Charles Lee

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Towards a comprehensive structural variation map of an individual human genome
    Andy W Pang
    Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Genome Biol 11:R52. 2010
  2. ncbi request reprint Copy number variations and clinical cytogenetic diagnosis of constitutional disorders
    Charles Lee
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Nat Genet 39:S48-54. 2007
  3. ncbi request reprint Multicolor fluorescence in situ hybridization in clinical cytogenetic diagnostics
    C Lee
    Department of Pathology, Brigham and Women s Hospital, Boston Massachusetts, USA
    Curr Opin Pediatr 13:550-5. 2001
  4. pmc A mutation in separase causes genome instability and increased susceptibility to epithelial cancer
    Jennifer L Shepard
    Children s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 21:55-9. 2007
  5. pmc Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC
    Alexa B Turke
    Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
    Cancer Cell 17:77-88. 2010
  6. doi request reprint Reporting of diagnostic cytogenetic results
    Azra H Ligon
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2011
  7. pmc Artemis and p53 cooperate to suppress oncogenic N-myc amplification in progenitor B cells
    Sean Rooney
    Howard Hughes Medical Institute, Children s Hospital, Department of Genetics, Harvard Medical School, and Center for Blood Research, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:2410-5. 2004
  8. ncbi request reprint TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer
    Sven Perner
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, EBRC 442A, 221 Longwood Avenue, Boston, MA 02115 6110, USA
    Cancer Res 66:8337-41. 2006
  9. doi request reprint Reporting of diagnostic cytogenetic results
    Azra H Ligon
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2010
  10. pmc Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model
    Kirsten D Mertz
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115 6110, USA
    Neoplasia 9:200-6. 2007

Research Grants

Detail Information

Publications91

  1. pmc Towards a comprehensive structural variation map of an individual human genome
    Andy W Pang
    Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Genome Biol 11:R52. 2010
    ..It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions...
  2. ncbi request reprint Copy number variations and clinical cytogenetic diagnosis of constitutional disorders
    Charles Lee
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Nat Genet 39:S48-54. 2007
    ..Ironically, the accumulation and annotation of such array CGH data can lead to the rapid identification of pathogenic CNVs and the definition of new genomic syndromes that, in turn, are useful for accurate clinical genetic diagnoses...
  3. ncbi request reprint Multicolor fluorescence in situ hybridization in clinical cytogenetic diagnostics
    C Lee
    Department of Pathology, Brigham and Women s Hospital, Boston Massachusetts, USA
    Curr Opin Pediatr 13:550-5. 2001
    ....
  4. pmc A mutation in separase causes genome instability and increased susceptibility to epithelial cancer
    Jennifer L Shepard
    Children s Hospital, Boston, Massachusetts 02115, USA
    Genes Dev 21:55-9. 2007
    ..These data strongly support a conserved cross-species role for mitotic checkpoint genes in genetic stability and epithelial carcinogenesis...
  5. pmc Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC
    Alexa B Turke
    Massachusetts General Hospital Cancer Center, Boston, MA 02129, USA
    Cancer Cell 17:77-88. 2010
    ..These findings highlight the potential to prospectively identify treatment naive, patients with EGFR-mutant lung cancer who will benefit from initial combination therapy...
  6. doi request reprint Reporting of diagnostic cytogenetic results
    Azra H Ligon
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2011
    ..Multi-specimen usage macros are included that can be applied to two or more specimen types...
  7. pmc Artemis and p53 cooperate to suppress oncogenic N-myc amplification in progenitor B cells
    Sean Rooney
    Howard Hughes Medical Institute, Children s Hospital, Department of Genetics, Harvard Medical School, and Center for Blood Research, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:2410-5. 2004
    ..We discuss this finding in the context of potential implications for mechanisms that may target IgH locus translocations to particular oncogenes...
  8. ncbi request reprint TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer
    Sven Perner
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, EBRC 442A, 221 Longwood Avenue, Boston, MA 02115 6110, USA
    Cancer Res 66:8337-41. 2006
    ..The deletion as cause of TMPRSS2:ERG fusion is associated with clinical features for prostate cancer progression compared with tumors that lack the TMPRSS2:ERG rearrangement...
  9. doi request reprint Reporting of diagnostic cytogenetic results
    Azra H Ligon
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2010
    ..Multi-specimen usage macros are included that can be applied to two or more specimen types...
