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Rameen Beroukhim, MD, PhD


Neuro-oncology

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Physician

  • Physician
  • Associate Professor of Medicine, Harvard Medical School

Centers/Programs

Clinical Interests

  • Glioma
  • Meningioma
  • Somatic genetics of cancer

Diseases Treated

  • Brain Metastasis
  • Brain Tumors
  • Glioblastoma
  • Low-Grade Glioma
  • Meningioma

Contact Information

  • Appointments617-632-2166
  • Office Phone Number617-632-2166
  • Fax617-632-4773

Board Certification:

  • Internal Medicine
  • Medical Oncology, 2005

Fellowship:

  • Dana-Farber/Partners CancerCare, Medical Oncology

Residency:

  • University of California, San Francisco, Internal Medicine

Medical School:

  • University of California, San Francisco

Recent Awards:

  • V Scholar Award 2009

Research

Cancer Genomics



Our research team focuses on understanding the genetic changes in cancer and how these genetic changes affect cancer behavior.  We have a particular focus on brain cancers, although we study many types of cancer.  All our projects involve collaborations with multiple other groups at the DFCI, Broad Institute, and multiple other institutions.



We have undertaken a variety of genomic approaches to profiling large numbers of cancers, including the use of SNP arrays, expression arrays, and sequencing.  We have also 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 published an analysis of over 3000 cancer copy-number profiles in 2010, which is one of the most-cited publications in cancer from that year.  This study identified two new amplified oncogenes (MCL1 and BCL2L1) and showed both lineage-specific genetic events and events that were shared across many cancer types.  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 have performed integrated genomic analyses across multiple datasets.  For example, we have integrated copy-number data with functional screens to identify novel vulnerabilities associated with genomic losses in cancer.



