Research Departments

Cancer Biology

Medical Oncology

Interests

Glioma, Meningioma, Somatic genetics of cancer

Area of Research

Recent Awards

• V Scholar Award, 2009

Research

Our research team focuses on understanding the heterogeneity observed across cancers through differences in their genomic profiles, with particular emphasis on the somatic genetic events driving cancer development and progression.

We have undertaken a variety of genomic approaches to profiling large numbers of cancers, including the use of SNP arrays, expression arrays, and sequencing, and have developed several computational approaches to understand these data.

For copy-number changes, which are some of the most frequent somatic genetic events in cancer, we developed an approach (GISTIC, for Genomic Identification of Significant Targets In Cancer) that simultaneously identifies those events that are most likely to drive cancer development and profiles individual specimens for the set of events they have undergone. We have used this approach to identify new oncogenes in several cancer types, including lung, esophageal, and colorectal cancers.

We have also used this approach to identify prognostic indicators in endometrial cancers and predictors of pathway dependency several cancer types, including glioblastoma and renal cancer.

We currently have particular interests in the use of high-throughput sequencing technologies to profile large numbers of cancers, and in applying these approaches to brain cancers in the context of clinical trials.

Select Publications

• Beroukhim R, Brunet JP, Di Napoli A, Mertz KD, Seeley A, Pires MM, Linhart D, Worrell RA, Moch H, Rubin MA, Sellers WR, Meyerson M, Linehan WM, Kaelin WG Jr, Signoretti S. Patterns of gene expression and copy-number alterations in von-hippel landau disease associated and sporadic clear cell carcinoma in the kidney. Cancer Res., 2009; 69:4674-81
• Salvesen HB, Carter SL, Mannelqvist M, Dutt A, Getz G, Stefansson IM, Raeder MB, Sos ML, Engelsen IB, Trovik J, Wik E, Greulich H, B TH, Jonassen I, Thomas RK, Zander T, Garraway LA, Oyan AM, Sellers WR, Kalland KH, Meyerson M, Akslen LA, Beroukhim R. Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation. Proc Natl Acad Sci USA, 2009; 106:4834-9.
• Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 2008; 455:1061-8.
• Beroukhim R1, Getz G1, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA. 2007;104:20007-12. PMC2148413.
• Beroukhim R1, Mermel C1, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffmann C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, DeMichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. The landscape of somatic copy-number alteration across human cancers. Nature, in press.
• Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar A, Giordano T, Greulich H, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna J, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd FA, Sougnez C, Spitz MR, Tsao MS, Twomey D, Verhaak R, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis W, Pao W, Rubin MA, Gabriel S, Gibbs R, Varmus H, Wilson RK, Lander ES, Meyerson M. Characterizing the cancer genome in lung adenocarcinoma. Nature, 2007; 450:893-8.
• Beroukhim R*, Lin M*, Park Y, Hao K, Zhao X, Garraway LA, Fox EA, Hochberg EP, Mellinghoff IK, Hofer MD, Descazeaud A, Rubin MA, Meyerson ML, Wong W, Sellers WR, Li C. Inferring Loss-of-Heterozygosity from Tumors without Paired Normals Using High-Density SNP Arrays. PLoS Comput Biol, 2006; 2:e41.
• Mellinghoff IK, Wang MY, Vivanco I, Haas-Kogan DA, Zhu S, Dia EQ, Lu KV, Yoshimoto K, Huang JH, Chute DJ, Riggs BL, Horvath S, Liau LM, Cavenee WK, Rao PN, Beroukhim R, Peck TC, Lee JC, Sellers WR, Stokoe D, Prados M, Cloughesy TF, Sawyers CL, Mischel PS. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med 2005; 353:2012-24.