  10. pmc Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model
    Kirsten D Mertz
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115 6110, USA
    Neoplasia 9:200-6. 2007
    ..The androgen receptor-negative NCI-H660 cell line expresses ERG in an androgen-independent fashion. This in vitro model system has the potential to provide important pathobiologic insights into TMPRSS2-ERG fusion prostate cancer...
  11. pmc Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis
    Kim H Brown
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:529-34. 2012
    ....
  12. pmc Construction and application of a zebrafish array comparative genomic hybridization platform
    Jennifer L Freeman
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Genes Chromosomes Cancer 48:155-70. 2009
    ..Hence, this platform should be a useful resource for genetic dissection of additional zebrafish developmental and disease models as well as a benchmark for future array CGH platform development...
  13. pmc Regulatory element copy number differences shape primate expression profiles
    Rebecca C Iskow
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:12656-61. 2012
    ..We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA...
  14. pmc Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
    Genome Biol 12:R52. 2011
    ..Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation...
  15. ncbi request reprint Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer
    Scott A Tomlins
    Department of Pathology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, MI 48109 0602, USA
    Science 310:644-8. 2005
    ..These results have implications in the development of carcinomas and the molecular diagnosis and treatment of prostate cancer...
  16. doi request reprint Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies
    Arthur S Lee
    Department of Pathology, Brigham and Women s Hospital, 221 Longwood Ave, Boston, MA 02115, USA
    Hum Mol Genet 17:1127-36. 2008
    ..Therefore, the rhesus macaque offers an intriguing, non-human primate outbred model organism with which hypotheses concerning the specific functions of phenotypically relevant human CNVs can be tested...
  17. ncbi request reprint Structural variation in the human genome: the impact of copy number variants on clinical diagnosis
    Laia Rodriguez-Revenga
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genet Med 9:600-6. 2007
    ..Herein, we review the literature from the past 3 years on this new source of genomic variability and comment on factors that should be considered when trying to differentiate between a pathogenic and a benign copy number variant...
  18. ncbi request reprint Copy number variation: new insights in genome diversity
    Jennifer L Freeman
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genome Res 16:949-61. 2006
    ..Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases...
  19. doi request reprint On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test
    Iuliana Ionita-Laza
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts, USA
    Genet Epidemiol 32:273-84. 2008
    ..A software implementation of the approach is freely available at http://www.hsph.harvard.edu/research/iuliana-ionita/software. The approach has also been completely integrated in the PBAT software package...
  20. pmc Definition of the zebrafish genome using flow cytometry and cytogenetic mapping
    Jennifer L Freeman
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    BMC Genomics 8:195. 2007
    ..Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data...
  21. pmc EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer
    Jussi P Koivunen
    Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, D820A, 44 Binney Street, Boston, MA 02115, USA
    Clin Cancer Res 14:4275-83. 2008
    ..We determined the frequency of EML4-ALK in Caucasian NSCLC and in NSCLC cell lines. We also determined whether TAE684, a specific ALK kinase inhibitor, would inhibit the growth of EML4-ALK-containing cell lines in vitro and in vivo...
  22. pmc Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis
    Iuliana Ionita-Laza
    Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
    Genomics 93:22-6. 2009
    ..Instead, development of novel technical, statistical, and epidemiologic methods will be necessary to optimally capture this newly-appreciated form of genetic variation in a meaningful manner...
  23. doi request reprint Genetic variation of genes involved in dihydrotestosterone metabolism and the risk of prostate cancer
    Sunita R Setlur
    Department of Pathology, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Cancer Epidemiol Biomarkers Prev 19:229-39. 2010
    ..Given PCA's strong genetic component, we evaluated the possibility that variation in genes involved in DHT metabolism influence PCA risk...
  24. pmc EGFR mutation is a better predictor of response to tyrosine kinase inhibitors in non-small cell lung carcinoma than FISH, CISH, and immunohistochemistry
    Lynette M Sholl
    Department of Pathology, Brigham and Women s Hospital, 75 Francis St, Boston, MA 02115, USA
    Am J Clin Pathol 133:922-34. 2010
    ..Thus, EGFR sequence analysis was the only method useful for predicting response and progression-free survival following TKI therapy in NSCLC...
  25. pmc Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence
    Omer Gokcumen
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts, United States of America
    PLoS Genet 9:e1003404. 2013
    ..We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European populations...
  26. pmc Disseminated peritoneal leiomyomatosis after laparoscopic supracervical hysterectomy with characteristic molecular cytogenetic findings of uterine leiomyoma
    Zehra Ordulu
    Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women s Hospital and Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115, USA
    Genes Chromosomes Cancer 49:1152-60. 2010
    ....