We have performed high-throughput sequencing analyses of several cancer types. For example, we found mutations in SMO and AKT1 in meningiomas, which may serve as therapeutic targets in these diseases.  We have also found rearrangements of MYBL1 in pediatric low-grade gliomas.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. 2021 Apr 02.
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Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 23; 34(8):108784.
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Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 02; 34(5):108707.
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Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature. 2021 02; 590(7846):486-491.
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Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell. 2020 Dec 10; 183(6):1617-1633.e22.
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Quantification of aneuploidy in targeted sequencing data using ASCETS. Bioinformatics. 2020 Nov 28.
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CloneSifter: enrichment of rare clones from heterogeneous cell populations. BMC Biol. 2020 11 24; 18(1):177.
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Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 01; 183(1):197-210.e32.
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Author Correction: Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020 Jul; 52(7):748-749.
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Tumor Interferon Signaling Is Regulated by a lncRNA INCR1 Transcribed from the PD-L1 Locus. Mol Cell. 2020 06 18; 78(6):1207-1223.e8.
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Ancestry-specific predisposing germline variants in cancer. Genome Med. 2020 05 29; 12(1):51.
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Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat Commun. 2020 05 20; 11(1):2517.
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Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020 07; 52(7):662-668.
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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell. 2020 05 11; 37(5):639-654.e6.
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Targeting Cancer Gene Dependencies with Anthrax-Mediated Delivery of Peptide Nucleic Acids. ACS Chem Biol. 2020 06 19; 15(6):1358-1369.
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Mechanisms and therapeutic implications of hypermutation in gliomas. Nature. 2020 04; 580(7804):517-523.
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The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128.
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Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2020 03; 52(3):294-305.
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 02; 578(7793):102-111.
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Patterns of somatic structural variation in human cancer genomes. Nature. 2020 02; 578(7793):112-121.
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Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020 03; 52(3):306-319.
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Early TP53 alterations engage environmental exposures to promote gastric premalignancy in an integrative mouse model. Nat Genet. 2020 02; 52(2):219-230.
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Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway. Cancer Cell. 2020 01 13; 37(1):104-122.e12.
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Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019 12; 576(7785):112-120.
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Phase II trial of ponatinib in patients with bevacizumab-refractory glioblastoma. Cancer Med. 2019 10; 8(13):5988-5994.
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Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nat Commun. 2019 08 19; 10(1):3731.
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Molecular profiling and targeted therapy in pediatric gliomas: review and consensus recommendations. Neuro Oncol. 2019 08 05; 21(8):968-980.
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Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019 06 03; 10(1):2400.
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Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science. 2019 03 15; 363(6432):1217-1222.
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Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. Elife. 2019 03 12; 8.
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MCL1 and DEDD Promote Urothelial Carcinoma Progression. Mol Cancer Res. 2019 06; 17(6):1294-1304.
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Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial. J Clin Oncol. 2019 03 20; 37(9):741-750.
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Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer. 2019 02; 19(2):97-109.
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miR-4516 predicts poor prognosis and functions as a novel oncogene via targeting PTPN14 in human glioblastoma. Oncogene. 2019 04; 38(16):2923-2936.
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Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling. Cancer Cell. 2018 12 10; 34(6):922-938.e7.
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PIK3CA Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma. Clin Cancer Res. 2019 01 01; 25(1):334-345.
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Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018 Oct; 24(10):1627.
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Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018 08; 560(7718):325-330.
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Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1290-1291.
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Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 Aug; 24(8):1292.
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The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19; 23(12):3698.
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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19.
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Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro Oncol. 2018 06 18; 20(7):873-884.
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Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome. Clin Cancer Res. 2018 09 15; 24(18):4416-4428.
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Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018 07; 24(7):968-977.
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Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 05; 24(5):679-690.
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Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 04 20; 360(6386):331-335.
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The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 04 03; 23(1):313-326.e5.
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Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 04 09; 33(4):676-689.e3.
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SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018 04; 28(4):581-591.
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Radiographic prediction of meningioma grade by semantic and radiomic features. PLoS One. 2017; 12(11):e0187908.
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Open data: Spot data glitches before publication. Nature. 2017 10 18; 550(7676):333.
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Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet. 2017 Nov; 49(11):1567-1575.
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Erratum: Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2:26.
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The whole-genome landscape of medulloblastoma subtypes. Nature. 2017 07 19; 547(7663):311-317.
