Victoria A VA; Jenkins, Dorea P DP; Wilson, Robert C RC; Carroll, Andrew J AJ; Wolff, Daynna J DJ; Roth, Kevin A KA; Carroll, Steven L SL
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
Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity.
Genome Biology
Lee, Won-Chul WC; Reuben, Alexandre A; Hu, Xin X; McGranahan, Nicholas N; Chen, Runzhe R; Jalali, Ali A; Negrao, Marcelo V MV; Hubert, Shawna M SM; Tang, Chad C; Wu, Chia-Chin CC; Lucas, Anthony San AS; Roh, Whijae W; Suda, Kenichi K; Kim, Jihye J; Tan, Aik-Choon AC; Peng, David H DH; Lu, Wei W; Tang, Ximing X; Chow, Chi-Wan CW; Fujimoto, Junya J; Behrens, Carmen C; Kalhor, Neda N; Fukumura, Kazutaka K; Coyle, Marcus M; Thornton, Rebecca R; Gumbs, Curtis C; Li, Jun J; Wu, Chang-Jiun CJ; Little, Latasha L; Roarty, Emily E; Song, Xingzhi X; Lee, J Jack JJ; Sulman, Erik P EP; Rao, Ganesh G; Swisher, Stephen S; Diao, Lixia L; Wang, Jing J; Heymach, John V JV; Huse, Jason T JT; Scheet, Paul P; Wistuba, Ignacio I II; Gibbons, Don L DL; Futreal, P Andrew PA; Zhang, Jianhua J; Gomez, Daniel D; Zhang, Jianjun J
Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer.
Esmo Open
Perakis, Samantha O SO; Weber, Sabrina S; Zhou, Qing Q; Graf, Ricarda R; Hojas, Sabine S; Riedl, Jakob M JM; Gerger, Armin A; Dandachi, Nadia N; Balic, Marija M; Hoefler, Gerald G; Schuuring, Ed E; Groen, Harry J M HJM; Geigl, Jochen B JB; Heitzer, Ellen E; Speicher, Michael R MR
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
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; ,
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
Establishment and genomic characterization of gingivobuccal carcinoma cell lines with smokeless tobacco associated genetic alterations and oncogenic PIK3CA mutation.
From uncertainty to pathogenicity: clinical and functional interrogation of a rare TP53 in-frame deletion.
Cold Spring Harbor Molecular Case Studies
Quinn, Emily A EA; Maciaszek, Jamie L JL; Pinto, Emilia M EM; Phillips, Aaron H AH; Berdy, David D; Khandwala, Mohammad M; Upadhyaya, Santhosh A SA; Zambetti, Gerard P GP; Kriwacki, Richard W RW; Ellison, David W DW; Nichols, Kim E KE; Kesserwan, Chimene C
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
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
TP53 exon-6 truncating mutations produce separation of function isoforms with pro-tumorigenic functions.
Elife
Shirole, Nitin H NH; Pal, Debjani D; Kastenhuber, Edward R ER; Senturk, Serif S; Boroda, Joseph J; Pisterzi, Paola P; Miller, Madison M; Munoz, Gustavo G; Anderluh, Marko M; Ladanyi, Marc M; Lowe, Scott W SW; Sordella, Raffaella R
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
Mutational landscape of MCPyV-positive and MCPyV-negative Merkel cell carcinomas with implications for immunotherapy.
Oncotarget
Goh, Gerald G; Walradt, Trent T; Markarov, Vladimir V; Blom, Astrid A; Riaz, Nadeem N; Doumani, Ryan R; Stafstrom, Krista K; Moshiri, Ata A; Yelistratova, Lola L; Levinsohn, Jonathan J; Chan, Timothy A TA; Nghiem, Paul P; Lifton, Richard P RP; Choi, Jaehyuk J
NOTCH, ASCL1, p53 and RB alterations define an alternative pathway driving neuroendocrine and small cell lung carcinomas.
International Journal Of Cancer
Meder, Lydia L; König, Katharina K; Ozretić, Luka L; Schultheis, Anne M AM; Ueckeroth, Frank F; Ade, Carsten P CP; Albus, Kerstin K; Boehm, Diana D; Rommerscheidt-Fuss, Ursula U; Florin, Alexandra A; Buhl, Theresa T; Hartmann, Wolfgang W; Wolf, Jürgen J; Merkelbach-Bruse, Sabine S; Eilers, Martin M; Perner, Sven S; Heukamp, Lukas C LC; Buettner, Reinhard R
Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.
Nature Communications
Nones, Katia K; Waddell, Nicola N; Wayte, Nicci N; Patch, Ann-Marie AM; Bailey, Peter P; Newell, Felicity F; Holmes, Oliver O; Fink, J Lynn JL; Quinn, Michael C J MCJ; Tang, Yue Hang YH; Lampe, Guy G; Quek, Kelly K; Loffler, Kelly A KA; Manning, Suzanne S; Idrisoglu, Senel S; Miller, David D; Xu, Qinying Q; Waddell, Nick N; Wilson, Peter J PJ; Bruxner, Timothy J C TJC; Christ, Angelika N AN; Harliwong, Ivon I; Nourse, Craig C; Nourbakhsh, Ehsan E; Anderson, Matthew M; Kazakoff, Stephen S; Leonard, Conrad C; Wood, Scott S; Simpson, Peter T PT; Reid, Lynne E LE; Krause, Lutz L; Hussey, Damian J DJ; Watson, David I DI; Lord, Reginald V RV; Nancarrow, Derek D; Phillips, Wayne A WA; Gotley, David D; Smithers, B Mark BM; Whiteman, David C DC; Hayward, Nicholas K NK; Campbell, Peter J PJ; Pearson, John V JV; Grimmond, Sean M SM; Barbour, Andrew P AP
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
Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.
Genome Biology
Brannon, A Rose AR; Vakiani, Efsevia E; Sylvester, Brooke E BE; Scott, Sasinya N SN; McDermott, Gregory G; Shah, Ronak H RH; Kania, Krishan K; Viale, Agnes A; Oschwald, Dayna M DM; Vacic, Vladimir V; Emde, Anne-Katrin AK; Cercek, Andrea A; Yaeger, Rona R; Kemeny, Nancy E NE; Saltz, Leonard B LB; Shia, Jinru J; D'Angelica, Michael I MI; Weiser, Martin R MR; Solit, David B DB; Berger, Michael F MF
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.
Nature Genetics
Gross, Andrew M AM; Orosco, Ryan K RK; Shen, John P JP; Egloff, Ann Marie AM; Carter, Hannah H; Hofree, Matan M; Choueiri, Michel M; Coffey, Charles S CS; Lippman, Scott M SM; Hayes, D Neil DN; Cohen, Ezra E EE; Grandis, Jennifer R JR; Nguyen, Quyen T QT; Ideker, Trey T