Research Topics
Genomes and GenesSpecies | Gad GetzSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
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Publications
Comment on "The consensus coding sequences of human breast and colorectal cancers"Gad Getz
Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
Science 317:1500. 2007..When these concerns are addressed, few genes with significantly elevated mutation rates remain. Although the biological methodology in Sjöblom et al. is sound, more samples are needed to achieve sufficient power...- Comparative gene marker selection suiteJoshua Gould
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Bioinformatics 22:1924-5. 2006..AVAILABILITY: The Comparative Marker Selection application suite is freely available as a GenePattern module. The GenePattern analysis environment is freely available at http://www.broad.mit.edu/genepattern... 
A landscape of driver mutations in melanomaEran Hodis
The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
Cell 150:251-63. 2012..Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis...
Sequence analysis of mutations and translocations across breast cancer subtypesShantanu Banerji
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 486:405-9. 2012..The MAGI3-AKT3 fusion leads to constitutive activation of AKT kinase, which is abolished by treatment with an ATP-competitive AKT small-molecule inhibitor...- Absolute quantification of somatic DNA alterations in human cancerScott L Carter
The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
Nat Biotechnol 30:413-21. 2012..ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity... - The mutational landscape of head and neck squamous cell carcinomaNicolas Stransky
The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Science 333:1157-60. 2011..More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms... - Melanoma genome sequencing reveals frequent PREX2 mutationsMichael F Berger
The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
Nature 485:502-6. 2012..Thus, whole-genome sequencing of human melanoma tumours revealed genomic evidence of ultraviolet pathogenesis and discovered a new recurrently mutated gene in melanoma... - The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivityJordi Barretina
The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
Nature 483:603-7. 2012..The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens... - GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancersCraig H Mermel
Cancer Program, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 12:R41. 2011..Here we detail this revised computational approach, GISTIC2.0, and validate its performance in real and simulated datasets... - Initial genome sequencing and analysis of multiple myelomaMichael A Chapman
The Eli and Edythe L Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02412, USA
Nature 471:467-72. 2011..These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge... - Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencingMarcin Imielinski
Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
Cell 150:1107-20. 2012..The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma... - Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencingJens G Lohr
Eli and Edythe Broad Institute, Cambridge, MA 02412, USA
Proc Natl Acad Sci U S A 109:3879-84. 2012..Our data provide an unbiased view of the landscape of mutations in DLBCL, and this in turn may point toward new therapeutic strategies for the disease... - Paired-end sequencing of Fosmid libraries by IlluminaLouise J S Williams
Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
Genome Res 22:2241-9. 2012..Our Fosill-powered assembly of the mouse genome has an N50 scaffold length of 17.0 Mb, rivaling the connectivity (16.9 Mb) of the Sanger-sequencing based draft assembly... - Medulloblastoma exome sequencing uncovers subtype-specific somatic mutationsTrevor J Pugh
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Nature 488:106-10. 2012.... - RNA-SeQC: RNA-seq metrics for quality control and process optimizationDavid S DeLuca
Broad Institute of MIT and Harvard, Cambridge, MA, USA
Bioinformatics 28:1530-2. 2012..Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool... - ContEst: estimating cross-contamination of human samples in next-generation sequencing dataKristian Cibulskis
Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
Bioinformatics 27:2601-2. 2011..We applied our tool to published cancer sequencing datasets and report their estimated contamination levels... - Integrative analysis of the melanoma transcriptomeMichael F Berger
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Genome Res 20:413-27. 2010..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types... - Integrative analysis reveals an outcome-associated and targetable pattern of p53 and cell cycle deregulation in diffuse large B cell lymphomaStefano Monti
Broad Institute, Cambridge, MA 02142, USA
Cancer Cell 22:359-72. 2012..CNAs of the CDKN2A-TP53-RB-E2F axis provide a structural basis for increased proliferation in DLBCL, predict outcome with current therapy, and suggest targeted treatment approaches... - The genomic complexity of primary human prostate cancerMichael F Berger
The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