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Clinical Identification of Oncogenic Drivers and Copy-Number Alterations in Pituitary Tumors. Endocrinology. 2017 07 01; 158(7):2284-2291.
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Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro Oncol. 2017 Jul 01; 19(7):908-917.
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Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. Neuro Oncol. 2017 Jul 01; 19(7):986-996.
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Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2017 06 30; 7:46873.
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Genomic profile of human meningioma cell lines. PLoS One. 2017; 12(5):e0178322.
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MicroRNA Signatures and Molecular Subtypes of Glioblastoma: The Role of Extracellular Transfer. Stem Cell Reports. 2017 06 06; 8(6):1497-1505.
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Genomic landscape of high-grade meningiomas. NPJ Genom Med. 2017; 2.
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Somatic copy number alterations in gastric adenocarcinomas among Asian and Western patients. PLoS One. 2017; 12(4):e0176045.
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Germline and somatic BAP1 mutations in high-grade rhabdoid meningiomas. Neuro Oncol. 2017 04 01; 19(4):535-545.
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SeqLib: a C?++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics. 2017 03 01; 33(5):751-753.
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Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Elife. 2017 02 08; 6.
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Copy number alterations unmasked as enhancer hijackers. Nat Genet. 2016 12 28; 49(1):5-6.
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Pan-Cancer Analysis Links PARK2 to BCL-XL-Dependent Control of Apoptosis. Neoplasia. 2017 02; 19(2):75-83.
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Genomic evolution and chemoresistance in germ-cell tumours. Nature. 2016 11 30; 540(7631):114-118.
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Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. Nat Genet. 2017 01; 49(1):10-16.
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Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373.
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The genomic landscape of schwannoma. Nat Genet. 2016 11; 48(11):1339-1348.
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Landscape of Genomic Alterations in Pituitary Adenomas. Clin Cancer Res. 2017 Apr 01; 23(7):1841-1851.
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Tyrosine receptor kinase B is a drug target in astrocytomas. Neuro Oncol. 2017 01; 19(1):22-30.
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The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis. Nat Genet. 2016 08; 48(8):848-55.
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Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2016 06 24; 6:27960.
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MAPK activation and HRAS mutation identified in pituitary spindle cell oncocytoma. Oncotarget. 2016 Jun 14; 7(24):37054-37063.
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Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep. 2016 05 10; 6:25521.
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Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46.
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Genomic and Epigenomic Landscape in Meningioma. Neurosurg Clin N Am. 2016 Apr; 27(2):167-79.
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CANCER. The oncogene makes its escape. Science. 2016 Mar 25; 351(6280):1398-9.
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Disseminated glioneuronal tumors occurring in childhood: treatment outcomes and BRAF alterations including V600E mutation. J Neurooncol. 2016 06; 128(2):293-302.
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VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. Bioinformatics. 2016 07 01; 32(13):2029-31.
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MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat Genet. 2016 Mar; 48(3):273-82.
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Oncogenic PI3K mutations are as common as AKT1 and SMO mutations in meningioma. Neuro Oncol. 2016 05; 18(5):649-55.
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Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28; 164(3):550-63.
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Case Report: Next generation sequencing identifies a NAB2-STAT6 fusion in Glioblastoma. Diagn Pathol. 2016 Jan 27; 11:13.
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Genomic landscape of intracranial meningiomas. J Neurosurg. 2016 09; 125(3):525-35.
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Myxopapillary ependymomas in children: imaging, treatment and outcomes. J Neurooncol. 2016 Jan; 126(1):165-174.
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MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. Cancer Discov. 2016 Jan; 6(1):45-58.
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Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14; 374(2):135-45.
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Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 2015 Nov; 5(11):1164-1177.
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Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background. Genome Res. 2015 Nov; 25(11):1634-45.
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A prognostic cytogenetic scoring system to guide the adjuvant management of patients with atypical meningioma. Neuro Oncol. 2016 Feb; 18(2):269-74.
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Extent of resection and overall survival for patients with atypical and malignant meningioma. Cancer. 2015 Dec 15; 121(24):4376-81.
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Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6. Nat Struct Mol Biol. 2015 Sep; 22(9):703-711.
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Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98.
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Incidence, risk factors, and reasons for hospitalization among glioblastoma patients receiving chemoradiation. J Neurooncol. 2015 Aug; 124(1):137-46.
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A Multicenter, Phase II, Randomized, Noncomparative Clinical Trial of Radiation and Temozolomide with or without Vandetanib in Newly Diagnosed Glioblastoma Patients. Clin Cancer Res. 2015 Aug 15; 21(16):3610-8.
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Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype. Neuro Oncol. 2015 Nov; 17(11):1486-96.
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ARID1A and TERT promoter mutations in dedifferentiated meningioma. Cancer Genet. 2015 Jun; 208(6):345-50.
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Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma. Neuro Oncol. 2015 Oct; 17(10):1344-55.
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Predicting clinical response to anticancer drugs using an ex vivo platform that captures tumour heterogeneity. Nat Commun. 2015 Feb 27; 6:6169.
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Molecular profiling of endometrial carcinoma precursor, primary and metastatic lesions suggests different targets for treatment in obese compared to non-obese patients. Oncotarget. 2015 Jan 20; 6(2):1327-39.
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Phase II study of panobinostat in combination with bevacizumab for recurrent glioblastoma and anaplastic glioma. Neuro Oncol. 2015 Jun; 17(6):862-7.
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An in-tumor genetic screen reveals that the BET bromodomain protein, BRD4, is a potential therapeutic target in ovarian carcinoma. Proc Natl Acad Sci U S A. 2015 Jan 06; 112(1):232-7.