  27. doi request reprint Reporting of diagnostic cytogenetic results
    Azra H Ligon
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2004
    ..Multi-specimen usage macros are included that can be applied to two or more specimen types...
  28. pmc XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice
    Catherine T Yan
    Howard Hughes Medical Institute, The Children s Hospital, CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:7378-83. 2006
    ....
  29. ncbi request reprint Common deletion polymorphisms in the human genome
    Steven A McCarroll
    Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
    Nat Genet 38:86-92. 2006
    ....
  30. ncbi request reprint Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
    Levi A Garraway
    Department of Medical Oncology, and Melanoma Program in Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 436:117-22. 2005
    ..Together, these data suggest that MITF represents a distinct class of 'lineage survival' or 'lineage addiction' oncogenes required for both tissue-specific cancer development and tumour progression...
  31. pmc A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility
    Jennifer L Shepard
    Children s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 102:13194-9. 2005
    ..Our findings show that zebrafish screens can uncover cancer pathways, and demonstrate that loss of function of bmyb is associated with cancer...
  32. doi request reprint Structural genomic variation and personalized medicine
    Charles Lee
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, USA
    N Engl J Med 358:740-1. 2008
  33. pmc Alu elements mediate MYB gene tandem duplication in human T-ALL
    Jennifer O'Neil
    Department of Pediatric Oncology, Belfer Foundation Institute for Innovative Cancer Science, Dana Farber Cancer Institute, Boston, MA 02115, USA
    J Exp Med 204:3059-66. 2007
    ..We conclude that Alu-mediated MYB tandem duplication occurs at low frequency during normal thymocyte development and is clonally selected during the molecular pathogenesis of human T-ALL...
  34. pmc Diverse mechanisms of somatic structural variations in human cancer genomes
    Lixing Yang
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Cell 153:919-29. 2013
    ....
  35. pmc Mapping copy number variation by population-scale genome sequencing
    Ryan E Mills
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Nature 470:59-65. 2011
    ..Our analytical framework and SV map serves as a resource for sequencing-based association studies...
  36. ncbi request reprint Detecting copy number variation in the human genome using comparative genomic hybridization
    Joelle Tchinda
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Biotechniques 41:385, 387, 389 passim. 2006
    ..g., allergic reactions), medications (e.g., pharmacogenomics), microscopic infections (i.e., immunity), and other aspects of our ever-changing environment...
  37. pmc Comparison of familial and sporadic chronic lymphocytic leukaemia using high resolution array comparative genomic hybridization
    Sunita R Setlur
    Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Br J Haematol 151:336-45. 2010
    ..This study is the first high resolution effort to investigate and report somatic genetic differences between familial and sporadic CLL...
  38. ncbi request reprint Histone H2AX: a dosage-dependent suppressor of oncogenic translocations and tumors
    Craig H Bassing
    Howard Hughes Medical Institute, The Children s Hospital, Department of Genetics, Harvard Medical School and The Center for Blood Research, Boston, MA 02115, USA
    Cell 114:359-70. 2003
    ..Notably, H2AX maps to a cytogenetic region frequently altered in human cancers, possibly implicating similar functions in man...
  39. doi request reprint Molecular cytogenetic methodologies and a BAC probe panel resource for genomic analyses in the zebrafish
    Kimberly P Dobrinski
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts, USA Harvard Medical School, Boston, Massachusetts, USA
    Methods Cell Biol 104:237-57. 2011
    ....
  40. pmc The fine-scale and complex architecture of human copy-number variation
    George H Perry
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Am J Hum Genet 82:685-95. 2008
    ..Future association studies that aim to capture the potential influences of CNVs on disease phenotypes will need to consider how to best ascertain this previously uncharacterized complexity...
  41. pmc Integrating common and rare genetic variation in diverse human populations
    David M Altshuler
    Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA
    Nature 467:52-8. 2010
    ....
  42. ncbi request reprint Characterization of familial Waldenstrom's macroglobulinemia
    S P Treon
    Bing Center for Waldenstrom s Macroglobulinemia, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Ann Oncol 17:488-94. 2006
    ..Familial clustering of B-cell disorders among Waldenström's macroglobulinemia (WM) patients has been reported, though the frequency and any differences in disease manifestation for familial patients remain to be defined...