Nature 470:214-20. 2011..Thus, genomic rearrangements may arise from transcriptional or chromatin aberrancies and engage prostate tumorigenic mechanisms... - Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1Roel G W Verhaak
The Eli and Edythe L Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
Cancer Cell 17:98-110. 2010..We provide a framework that unifies transcriptomic and genomic dimensions for GBM molecular stratification with important implications for future studies... - High-resolution mapping of copy-number alterations with massively parallel sequencingDerek Y Chiang
Broad Institute, Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
Nat Methods 6:99-103. 2009.... - MicroRNA expression profiles classify human cancersJun Lu
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
Nature 435:834-8. 2005..These findings highlight the potential of miRNA profiling in cancer diagnosis... - Assessing the significance of chromosomal aberrations in cancer: methodology and application to gliomaRameen Beroukhim
Broad Institute, Massachusetts Institute of Technology and Harvard University, 7 Cambridge Center, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 104:20007-12. 2007..Our results support the feasibility and utility of systematic characterization of the cancer genome... - Design principle of gene expression used by human stem cells: implication for pluripotencyMichal Golan-Mashiach
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
FASEB J 19:147-9. 2005..Concomitantly, genes specific to the target tissue are up-regulated toward mature cells of skin or blood... - Coupled two-way clustering analysis of breast cancer and colon cancer gene expression dataGad Getz
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Bioinformatics 19:1079-89. 2003..AVAILABILITY: Free, at http://ctwc.weizmann.ac.il.. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/.. - Coupled two-way clustering serverGad Getz
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Bioinformatics 19:1153-4. 2003..2000), a method designed to mine gene expression data Availability: Free, at http://ctwc.weizmann.ac.il. SUPPLEMENTARY INFORMATION: The site has a link to an example which provides figures and detailed explanations.. - Outcome signature genes in breast cancer: is there a unique set?Liat Ein-Dor
Department of Physics of Complex Systems, Weizmann Institute of Science Rehovot 76100, Israel
Bioinformatics 21:171-8. 2005..One of the main open questions in this context is whether the disparity can be attributed only to trivial reasons such as different technologies, different patients and different types of analyses... - Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypesSophie Godard
Laboratory of Tumor Biology and Genetics, University Hospital (CHUV, 1011 Lausanne, Switzerland
Cancer Res 63:6613-25. 2003..The separating groups of genes were found by the unsupervised coupled two-way clustering method, and their classification power was validated by a supervised construction of a nearly perfect glioma classifier... - F2CS: FSSP to CATH and SCOP prediction serverGad Getz
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Bioinformatics 20:2150-2. 2004..AVAILABILITY: Free at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/ SUPPLEMENTARY INFORMATION: The site contains links to additional figures and tables... - Modeling genomic diversity and tumor dependency in malignant melanomaWilliam M Lin
Department of Medical Oncology, Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
Cancer Res 68:664-73. 2008..Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors... - Finding motifs in promoter regionsLibi Hertzberg
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
J Comput Biol 12:314-30. 2005..Our results were significantly better. In contrast with us, MatInspector doesn't calculate the exact statistical significance of its results... - Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysRoger McLendon
Nature 455:1061-8. 2008..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer... - Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancerUri Einav
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Oncogene 24:6367-75. 2005.... - Identification of the JNK signaling pathway as a functional target of the tumor suppressor PTENIgor Vivanco
Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
Cancer Cell 11:555-69. 2007..Akt and JNK activation are highly correlated in human prostate cancer. These findings implicate JNK in PI3K-driven cancers and demonstrate the utility of GSEA to identify functional pathways using genetically defined systems... - Characterizing the cancer genome in lung adenocarcinomaBarbara A Weir
Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
Nature 450:893-8. 2007..More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered... - High-resolution genomic and expression analyses of copy number alterations in breast tumorsPeter M Haverty
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
Genes Chromosomes Cancer 47:530-42. 2008..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat... - Automated assignment of SCOP and CATH protein structure classifications from FSSP scoresGad Getz
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
Proteins 46:405-15. 2002..quot; We further suggest that to resolve these ambiguous cases, other criteria of classification, based also on information about sequence and function, must be used...