Gad Getz

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint 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
  2. ncbi request reprint Comparative gene marker selection suite
    Joshua Gould
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Bioinformatics 22:1924-5. 2006
  3. pmc Discovery and saturation analysis of cancer genes across 21 tumour types
    Michael S Lawrence
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 505:495-501. 2014
  4. pmc Mutational heterogeneity in cancer and the search for new cancer-associated genes
    Michael S Lawrence
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 499:214-8. 2013
  5. doi request reprint Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy
    Jens G Lohr
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
    Cancer Cell 25:91-101. 2014
  6. pmc Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    Kristian Cibulskis
    The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:213-9. 2013
  7. doi request reprint Sequence analysis of mutations and translocations across breast cancer subtypes
    Shantanu Banerji
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 486:405-9. 2012
  8. pmc A landscape of driver mutations in melanoma
    Eran Hodis
    The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Cell 150:251-63. 2012
  9. doi request reprint Absolute quantification of somatic DNA alterations in human cancer
    Scott L Carter
    The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 30:413-21. 2012
  10. ncbi request reprint Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
    Elena Helman
    Harvard MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
    Genome Res 24:1053-63. 2014

Detail Information

Publications47

  1. ncbi request reprint 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...
  2. ncbi request reprint Comparative gene marker selection suite
    Joshua Gould
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Bioinformatics 22:1924-5. 2006
    ....
  3. pmc Discovery and saturation analysis of cancer genes across 21 tumour types
    Michael S Lawrence
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 505:495-501. 2014
    ..We estimate that near-saturation may be achieved with 600-5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics. ..
  4. pmc Mutational heterogeneity in cancer and the search for new cancer-associated genes
    Michael S Lawrence
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 499:214-8. 2013
    ..By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer. ..
  5. doi request reprint Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy
    Jens G Lohr
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02412, USA Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
    Cancer Cell 25:91-101. 2014
    ..These results emphasize the importance of heterogeneity analysis for treatment decisions...
  6. pmc Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    Kristian Cibulskis
    The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:213-9. 2013
    ..1 and below, making MuTect particularly useful for studying cancer subclones and their evolution in standard exome and genome sequencing data...
  7. doi request reprint Sequence analysis of mutations and translocations across breast cancer subtypes
    Shantanu 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...
  8. pmc A landscape of driver mutations in melanoma
    Eran 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...
  9. doi request reprint Absolute quantification of somatic DNA alterations in human cancer
    Scott 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...
  10. ncbi request reprint Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
    Elena Helman
    Harvard MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
    Genome Res 24:1053-63. 2014
    ..The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer. ..
  11. pmc Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
    Maura Costello
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Nucleic Acids Res 41:e67. 2013
    ....
  12. pmc The mutational landscape of head and neck squamous cell carcinoma
    Nicolas 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...
  13. pmc Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing
    David G McFadden
    Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Cell 156:1298-311. 2014
    ..We propose a temporal model of SCLC tumorigenesis with implications for human SCLC therapeutics and the nature of cancer-genome evolution in GEMMs. ..
  14. pmc RNA-SeQC: RNA-seq metrics for quality control and process optimization
    David 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...
  15. pmc Melanoma genome sequencing reveals frequent PREX2 mutations
    Michael 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...
  16. pmc The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
    Jordi 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...
  17. pmc GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
    Craig 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...
  18. pmc Initial genome sequencing and analysis of multiple myeloma
    Michael 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...
  19. pmc Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
    Eliezer M Van Allen
    1 Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Med 20:682-8. 2014
    ..In one patient, previously undetected findings guided clinical trial enrollment, leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine. ..
  20. pmc The genetic landscape of high-risk neuroblastoma
    Trevor J Pugh
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 45:279-84. 2013
    ..The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies that rely on frequently altered oncogenic drivers...
  21. pmc Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing
    Marcin 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...
  22. pmc Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
    Jens 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...
  23. pmc Paired-end sequencing of Fosmid libraries by Illumina
    Louise 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...
  24. pmc Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
    Trevor J Pugh
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 488:106-10. 2012
    ....
  25. pmc Integrative analysis of the melanoma transcriptome
    Michael 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...
  26. pmc ContEst: estimating cross-contamination of human samples in next-generation sequencing data
    Kristian 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...
  27. pmc Integrative analysis reveals an outcome-associated and targetable pattern of p53 and cell cycle deregulation in diffuse large B cell lymphoma
    Stefano 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...
  28. pmc High-resolution mapping of copy-number alterations with massively parallel sequencing
    Derek Y Chiang
    Broad Institute, Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, MA 02142, USA
    Nat Methods 6:99-103. 2009
    ....
  29. pmc The genomic complexity of primary human prostate cancer
    Michael 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...
  30. pmc Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
    Roel 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...
  31. pmc Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
    Rameen 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...
  32. ncbi request reprint MicroRNA expression profiles classify human cancers
    Jun 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...
  33. ncbi request reprint Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data
    Gad Getz
    Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 19:1079-89. 2003
    ..We demonstrate, on data from colon and breast cancer, that we are able to identify partitions that elude standard clustering analysis...
  34. ncbi request reprint Coupled two-way clustering server
    Gad Getz
    Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 19:1153-4. 2003
    ..The CTWC server provides access to the software, CTWC1.00, that implements Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data Availability: Free, at http://ctwc.weizmann.ac.il...
  35. ncbi request reprint 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...
  36. ncbi request reprint Design principle of gene expression used by human stem cells: implication for pluripotency
    Michal 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...
  37. ncbi request reprint 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 subtypes
    Sophie 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...
  38. ncbi request reprint F2CS: FSSP to CATH and SCOP prediction server
    Gad 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...
  39. ncbi request reprint Identification of the JNK signaling pathway as a functional target of the tumor suppressor PTEN
    Igor 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...
  40. ncbi request reprint Finding motifs in promoter regions
    Libi 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...
  41. pmc Characterizing the cancer genome in lung adenocarcinoma
    Barbara 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...
  42. ncbi request reprint Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer
    Uri Einav
    Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Oncogene 24:6367-75. 2005
    ....
  43. doi request reprint High-resolution genomic and expression analyses of copy number alterations in breast tumors
    Peter 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...
  44. doi request reprint Modeling genomic diversity and tumor dependency in malignant melanoma
    William 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...
  45. ncbi request reprint Automated assignment of SCOP and CATH protein structure classifications from FSSP scores
    Gad 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...