  43. pmc Cross-species array comparative genomic hybridization identifies novel oncogenic events in zebrafish and human embryonal rhabdomyosarcoma
    Eleanor Y Chen
    Division of Molecular Pathology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America Harvard Stem Cell Institute, Boston, Massachusetts, United States of America Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 9:e1003727. 2013
    ..Our results demonstrate the utility of array CGH and cross-species comparisons to identify candidate oncogenes essential for the pathogenesis of human cancer. ..
  44. pmc Copy number variation genotyping using family information
    Jen hwa Chu
    Channing Division of Network Medicine, Brigham and Women s Hospital, MA, USA
    BMC Bioinformatics 14:157. 2013
    ....
  45. pmc Exploring the role of copy number variants in human adaptation
    Rebecca C Iskow
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Trends Genet 28:245-57. 2012
    ..We expect that many more adaptive CNVs will be discovered in the coming years, and we believe that these new findings will contribute to our understanding of human-specific phenotypes...
  46. pmc Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration
    Colby Chiang
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Genet 44:390-7, S1. 2012
    ....
  47. ncbi request reprint Molecular cytogenetic methodologies and a bacterial artificial chromosome (BAC) probe panel resource for genomic analyses in zebrafish
    Charles Lee
    Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Methods Cell Biol 77:241-54. 2004
  48. ncbi request reprint Detection of large-scale variation in the human genome
    A John Iafrate
    Department of Pathology, Brigham and Women s Hospital, 20 Shattuck St, Thorn 6 28, Boston, Massachusetts 02115, USA
    Nat Genet 36:949-51. 2004
    ..This previously unappreciated heterogeneity may underlie certain human phenotypic variation and susceptibility to disease and argues for a more dynamic human genome structure...
  49. doi request reprint The clinical context of copy number variation in the human genome
    Charles Lee
    Department of Pathology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Expert Rev Mol Med 12:e8. 2010
    ..Challenges remain for understanding the relationship between genomic changes and the phenotypes that might be predicted and prevented by such knowledge...
  50. pmc Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies
    David T Miller
    Division of Genetics and Department of Laboratory Medicine, Children s Hospital Boston and Harvard Medical School, Boston, MA, USA
    Am J Hum Genet 86:749-64. 2010
    ..G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages...
  51. pmc Limitations of chromosome classification by multicolor karyotyping
    C Lee
    Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA 02115, USA
    Am J Hum Genet 68:1043-7. 2001
    ..In this report, we present nine cases, which fall into five categories, in which multicolor karyotyping has produced erroneous interpretations. Most errors appear to have a similar mechanistic basis...
  52. pmc Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks
    Mauro Longoni
    Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Am J Med Genet A 158:3148-58. 2012
    ..This combination of bioinformatics and expression studies can be applied to other chromosomal hotspots, as well as private microdeletions or microduplications, to identify causative genes and their interaction networks...
  53. pmc A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response
    Zhao Chen
    Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 483:613-7. 2012
    ....
  54. pmc Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization
    Omer Gokcumen
    Cytogenetics Research Laboratory, Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC 404, Boston, MA 02115, USA
    Methods 49:18-25. 2009
    ....
  55. pmc Germ cell aneuploidy in zebrafish with mutations in the mitotic checkpoint gene mps1
    Kenneth D Poss
    Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 18:1527-32. 2004
    ....
  56. pmc Detection of low-copy-number genomic DNA sequences in individual bacterial cells by using peptide nucleic acid-assisted rolling-circle amplification and fluorescence in situ hybridization
    Irina Smolina
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington St, Boston, MA 02215, USA
    Appl Environ Microbiol 73:2324-8. 2007
    ..The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes...
  57. ncbi request reprint MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling
    Jeffrey A Engelman
    Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
    Science 316:1039-43. 2007
    ..Thus, we propose that MET amplification may promote drug resistance in other ERBB-driven cancers as well...
  58. doi request reprint Genomic alterations in myeloid neoplasms with novel, apparently balanced translocations
    Jennifer L Poitras
    Department of Pathology, Brigham and Women s Hospital, Boston, MA, USA
    Cancer Genet 204:68-76. 2011
    ..Such imbalances may portend important hitherto unrecognized prognostic and diagnostic categories...
  59. pmc Findings from aCGH in patients with congenital diaphragmatic hernia (CDH): a possible locus for Fryns syndrome
    S Kantarci
    Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
    Am J Med Genet A 140:17-23. 2006
    ..12 that was confirmed by FISH. Given prior reports of CDH in association with cytogenetic abnormalities in this region, we propose that this represents a locus for Fryns syndrome, a Fryns syndrome phenocopy, or CDH...
