Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.
Nature Communications
Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA
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
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
Uterine lavage identifies cancer mutations and increased TP53 somatic mutation burden in individuals with ovarian cancer.
Cancer Research Communications
Ghezelayagh, Talayeh S TS; Kohrn, Brendan F BF; Fredrickson, Jeanne J; Manhardt, Enna E; Radke, Marc R MR; Katz, Ronit R; Gray, Heidi J HJ; Urban, Renata R RR; Pennington, Kathryn P KP; Liao, John B JB; Doll, Kemi M KM; Simons, Elise J EJ; Burzawa, Jennifer K JK; Goff, Barbara A BA; Speiser, Paul P; Swisher, Elizabeth M EM; Norquist, Barbara M BM; Risques, Rosa Ana RA
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis.
Nature Genetics
Kar, Siddhartha P SP; Quiros, Pedro M PM; Gu, Muxin M; Jiang, Tao T; Mitchell, Jonathan J; Langdon, Ryan R; Iyer, Vivek V; Barcena, Clea C; Vijayabaskar, M S MS; Fabre, Margarete A MA; Carter, Paul P; Petrovski, Slavé S; Burgess, Stephen S; Vassiliou, George S GS
The longitudinal dynamics and natural history of clonal haematopoiesis.
Nature
Fabre, Margarete A MA; de Almeida, José Guilherme JG; Fiorillo, Edoardo E; Mitchell, Emily E; Damaskou, Aristi A; Rak, Justyna J; Orrù, Valeria V; Marongiu, Michele M; Chapman, Michael Spencer MS; Vijayabaskar, M S MS; Baxter, Joanna J; Hardy, Claire C; Abascal, Federico F; Williams, Nicholas N; Nangalia, Jyoti J; Martincorena, Iñigo I; Campbell, Peter J PJ; McKinney, Eoin F EF; Cucca, Francesco F; Gerstung, Moritz M; Vassiliou, George S GS
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages.
Nature Communications
Ng, Charlotte K Y CKY; Dazert, Eva E; Boldanova, Tuyana T; Coto-Llerena, Mairene M; Nuciforo, Sandro S; Ercan, Caner C; Suslov, Aleksei A; Meier, Marie-Anne MA; Bock, Thomas T; Schmidt, Alexander A; Ketterer, Sylvia S; Wang, Xueya X; Wieland, Stefan S; Matter, Matthias S MS; Colombi, Marco M; Piscuoglio, Salvatore S; Terracciano, Luigi M LM; Hall, Michael N MN; Heim, Markus H MH
Publication Date: 2022-05-04
Variant appearance in text: TP53: 709A>G; M237V; rs730882004
Oral Squamous Cell Carcinoma in Young Patients Show Higher Rates of EGFR Amplification: Implications for Novel Personalized Therapy.
Frontiers In Oncology
Satgunaseelan, Laveniya L; Porazinski, Sean S; Strbenac, Dario D; Istadi, Aji A; Willet, Cali C; Chew, Tracy T; Sadsad, Rosemarie R; Palme, Carsten E CE; Lee, Jenny H JH; Boyer, Michael M; Yang, Jean Y H JYH; Clark, Jonathan R JR; Pajic, Marina M; Gupta, Ruta R
Targeted Therapy of Papillary Thyroid Cancer: A Comprehensive Genomic Analysis.
Frontiers In Endocrinology
Hescheler, Daniel A DA; Riemann, Burkhard B; Hartmann, Milan J M MJM; Michel, Maximilian M; Faust, Michael M; Bruns, Christiane J CJ; Alakus, Hakan H; Chiapponi, Costanza C
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
Defining phenotypic and functional heterogeneity of glioblastoma stem cells by mass cytometry.
Jci Insight
Galdieri, Luciano L; Jash, Arijita A; Malkova, Olga O; Mao, Diane D DD; DeSouza, Patrick P; Chu, Yunli E YE; Salter, Amber A; Campian, Jian L JL; Naegle, Kristen M KM; Brennan, Cameron W CW; Wakimoto, Hiroaki H; Oh, Stephen T ST; Kim, Albert H AH; Chheda, Milan G MG
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
Criteria of the German Consortium for Hereditary Breast and Ovarian Cancer for the Classification of Germline Sequence Variants in Risk Genes for Hereditary Breast and Ovarian Cancer.
Geburtshilfe Und Frauenheilkunde
Wappenschmidt, Barbara B; Hauke, Jan J; Faust, Ulrike U; Niederacher, Dieter D; Wiesmüller, Lisa L; Schmidt, Gunnar G; Groß, Evi E; Gehrig, Andrea A; Sutter, Christian C; Ramser, Juliane J; Rump, Andreas A; Arnold, Norbert N; Meindl, Alfons A
Identification of targeted therapy options for gastric adenocarcinoma by comprehensive analysis of genomic data.
