Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

Brat, D.J.; Verhaak, R.G.W.; Aldape, K.D.; Yung, W.K.A.; Salama, S.R.; Cooper, L.A.D.; Rheinbay, E.; Miller, C.R.; Vitucci, M.; Morozova, O.; Robertson, A.G.; Noushmehr, H.; Laird, P.W.; Cherniack, A.D.; Akbani, R.; Huse, J.T.; Ciriello, G.; Poisson, L.M.; Barnholtz-Sloan, J.S.; Berger, M.S.; Brennan, C.; Colen, R.R.; Colman, H.; Flanders, A.E.; Giannini, C.; Grifford, M.; Iavarone, A.; Jain, R.; Joseph, I.; Kim, J.; Kasaian, K.; Mikkelsen, T.; Murray, B.A.; O'Neill, B.P.; Pachter, L.; Parsons, D.W.; Sougnez, C.; Sulman, E.P.; Vandenberg, S.R.; Van Meir, E.G.; von Deimling, A.; Zhang, H.; Crain, D.; Lau, K.; Mallery, D.; Morris, S.; Paulauskis, J.; Penny, R.; Shelton, T.; Sherman, M.; Yena, P.; Black, A.; Bowen, J.; Dicostanzo, K.; Gastier-Foster, J.; Leraas, K.M.; Lichtenberg, T.M.; Pierson, C.R.; Ramirez, N.C.; Taylor, C.; Weaver, S.; Wise, L.; Zmuda, E.; Davidsen, T.; Demchok, J.A.; Eley, G.; Ferguson, M.L.; Hutter, C.M.; Mills Shaw, K.R.; Ozenberger, B.A.; Sheth, M.; Sofia, H.J.; Tarnuzzer, R.; Wang, Z.; Yang, L.; Zenklusen, J.C.; Ayala, B.; Baboud, J.; Chudamani, S.; Jensen, M.A.; Liu, J.; Pihl, T.; Raman, R.; Wan, Y.; Ye, W.; Ally, A.; Auman, J.T.; Balasundaram, M.; Balu, S.; Baylin, S.B.; Beroukhim, R.; Bootwalla, M.S.; Bowlby, R.; Bristow, C.A.; Brooks, D.; Butterfield, Y.; Carlsen, R.; Carter, S.; Chin, L.; Chu, A.; Chuah, E.; Cibulskis, K.; Clarke, A.; Coetzee, S.G.; Dhalla, N.; Fennell, T.; Fisher, S.; Gabriel, S.; Getz, G.; Gibbs, R.; Guin, R.; Hadjipanayis, A.; Hayes, D.N.; Hinoue, T.; Hoadley, K.; Holt, R.A.; Hoyle, A.P.; Jefferys, S.R.; Jones, S.; Jones, C.D.; Kucherlapati, R.; Lai, P.H.; Lander, E.; Lee, S.; Lichtenstein, L.; Yussanne, M.; Maglinte, D.T.; Mahadeshwar, H.S.; Marra, M.A.; Mayo, M.; Meng, S.; Meyerson, M.L.; Mieczkowski, P.A.; Moore, R.A.; Mose, L.E.; Mungall, A.J.; Pantazi, A.; Parfenov, M.; Park, P.J.; Parker, J.S.; Perou, C.M.; Protopopov, A.; Ren, X.; Roach, J.; Sabedot, T.S.; Schein, J.; Schumacher, S.E.; Seidman, J.G.; Seth, S.; Shen, H.; Simons, J.V.; Sipahimalani, P.; Soloway, M.G.; Song, X.; Sun, H.; Tabak, B.; Tam, A.; Tan, D.; Tang, J.; Thiessen, N.; Triche, T.; Van Den Berg, D.J.; Veluvolu, U.; Waring, S.; Weisenberger, D.J.; Wilkerson, M.D.; Wong, T.; Junyuan, W.; Liu, X.; Andrew