  60. pmc Landscape of somatic retrotransposition in human cancers
    Eunjung Lee
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Science 337:967-71. 2012
    ....
  61. ncbi request reprint Tumor Archaeology Reveals that Mutations Love Company
    Sunita R Setlur
    Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Cell 149:959-61. 2012
    ..The bulk of a tumor's life span is shown to involve the development of subclones, many of which harbor mutations that are clustered in subchromosomal regions and appear to result from catastrophic mutational events...
  62. ncbi request reprint Copy number variants and pharmacogenomics
    Karim Ouahchi
    Brigham and Women s Hospital, Department of Pathology, and Harvard Medical School, Boston, MA 02115, USA
    Pharmacogenomics 7:25-9. 2006
    ..Here we review the discovery of copy number variants and speculate on their implications for pathophysiology and pharmacogenomics...
  63. ncbi request reprint Cell-specific mitotic defect and dyserythropoiesis associated with erythroid band 3 deficiency
    Barry H Paw
    Department of Medicine, Division of Hematology Oncology, Children s Hospital, Boston, Massachusetts, USA
    Nat Genet 34:59-64. 2003
    ..1R-binding domains. Our report establishes an evolutionarily conserved role for band 3 in erythroid-specific cell division and illustrates the concept of cell-specific adaptation for mitosis...
  64. ncbi request reprint BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in the genesis of melanoma
    E Elizabeth Patton
    Howard Hughes Medical Institute, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
    Curr Biol 15:249-54. 2005
    ....
  65. ncbi request reprint Multicolor Fluorescence In Situ Hybridization (FISH) approaches for simultaneous analysis of the entire human genome
    C Lee
    Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Curr Protoc Hum Genet . 2001
    ..This overview discusses each of these systems and the recent advances which have made them possible...
  66. ncbi request reprint Prenatal diagnosis and molecular cytogenetics in a case of partial trisomy 14 and monosomy 21
    C Lee
    Department of Obstetrics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
    Am J Med Genet 100:246-50. 2001
    ..More precise definitions of chromosomal breakpoints in such clinical cases should provide more accurate prognosis for individuals with unbalanced karyotypes and assist in the identification of putative developmentally important genes...
  67. ncbi request reprint Identification and characterization of a novel polycystin family member, polycystin-L2, in mouse and human: sequence, expression, alternative splicing, and chromosomal localization
    L Guo
    Renal Division, Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genomics 64:241-51. 2000
    ..PKD2L2 consists of 17 exons spanning approximately 50 kb of genomic DNA. PKD2L2 was mapped to human chromosome 5q31 and Pkd2l2 to mouse chromosome 18 in band C...
  68. ncbi request reprint Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions
    N E Sharpless
    Department of Adult Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 8:1187-96. 2001
    ..Together, these findings support the view that loss of a single lig4 allele results in NHEJ activity being sufficiently reduced to engender chromosomal aberrations that drive non-lymphoid tumorigenesis...
  69. ncbi request reprint Genomic structure, functional comparison, and tissue distribution of mouse Cd59a and Cd59b
    X Qin
    Harvard Medical School, Laboratory for Membrane Transport, 240 Longwood Ave, C1 607, Boston, Massachusetts 02115, USA
    Mamm Genome 12:582-9. 2001
    ..These results suggest that even though Cd59a and Cd59b are expressed in multiple tissues, they may play some different roles, particularly in reproduction...
  70. ncbi request reprint TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort
    F Demichelis
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115 6110, USA
    Oncogene 26:4596-9. 2007
    ..005). These data suggest that TMPRSS2:ERG fusion prostate cancers may have a more aggressive phenotype, possibly mediated through increased ERG expression...
  71. pmc Hotspots for copy number variation in chimpanzees and humans
    George H Perry
    School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
    Proc Natl Acad Sci U S A 103:8006-11. 2006
    ..Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species...
  72. ncbi request reprint Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridization
    Mi Young Kim
    Department of Microbiology, College of Medicine, Catholic University of Korea, Socho gu, Seoul, Korea
    Gastroenterology 131:1913-24. 2006
    ..We aimed to identify recurrently altered genomic regions (RAR) in CRC with high resolution, to investigate their implications on survival and to explore novel cancer-related genes in prognosis-associated RARs...
  73. pmc Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
    Daisuke Komura
    Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153 8904, Japan
    Genome Res 16:1575-84. 2006
    ....
  74. pmc Accurate and reliable high-throughput detection of copy number variation in the human genome
    Heike Fiegler
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 16:1566-74. 2006
    ..Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method...