Gastric Cancer : Official Journal Of The International Gastric Cancer Association And The Japanese Gastric Cancer Association
Hescheler, Daniel A DA; Plum, Patrick S PS; Zander, Thomas T; Quaas, Alexander A; Korenkov, Michael M; Gassa, Asmae A; Michel, Maximilian M; Bruns, Christiane J CJ; Alakus, Hakan H
REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.
Scientific Reports
Tian, Yuan Y; Pesaran, Tina T; Chamberlin, Adam A; Fenwick, R Bryn RB; Li, Shuwei S; Gau, Chia-Ling CL; Chao, Elizabeth C EC; Lu, Hsiao-Mei HM; Black, Mary Helen MH; Qian, Dajun D
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
Publication Date: 2019-08
Variant appearance in text: TP53: 709A>G; Met237Val
A Bayesian framework for efficient and accurate variant prediction.
Plos One
Qian, Dajun D; Li, Shuwei S; Tian, Yuan Y; Clifford, Jacob W JW; Sarver, Brice A J BAJ; Pesaran, Tina T; Gau, Chia-Ling CL; Elliott, Aaron M AM; Lu, Hsiao-Mei HM; Black, Mary Helen MH
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
Analytical Validation of a Hybrid Capture-Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA.
The Journal Of Molecular Diagnostics : Jmd
Clark, Travis A TA; Chung, Jon H JH; Kennedy, Mark M; Hughes, Jason D JD; Chennagiri, Niru N; Lieber, Daniel S DS; Fendler, Bernard B; Young, Lauren L; Zhao, Mandy M; Coyne, Michael M; Breese, Virginia V; Young, Geneva G; Donahue, Amy A; Pavlick, Dean D; Tsiros, Alyssa A; Brennan, Timothy T; Zhong, Shan S; Mughal, Tariq T; Bailey, Mark M; He, Jie J; Roels, Steven S; Frampton, Garrett M GM; Spoerke, Jill M JM; Gendreau, Steven S; Lackner, Mark M; Schleifman, Erica E; Peters, Eric E; Ross, Jeffrey S JS; Ali, Siraj M SM; Miller, Vincent A VA; Gregg, Jeffrey P JP; Stephens, Philip J PJ; Welsh, Allison A; Otto, Geoff A GA; Lipson, Doron D
Integrative genomic and transcriptomic analysis of leiomyosarcoma.
Nature Communications
Chudasama, Priya P; Mughal, Sadaf S SS; Sanders, Mathijs A MA; Hübschmann, Daniel D; Chung, Inn I; Deeg, Katharina I KI; Wong, Siao-Han SH; Rabe, Sophie S; Hlevnjak, Mario M; Zapatka, Marc M; Ernst, Aurélie A; Kleinheinz, Kortine K; Schlesner, Matthias M; Sieverling, Lina L; Klink, Barbara B; Schröck, Evelin E; Hoogenboezem, Remco M RM; Kasper, Bernd B; Heilig, Christoph E CE; Egerer, Gerlinde G; Wolf, Stephan S; von Kalle, Christof C; Eils, Roland R; Stenzinger, Albrecht A; Weichert, Wilko W; Glimm, Hanno H; Gröschel, Stefan S; Kopp, Hans-Georg HG; Omlor, Georg G; Lehner, Burkhard B; Bauer, Sebastian S; Schimmack, Simon S; Ulrich, Alexis A; Mechtersheimer, Gunhild G; Rippe, Karsten K; Brors, Benedikt B; Hutter, Barbara B; Renner, Marcus M; Hohenberger, Peter P; Scholl, Claudia C; Fröhling, Stefan S
Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction.
Oncotarget
Sung, Jae Sook JS; Chong, Hyon Yong HY; Kwon, Nak-Jung NJ; Kim, Hae Mi HM; Lee, Jong Won JW; Kim, Boyeon B; Lee, Saet Byeol SB; Park, Chang Won CW; Choi, Jung Yoon JY; Chang, Won Jin WJ; Choi, Yoon Ji YJ; Lee, Sung Yong SY; Kang, Eun Joo EJ; Park, Kyong Hwa KH; Kim, Yeul Hong YH
The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy.
Nature Communications
Landau, Dan A DA; Sun, Clare C; Rosebrock, Daniel D; Herman, Sarah E M SEM; Fein, Joshua J; Sivina, Mariela M; Underbayev, Chingiz C; Liu, Delong D; Hoellenriegel, Julia J; Ravichandran, Sarangan S; Farooqui, Mohammed Z H MZH; Zhang, Wandi W; Cibulskis, Carrie C; Zviran, Asaf A; Neuberg, Donna S DS; Livitz, Dimitri D; Bozic, Ivana I; Leshchiner, Ignaty I; Getz, Gad G; Burger, Jan A JA; Wiestner, Adrian A; Wu, Catherine J CJ
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