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Phase II study of monthly pasireotide LAR (SOM230C) for recurrent or progressive meningioma. Neurology. 2015 Jan 20; 84(3):280-6.
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Vandetanib plus sirolimus in adults with recurrent glioblastoma: results of a phase I and dose expansion cohort study. J Neurooncol. 2015 Feb; 121(3):627-34.
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Prioritizing causal disease genes using unbiased genomic features. Genome Biol. 2014 Dec 03; 15(12):534.
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Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5. Oncotarget. 2014 Nov 15; 5(21):10596-606.
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SGK3 mediates INPP4B-dependent PI3K signaling in breast cancer. Mol Cell. 2014 Nov 20; 56(4):595-607.
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Clinical multiplexed exome sequencing distinguishes adult oligodendroglial neoplasms from astrocytic and mixed lineage gliomas. Oncotarget. 2014 Sep 30; 5(18):8083-92.
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Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev. 2014 Sep 01; 28(17):1957-75.
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Beating the odds: extreme long-term survival with glioblastoma. Neuro Oncol. 2014 Sep; 16(9):1159-60.
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Epigenetic targeting of hedgehog pathway transcriptional output. Neuro Oncol. 2014 Jul; 16 Suppl 3:iii25.
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Epigenetic targeting of Hedgehog pathway transcriptional output through BET bromodomain inhibition. Nat Med. 2014 Jul; 20(7):732-40.
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Retrospective study of carmustine or lomustine with bevacizumab in recurrent glioblastoma patients who have failed prior bevacizumab. Neuro Oncol. 2014 Nov; 16(11):1523-9.
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Adjuvant radiation therapy, local recurrence, and the need for salvage therapy in atypical meningioma. Neuro Oncol. 2014 Nov; 16(11):1547-53.
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Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet. 2014 Jun; 46(6):588-94.
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Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell. 2014 Mar 17; 25(3):393-405.
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Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study. Epilepsy Res. 2014 Jul; 108(5):843-52.
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Pediatric low-grade gliomas: how modern biology reshapes the clinical field. Biochim Biophys Acta. 2014 Apr; 1845(2):294-307.
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Long-term outcome of 4,040 children diagnosed with pediatric low-grade gliomas: an analysis of the Surveillance Epidemiology and End Results (SEER) database. Pediatr Blood Cancer. 2014 Jul; 61(7):1173-9.
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In vivo multiplexed interrogation of amplified genes identifies GAB2 as an ovarian cancer oncogene. Proc Natl Acad Sci U S A. 2014 Jan 21; 111(3):1102-7.
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SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer. Cancer Cell. 2013 Dec 09; 24(6):738-50.
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BET bromodomain inhibition of MYC-amplified medulloblastoma. Clin Cancer Res. 2014 Feb 15; 20(4):912-25.
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The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77.
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Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013 Oct; 45(10):1134-40.
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The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20.
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Coordinate activation of Shh and PI3K signaling in PTEN-deficient glioblastoma: new therapeutic opportunities. Nat Med. 2013 Nov; 19(11):1518-23.
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The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell. 2013 Sep 09; 24(3):365-78.
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Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9.
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Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Cancer Discov. 2013 Sep; 3(9):1044-57.
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Update on bevacizumab and other angiogenesis inhibitors for brain cancer. Expert Opin Emerg Drugs. 2013 Jun; 18(2):137-53.
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Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73.
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Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1. Proc Natl Acad Sci U S A. 2013 May 14; 110(20):8188-93.
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Phase 2 study of dose-intense temozolomide in recurrent glioblastoma. Neuro Oncol. 2013 Jul; 15(7):930-5.
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Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet. 2013 May; 45(5):478-86.
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Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. PLoS One. 2013; 8(2):e54873.
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Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. Nat Genet. 2013 Mar; 45(3):285-9.
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Integrative molecular analysis of intrahepatic cholangiocarcinoma reveals 2 classes that have different outcomes. Gastroenterology. 2013 Apr; 144(4):829-40.
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ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013 Apr; 23(4):665-78.
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ß-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell. 2012 Dec 21; 151(7):1457-73.
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Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 2013 Feb; 23(2):228-35.
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Integrative analysis reveals an outcome-associated and targetable pattern of p53 and cell cycle deregulation in diffuse large B cell lymphoma. Cancer Cell. 2012 Sep 11; 22(3):359-72.
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Cancer vulnerabilities unveiled by genomic loss. Cell. 2012 Aug 17; 150(4):842-54.
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Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012 Aug 02; 488(7409):49-56.
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Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 2012 Jul 26; 487(7408):491-5.
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Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis. Cancer Res. 2012 Sep 01; 72(17):4383-93.
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Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012 Jun 20; 486(7403):405-9.
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Recurrent hemizygous deletions in cancers may optimize proliferative potential. Science. 2012 Jul 06; 337(6090):104-9.
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Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012 May; 30(5):413-21.
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Chemical genomics identifies small-molecule MCL1 repressors and BCL-xL as a predictor of MCL1 dependency. Cancer Cell. 2012 Apr 17; 21(4):547-62.
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Somatic activation of AKT3 causes hemispheric developmental brain malformations. Neuron. 2012 Apr 12; 74(1):41-8.
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A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol. 2012 Jan; 8(1):e1002337.
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Oncogenic PIK3CA-driven mammary tumors frequently recur via PI3K pathway-dependent and PI3K pathway-independent mechanisms. Nat Med. 2011 Aug 07; 17(9):1116-20.