  75. pmc Linkage to chromosome 2q36.1 in autosomal dominant Dandy-Walker malformation with occipital cephalocele and evidence for genetic heterogeneity
    Ali Jalali
    Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
    Hum Genet 123:237-45. 2008
    ..1 chromosomal region. The Brazilian pedigree did not show linkage to this 2q36.1 region. Taken together, these results demonstrate a locus for ADDWOC on 2q36.1 and also suggest locus heterogeneity for ADDWOC...
  76. pmc Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
    Joshua M Korn
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:1253-60. 2008
    ..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
  77. pmc Completing the map of human genetic variation
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 447:161-5. 2007
  78. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  79. pmc Global variation in copy number in the human genome
    Richard Redon
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 444:444-54. 2006
    ..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
  80. ncbi request reprint Genetics: copies count
    Joseph H Nadeau
    Nature 439:798-9. 2006
  81. pmc Adaptive evolution of UGT2B17 copy-number variation
    Yali Xue
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Am J Hum Genet 83:337-46. 2008
    ..In contrast, diversity was low in East Asia where a single haplotype predominated, suggesting positive selection for the deletion in this part of the world...
  82. pmc Genome assembly comparison identifies structural variants in the human genome
    Razi Khaja
    Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular and Medical Genetics, University of Toronto and The Centre for Applied Genomics, MaRS Centre, Toronto, Ontario, M5G 1L7, Canada
    Nat Genet 38:1413-8. 2006
    ..Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects...
  83. ncbi request reprint Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations
    Chengming Zhu
    Howard Hughes Medical Institute, The Children s Hospital and The Center for Blood Research, Boston MA 02115, USA
    Cell 109:811-21. 2002
    ..This recombination event employs a microhomology-based end-joining repair pathway, as opposed to classic NHEJ or homologous recombination. These findings suggest a general model for oncogenic complicon formation...
  84. ncbi request reprint Multicolor karyotypic interpretation of a heterochromatin-associated marker chromosome in a dysmorphic girl with developmental delay
    Jonathan D Picker
    Am J Med Genet 110:393-6. 2002
  85. ncbi request reprint Description of a case of distal 2p trisomy by array-based comparative genomic hybridization: a high resolution genome-wide investigation for chromosomal aneuploidy in a single assay
    Amy E Roberts
    Am J Med Genet A 130:204-7. 2004
  86. pmc Diet and the evolution of human amylase gene copy number variation
    George H Perry
    School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287, USA
    Nat Genet 39:1256-60. 2007
    ..Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease...
  87. ncbi request reprint The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia
    Pieter Van Vlierberghe
    Erasmus MC Sophia Children s Hospital, Department of Pediatric Oncology Hematology, 3000 CB Rotterdam, The Netherlands
    Blood 108:3520-9. 2006
    ..LMO2 abnormalities represent about 9% (13/138) of pediatric T-ALL cases and are more frequent in pediatric T-ALL than appreciated until now...
  88. ncbi request reprint Vive la difference!
    Charles Lee
    Nat Genet 37:660-1. 2005
  89. pmc Challenges and standards in integrating surveys of structural variation
    Stephen W Scherer
    The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14 701, Ontario M5G 1L7, Canada
    Nat Genet 39:S7-15. 2007
    ..From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research...
  90. pmc EMBL Nucleotide Sequence Database: developments in 2005
    Guy Cochrane
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 34:D10-5. 2006
    ..New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information...
  91. pmc Temporal profile of replication of human chromosomes
    Yesu Jeon
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
    Proc Natl Acad Sci U S A 102:6419-24. 2005
    ..Thus, at least for aneuploid cancer cells, a typical discrete time of replication in S phase is not seen for large segments of the chromosomes...

Research Grants10

  1. Copy number variation in the human genome
    Charles Lee; Fiscal Year: 2007
    ..All information generated will be made available in public databases that will have great utility for the clinical and research genetics community. ..
  2. Molecular Cytogenetic Tools for the Zebrafish
    Charles Lee; Fiscal Year: 2007
    ..This tool will be used to identify genomic DNA gains and losses which could lead to the identification of novel oncogenes and tumor-suppresor genes that lead to tumorigenesis in many zebrafish mutants. ..
  3. Characterization and Evolution of Copy Number Variation Among Primates
    Charles Lee; Fiscal Year: 2010
    ..Our research team, which includes leaders in both the primate copy number variation and gene expression fields, is well positioned to collaboratively address these important issues. ..