W, X.; Yang, L.; Zack, T.I.; Zhang, J.; Aksoy, B.A.; Arachchi, H.; Benz, C.; Bernard, B.; Carlin, D.; Cho, J.; Dicara, D.; Frazer, S.; Fuller, G.N.; Gao, J.; Gehlenborg, N.; Haussler, D.; Heiman, D.I.; Iype, L.; Jacobsen, A.; Zhenlin, J.; Katzman, S.; Kim, H.; Knijnenburg, T.; Kreisberg, R.B.; Lawrence, M.S.; Lee, W.; Leinonen, K.; Lin, P.; Ling, S.; Liu, W.; Liu, Y.; Liu, Y.; Yiling, L.; Mills, G.; Sam, N.; Noble, M.S.; Paull, E.; Rao, A.; Reynolds, S.; Saksena, G.; Sanborn, Z.; Sander, C.; Schultz, N.; Senbabaoglu, Y.; Shen, R.; Shmulevich, I.; Sinha, R.; Stuart, J.; Sumer, S.O.; Sun, Y.; Tasman, N.; Taylor, B.S.; Voet, D.; Weinhold, N.; Weinstein, J.N.; Yang, D.; Yoshihara, K.; Zheng, S.; Zhang, W.; Zou, L.; Abel, T.; Sadeghi, S.; Cohen, M.L.; Eschbacher, J.; Hattab, E.M.; Raghunathan, A.; Schniederjan, M.J.; Aziz, D.; Barnett, G.; Barrett, W.; Bigner, D.D.; Boice, L.; Brewer, C.; Calatozzolo, C.; Campos, B.; Carlotti, C.G.; Chan, T.A.; Cuppini, L.; Curley, E.; Cuzzubbo, S.; Devine, K.; Dimeco, F.; Duell, R.; Elder, J.B.; Fehrenbach, A.; Finocchiaro, G.; Friedman, W.; Fulop, J.; Gardner, J.; Hermes, B.; Herold-Mende, C.; Jungk, C.; Kendler, A.; Lehman, N.L.; Lipp, E.; Liu, O.; Mandt, R.; Mcgraw, M.; Mclendon, R.; Mcpherson, C.; Neder, L.; Nguyen, P.; Noss, A.; Nunziata, R.; Ostrom, Q.T.; Palmer, C.; Perin, A.; Pollo, B.; Potapov, A.; Potapova, O.; Rathmell, W.K.; Rotin, D.; Scarpace, L.; Schilero, C.; Senecal, K.; Shimmel, K.; Shurkhay, V.; Sifri, S.; Singh, R.; Sloan, A.E.; Smolenski, K.; Staugaitis, S.M.; Steele, R.; Thorne, L.; Tirapelli, D.P.C.; Unterberg, A.; Vallurupalli, M.; Wang, Y.; Warnick, R.; Williams, F.; Wolinsky, Y.; Bell, S.; Rosenberg, M.; Stewart, C.; Huang, F.; Grimsby, J.L.; Radenbaugh, A.J.; Zhang, J.

doi:10.1056/NEJMoa1402121

BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma.

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas / D.J. Brat, R.G.W. Verhaak, K.D. Aldape, W.K.A. Yung, S.R. Salama, L.A.D. Cooper, E. Rheinbay, C.R. Miller, M. Vitucci, O. Morozova, A.G. Robertson, H. Noushmehr, P.W. Laird, A.D. Cherniack, R. Akbani, J.T. Huse, G. Ciriello, L.M. Poisson, J.S. Barnholtz-Sloan, M.S. Berger, C. Brennan, R.R. Colen, H. Colman, A.E. Flanders, C. Giannini, M. Grifford, A. Iavarone, R. Jain, I. Joseph, J. Kim, K. Kasaian, T. Mikkelsen, B.A. Murray, B.P. O'Neill, L. Pachter, D.W. Parsons, C. Sougnez, E.P. Sulman, S.R. Vandenberg, E.G. Van Meir, A. von Deimling, H. Zhang, D. Crain, K. Lau, D. Mallery, S. Morris, J. Paulauskis, R. Penny, T. Shelton, M. Sherman, P. Yena, A. Black, J. Bowen, K. Dicostanzo, J. Gastier-Foster, K.M. Leraas, T.M. Lichtenberg, C.R. Pierson, N.C. Ramirez, C. Taylor, S. Weaver, L. Wise, E. Zmuda, T. Davidsen, J.A. Demchok, G. Eley, M.L. Ferguson, C.M. Hutter, K.R. Mills