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Robertson, A. Gordon; Gibb, Ewan A.; Oba, Junna; Uzunangelov, Vladislav; Walter, Vonn; Danilova, Ludmila; Kimes, Patrick K.; Babur, Ozgun; Akbani, Rehan; Bristow, Christopher A.; Iype, Lisa; Beroukhim, Rameen; Bowen, Jay; Bowlby, Reanne; Bristow, Christopher A.; Carlsen, Rebecca; Cebulla, Colleen M.; Chin, Lynda; Chuah, Eric; Chudamani, Sudha; Cibulskis, Carrie; Cibulskis, Kristian; Cope, Leslie; Coupland, Sarah E.; Defreitas, Timothy; Demchok, John A.; Desjardins, Laurence; Esmaeli, Bita; Felau, Ina; Ferguson, Martin L.; Frazer, Scott; Gehlenborg, Nils; Gerken, Mark; Getz, Gad; Gibb, Ewan A.; Griewank, Klaus G.; Heiman, David I.; Helsel, Carmen; Hu, Xin; Jefferys, Stuart R.; Leraas, Kristen M.; Lichtenberg, Tara M.; Liu, Jia; Iype, Lisa; Ma, Yussanne; Mariani, Odette; Marra, Marco A.; Meier, Sam; Meyerson, Matthew; Mungall, Andrew J.; Mungall, Karen L.; Murray, Bradley A.; Naresh, Rashi; Oba, Junna; Pantazi, Angeliki; Parfenov, Michael; Park, Peter J.; Protopopov, Alexei; Radenbaugh, Amie; Rai, Karan; Ramirez, Nilsa C.; Ren, Xiaojia; Reynolds, Sheila M.; Roach, Jeffrey; Robertson, A. Gordon; Schadendorf, Dirk; Schumacher, Steven E.; Seidman, Jonathan; Seth, Sahil; Sethi, Geetika; Sheth, Margi; Shi, Yan; Singh, Arun D.; Sipahimalani, Payal; Soloway, Matthew G.; Sun, Huandong; Tan, Donghui; Tang, Ming; Tse, Kane; Uzunangelov, Vladislav; Verhaak, Roel G.W.; Walter, Vonn; Wan, Yunhu; Weinstein, John N.; Williams, Michelle D.; Woodman, Scott E.; Yang, Liming; Yang, Lixing; Yau, Christina; Zhang, Hailei; Zmuda, Erik; Benz, Christopher; Mills, Gordon B.; Verhaak, Roel G.W.; Gershenwald, Jeffrey E.; Schoenfield, Lynn; Abdel-Rahman, Mohamed H.; Stern, Marc-Henri; Cebulla, Colleen M.; Woodman, Scott E.
Cancer cell, 08/2017, Volume: 32, Issue: 2Journal Article
Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes. Display omitted •Both D3 and M3-UM divide into molecularly distinct subsets with different outcomes•Poor-prognosis M3-UM are characterized by a global DNA methylation pattern•Poor-prognosis M3-UM subsets have distinct genomic, signaling, and immune profiles•EIF1AX and SRSF2/SF3B1 mutant D3-UM have different genomic/DNA methylation profiles Robertson et al. analyze 80 uveal melanomas (UM) and divide poor-prognosis monosomy 3 UM into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. Somatic copy number changes and DNA methylation profiles separate better-prognosis disomy 3 UM into low or intermediate risk.
