Gad Getz

Summary

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. pmc Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    Adam J Bass
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Genet 43:964-8. 2011
  9. 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
  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

Publications42

  1. 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...
  2. 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. ..
  3. 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. ..
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. pmc Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    Adam J Bass
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Genet 43:964-8. 2011
    ..This study shows previously unidentified levels of genomic rearrangements in colorectal carcinoma that can lead to essential gene fusions and other oncogenic events...
  9. 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...
  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 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. ..
  12. pmc Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
    Austin M Dulak
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Genet 45:478-86. 2013
    ..Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis...
  13. 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
    ....
  14. 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...
  15. 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...
  16. 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...
  17. pmc Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
    Jens G Lohr
    1 The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Dana Farber Cancer Institute, Boston, Massachusetts, USA 3 Harvard Medical School, Boston, Massachusetts, USA 4
    Nat Biotechnol 32:479-84. 2014
    ..This study establishes a foundation for CTC genomics in the clinic. ..
  18. doi request reprint Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
    JOSHUA M FRANCIS
    1 Broad Institute, Cambridge, Massachusetts, USA 2 Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA 3
    Nat Genet 45:1483-6. 2013
    ....
  19. ncbi request reprint Resistance to CDK2 inhibitors is associated with selection of polyploid cells in CCNE1-amplified ovarian cancer
    Dariush Etemadmoghadam
    Authors Affiliations Peter MacCallum Cancer Centre, East Melbourne Victorian Cancer Cytogenetics Service, St Vincent s Hospital, Melbourne Sir Peter MacCallum Department of Oncology Departments of Pathology, Biochemistry and Molecular Biology, and Medicine Centre for Translational Pathology, University of Melbourne, Parkville, Victoria, Australia Dana Farber Cancer Institute, Boston and The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
    Clin Cancer Res 19:5960-71. 2013
    ..We have previously shown that CCNE1-amplified tumors show amplicon-dependent sensitivity to CCNE1 suppression. Here, we explore targeting CDK2 as a novel therapeutic strategy in CCNE1-amplified cancers and mechanisms of resistance...
  20. 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...
  21. 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...
  22. pmc High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
    Geoff Fudenberg
    Harvard University, Program in Biophysics, Boston, Massachusetts, USA
    Nat Biotechnol 29:1109-13. 2011
    ....
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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
    ....
  28. pmc Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
    Priscilla K Brastianos
    1 Division of Hematology Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA 2 Division of Neuro Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA 3 Harvard Medical School, Boston, Massachusetts, USA 4 Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA 5 Broad Institute of MIT and Harvard, Boston, Massachusetts, USA 6
    Nat Genet 46:161-5. 2014
    ..Adamantinomatous and papillary craniopharyngiomas harbor mutations that are mutually exclusive and clonal. These findings have important implications for the diagnosis and treatment of these neoplasms. ..
  29. pmc A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
    Angela N Brooks
    Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS ONE 9:e87361. 2014
    ..This report demonstrates consistent effects of U2AF1 mutation on splicing in distinct cancer cell types. ..
  30. 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. ..
  31. ncbi request reprint Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair
    Paz Polak
    1 Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts, USA 2 Harvard Medical School, Boston, Massachusetts, USA 3 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 4
    Nat Biotechnol 32:71-5. 2014
    ..Together, our results connect chromatin structure, gene regulation and cancer-associated somatic mutation. ..
  32. pmc Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations
    Priscilla K Brastianos
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Genet 45:285-9. 2013
    ..These mutations were present in therapeutically challenging tumors of the skull base and higher grade. These results begin to define the spectrum of genetic alterations in meningiomas and identify potential therapeutic targets...
  33. 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
    ....
  34. 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...
  35. 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...
  36. 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...
  37. pmc Punctuated evolution of prostate cancer genomes
    Sylvan C Baca
    Harvard Medical School, Boston, MA 02115, USA
    Cell 153:666-77. 2013
    ..By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis...
  38. 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...
  39. 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...
  40. 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...
  41. 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...