Shaw, B.A. Ozenberger, M. Sheth, H.J. Sofia, R. Tarnuzzer, Z. Wang, L. Yang, J.C. Zenklusen, B. Ayala, J. Baboud, S. Chudamani, M.A. Jensen, J. Liu, T. Pihl, R. Raman, Y. Wan, W. Ye, A. Ally, J.T. Auman, M. Balasundaram, S. Balu, S.B. Baylin, R. Beroukhim, M.S. Bootwalla, R. Bowlby, C.A. Bristow, D. Brooks, Y. Butterfield, R. Carlsen, S. Carter, L. Chin, A. Chu, E. Chuah, K. Cibulskis, A. Clarke, S.G. Coetzee, N. Dhalla, T. Fennell, S. Fisher, S. Gabriel, G. Getz, R. Gibbs, R. Guin, A. Hadjipanayis, D.N. Hayes, T. Hinoue, K. Hoadley, R.A. Holt, A.P. Hoyle, S.R. Jefferys, S. Jones, C.D. Jones, R. Kucherlapati, P.H. Lai, E. Lander, S. Lee, L. Lichtenstein, M. Yussanne, D.T. Maglinte, H.S. Mahadeshwar, M.A. Marra, M. Mayo, S. Meng, M.L. Meyerson, P.A. Mieczkowski, R.A. Moore, L.E. Mose, A.J. Mungall, A. Pantazi, M. Parfenov, P.J. Park, J.S. Parker, C.M. Perou, A. Protopopov, X. Ren, J. Roach, T.S. Sabedot, J. Schein, S.E. Schumacher, J.G. Seidman, S. Seth, H. Shen, J.V. Simons, P. Sipahimalani, M.G. Soloway, X. Song, H. Sun, B. Tabak, A. Tam, D. Tan, J. Tang, N. Thiessen, T. Triche, D.J. Van Den Berg, U. Veluvolu, S. Waring, D.J. Weisenberger, M.D. Wilkerson, T. Wong, W. Junyuan, X. Liu, X. Andrew W, L. Yang, T.I. Zack, J. Zhang, B.A. Aksoy, H. Arachchi, C. Benz, B. Bernard, D. Carlin, J. Cho, D. Dicara, S. Frazer, G.N. Fuller, J. Gao, N. Gehlenborg, D. Haussler, D.I. Heiman, L. Iype, A. Jacobsen, J. Zhenlin, S. Katzman, H. Kim, T. Knijnenburg, R.B. Kreisberg, M.S. Lawrence, W. Lee, K. Leinonen, P. Lin, S. Ling, W. Liu, Y. Liu, Y. Liu, L. Yiling, G. Mills, N. Sam, M.S. Noble, E. Paull, A. Rao, S. Reynolds, G. Saksena, Z. Sanborn, C. Sander, N. Schultz, Y. Senbabaoglu, R. Shen, I. Shmulevich, R. Sinha, J. Stuart, S.O. Sumer, Y. Sun, N. Tasman, B.S. Taylor, D. Voet, N. Weinhold, J.N. Weinstein, D. Yang, K. Yoshihara, S. Zheng, W. Zhang, L. Zou, T. Abel, S. Sadeghi, M.L. Cohen, J. Eschbacher, E.M. Hattab, A. Raghunathan, M.J. Schniederjan, D. Aziz, G. Barnett, W. Barrett, D.D. Bigner, L. Boice, C. Brewer, C. Calatozzolo, B. Campos, C.G. Carlotti, T.A. Chan, L. Cuppini, E. Curley, S. Cuzzubbo, K. Devine, F. Dimeco, R. Duell, J.B. Elder, A. Fehrenbach, G. Finocchiaro, W. Friedman, J. Fulop, J. Gardner, B. Hermes, C. Herold-Mende, C. Jungk, A. Kendler, N.L. Lehman, E. Lipp, O. Liu, R. Mandt, M. Mcgraw, R. Mclendon, C. Mcpherson, L. Neder, P. Nguyen, A. Noss, R. Nunziata, Q.T. Ostrom, C. Palmer, A. Perin, B. Pollo, A. Potapov, O. Potapova, W.K. Rathmell, D. Rotin, L. Scarpace, C. Schilero, K. Senecal, K. Shimmel, V. Shurkhay, S. Sifri, R. Singh, A.E. Sloan, K. Smolenski, S.M. Staugaitis, R. Steele, L. Thorne, D.P.C. Tirapelli, A. Unterberg, M. Vallurupalli, Y. Wang, R. Warnick, F. Williams, Y. Wolinsky, S. Bell, M. Rosenberg, C. Stewart, F. Huang, J.L. Grimsby, A.J. Radenbaugh, J. Zhang. - In: NEW ENGLAND JOURNAL OF MEDICINE. - ISSN 0028-4793. - 372:26(2015 Jun 25), pp. 2481-2498.