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Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet. 2011 Jul 31; 43(9):869-74.
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Orthotopic xenografts of RCC retain histological, immunophenotypic and genetic features of tumours in patients. J Pathol. 2011 Oct; 225(2):212-21.
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Safety of concurrent bevacizumab therapy and anticoagulation in glioma patients. J Neurooncol. 2012 Jan; 106(1):121-5.
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Genetic and functional studies implicate HIF1a as a 14q kidney cancer suppressor gene. Cancer Discov. 2011 Aug; 1(3):222-35.
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GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011; 12(4):R41.
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The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature. 2011 Mar 24; 471(7339):513-7.
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Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer. Sci Transl Med. 2010 Dec 15; 2(62):62ra93.
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Stathmin is superior to AKT and phospho-AKT staining for the detection of phosphoinositide 3-kinase activation and aggressive endometrial cancer. Histopathology. 2010 Oct; 57(4):641-6.
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A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A. 2010 Oct 12; 107(41):17604-9.
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Medical therapies for meningiomas. J Neurooncol. 2010 Sep; 99(3):365-78.
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Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet. 2010 Aug; 42(8):715-21.
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The design and validation of a novel phenotypic assay to determine HIV-1 coreceptor usage of clinical isolates. J Virol Methods. 2010 Oct; 169(1):39-46.
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ERG rearrangement is specific to prostate cancer and does not occur in any other common tumor. Mod Pathol. 2010 Aug; 23(8):1061-7.
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The landscape of somatic copy-number alteration across human cancers. Nature. 2010 Feb 18; 463(7283):899-905.
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An oncogene-tumor suppressor cascade drives metastatic prostate cancer by coordinately activating Ras and nuclear factor-kappaB. Nat Med. 2010 Mar; 16(3):286-94.
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Amplification of chromosomal segment 4q12 in non-small cell lung cancer. Cancer Biol Ther. 2009 Nov; 8(21):2042-50.
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Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer. Proc Natl Acad Sci U S A. 2009 Oct 27; 106(43):18351-6.
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SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet. 2009 Nov; 41(11):1238-42.
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Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56.
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Proteasomal and genetic inactivation of the NF1 tumor suppressor in gliomagenesis. Cancer Cell. 2009 Jul 07; 16(1):44-54.
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Oncosome formation in prostate cancer: association with a region of frequent chromosomal deletion in metastatic disease. Cancer Res. 2009 Jul 01; 69(13):5601-9.
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Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney. Cancer Res. 2009 Jun 01; 69(11):4674-81.
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Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet. 2009 Jul; 41(7):843-8.
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Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J Clin Invest. 2009 Jun; 119(6):1727-40.
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Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer. 2009 Apr; 48(4):366-80.
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Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas. Clin Cancer Res. 2009 Feb 15; 15(4):1417-27.
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Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotechnol. 2009 Jan; 27(1):77-83.
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Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A. 2008 Dec 23; 105(51):20380-5.
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High-resolution genomic and expression analyses of copy number alterations in breast tumors. Genes Chromosomes Cancer. 2008 Jun; 47(6):530-42.
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Major copy proportion analysis of tumor samples using SNP arrays. BMC Bioinformatics. 2008 Apr 21; 9:204.
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SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res. 2008 Apr; 36(7):2446-56.
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HER-2/neu expression is associated with high tumor cell proliferation and aggressive phenotype in a population based patient series of endometrial carcinomas. Int J Oncol. 2008 Feb; 32(2):307-16.
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Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res. 2008 Feb 01; 68(3):664-73.
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Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A. 2007 Dec 11; 104(50):20007-12.
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Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007 Dec 06; 450(7171):893-8.
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Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model. Neoplasia. 2007 Mar; 9(3):200-6.
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Molecular definition of breast tumor heterogeneity. Cancer Cell. 2007 Mar; 11(3):259-73.
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High-throughput oncogene mutation profiling in human cancer. Nat Genet. 2007 Mar; 39(3):347-51.
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Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol. 2007 Jan; 19(1):43-9.
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Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain. PLoS Med. 2006 Dec; 3(12):e485.
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TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res. 2006 Sep 01; 66(17):8337-41.
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Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol. 2006 May; 2(5):e41.
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Amplification and overexpression of prosaposin in prostate cancer. Genes Chromosomes Cancer. 2005 Dec; 44(4):351-64.
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Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol. 2005 Nov; 1(6):e65.
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Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med. 2005 Nov 10; 353(19):2012-24.
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Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature. 2005 Jul 07; 436(7047):117-22.
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Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res. 2005 Jul 01; 65(13):5561-70.
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Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell. 2004 Jul; 6(1):17-32.
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Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer. Cancer Res. 2004 Jun 01; 64(11):3814-22.
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Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res. 2004 May 18; 32(9):e71.
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Neonatal thyrotoxicosis and conjugated hyperbilirubinemia. J Matern Fetal Neonatal Med. 2003 Jun; 13(6):426-8.
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