Research Topics
Genomes and Genes
| Charles LeeSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
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Detail Information
Publications
Towards a comprehensive structural variation map of an individual human genomeAndy 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...
Copy number variations and clinical cytogenetic diagnosis of constitutional disordersCharles 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...- Multicolor fluorescence in situ hybridization in clinical cytogenetic diagnosticsC Lee
Department of Pathology, Brigham and Women s Hospital, Boston Massachusetts, USA
Curr Opin Pediatr 13:550-5. 2001.... - A mutation in separase causes genome instability and increased susceptibility to epithelial cancerJennifer 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... - Preexistence and clonal selection of MET amplification in EGFR mutant NSCLCAlexa 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... 
Reporting of diagnostic cytogenetic resultsAzra 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...- Artemis and p53 cooperate to suppress oncogenic N-myc amplification in progenitor B cellsSean 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... - TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancerSven 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... - Reporting of diagnostic cytogenetic resultsAzra 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... - Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old modelKirsten 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... - Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysisKim 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.... - Construction and application of a zebrafish array comparative genomic hybridization platformJennifer 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... - Regulatory element copy number differences shape primate expression profilesRebecca 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... - Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selectionOmer 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... - Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studiesArthur 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... - Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancerScott 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... - On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association testIuliana 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... - Structural variation in the human genome: the impact of copy number variants on clinical diagnosisLaia 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... - Copy number variation: new insights in genome diversityJennifer 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... - Definition of the zebrafish genome using flow cytometry and cytogenetic mappingJennifer 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... - EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancerJussi 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... - Genetic association analysis of copy-number variation (CNV) in human disease pathogenesisIuliana 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... - Genetic variation of genes involved in dihydrotestosterone metabolism and the risk of prostate cancerSunita 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... - EGFR mutation is a better predictor of response to tyrosine kinase inhibitors in non-small cell lung carcinoma than FISH, CISH, and immunohistochemistryLynette 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... - Disseminated peritoneal leiomyomatosis after laparoscopic supracervical hysterectomy with characteristic molecular cytogenetic findings of uterine leiomyomaZehra 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.... - Alu elements mediate MYB gene tandem duplication in human T-ALLJennifer 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... - Reporting of diagnostic cytogenetic resultsAzra 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... - Structural genomic variation and personalized medicineCharles Lee
Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
N Engl J Med 358:740-1. 2008 - Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanomaLevi 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... - XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient miceCatherine 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.... - A zebrafish bmyb mutation causes genome instability and increased cancer susceptibilityJennifer 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... - Common deletion polymorphisms in the human genomeSteven A McCarroll
Department of Molecular Biology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA
Nat Genet 38:86-92. 2006.... - Mapping copy number variation by population-scale genome sequencingRyan 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... - Histone H2AX: a dosage-dependent suppressor of oncogenic translocations and tumorsCraig 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... - Molecular cytogenetic methodologies and a BAC probe panel resource for genomic analyses in the zebrafishKimberly 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.... - The fine-scale and complex architecture of human copy-number variationGeorge 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... - Detecting copy number variation in the human genome using comparative genomic hybridizationJoelle 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... - Comparison of familial and sporadic chronic lymphocytic leukaemia using high resolution array comparative genomic hybridizationSunita 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... - Integrating common and rare genetic variation in diverse human populationsDavid M Altshuler
Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA
Nature 467:52-8. 2010.... - Characterization of familial Waldenstrom's macroglobulinemiaS 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... - Exploring the role of copy number variants in human adaptationRebecca 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... - Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integrationColby Chiang
Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
Nat Genet 44:390-7, S1. 2012.... - Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomaliesDavid 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... - The clinical context of copy number variation in the human genomeCharles 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... - Molecular cytogenetic methodologies and a bacterial artificial chromosome (BAC) probe panel resource for genomic analyses in zebrafishCharles Lee
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
Methods Cell Biol 77:241-54. 2004 - Detection of large-scale variation in the human genomeA 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... - Limitations of chromosome classification by multicolor karyotypingC 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... - Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergenceOmer Gokcumen
Department of Pathology, Brigham and Women s Hospital, Boston, Massachusetts, United States of America Harvard Medical School, 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... - A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic responseZhao Chen
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 483:613-7. 2012.... - Genomic alterations in myeloid neoplasms with novel, apparently balanced translocationsJennifer 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... - Germ cell aneuploidy in zebrafish with mutations in the mitotic checkpoint gene mps1Kenneth D Poss
Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Genes Dev 18:1527-32. 2004.... - 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 hybridizationIrina 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... - Copy number variants (CNVs) in primate species using array-based comparative genomic hybridizationOmer 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.... - MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signalingJeffrey 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... - Findings from aCGH in patients with congenital diaphragmatic hernia (CDH): a possible locus for Fryns syndromeS 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... - Landscape of somatic retrotransposition in human cancersEunjung Lee
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
Science 337:967-71. 2012.... - Tumor Archaeology Reveals that Mutations Love CompanySunita 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... - BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in the genesis of melanomaE Elizabeth Patton
Howard Hughes Medical Institute, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
Curr Biol 15:249-54. 2005.... - Cell-specific mitotic defect and dyserythropoiesis associated with erythroid band 3 deficiencyBarry 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... - Copy number variants and pharmacogenomicsKarim 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... - Multicolor Fluorescence In Situ Hybridization (FISH) approaches for simultaneous analysis of the entire human genomeC 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... - Prenatal diagnosis and molecular cytogenetics in a case of partial trisomy 14 and monosomy 21C 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... - Genomic structure, functional comparison, and tissue distribution of mouse Cd59a and Cd59bX 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... - TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohortF 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... - Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletionsN 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... - Identification and characterization of a novel polycystin family member, polycystin-L2, in mouse and human: sequence, expression, alternative splicing, and chromosomal localizationL 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... - Linkage to chromosome 2q36.1 in autosomal dominant Dandy-Walker malformation with occipital cephalocele and evidence for genetic heterogeneityAli 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... - Relative impact of nucleotide and copy number variation on gene expression phenotypesBarbara 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... - Global variation in copy number in the human genomeRichard 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... - Accurate and reliable high-throughput detection of copy number variation in the human genomeHeike 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... - Hotspots for copy number variation in chimpanzees and humansGeorge 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... - Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVsJoshua 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... - Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arraysDaisuke Komura
Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
Genome Res 16:1575-84. 2006.... - Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridizationMi-Young Kim
Department of Microbiology, College of Medicine, Catholic University of Korea, Socho-gu, Seoul, Korea
Gastroenterology 131:1913-24. 2006..Our results and analysis strategy will be helpful to elucidate pathogenesis of CRCs or to develop biomarkers for predicting prognosis... - Completing the map of human genetic variationEvan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nature 447:161-5. 2007 - Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocationsChengming 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... - Multicolor karyotypic interpretation of a heterochromatin-associated marker chromosome in a dysmorphic girl with developmental delayJonathan D Picker
Am J Med Genet 110:393-6. 2002 - Challenges and standards in integrating surveys of structural variationStephen 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... - The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemiaPieter 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... - Adaptive evolution of UGT2B17 copy-number variationYali 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... - Genetics: copies countJoseph H Nadeau
Nature 439:798-9. 2006 - EMBL Nucleotide Sequence Database: developments in 2005Guy 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... - Vive la difference!Charles Lee
Nat Genet 37:660-1. 2005 - Temporal profile of replication of human chromosomesYesu 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... - 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 assayAmy E Roberts
Am J Med Genet A 130:204-7. 2004 - Diet and the evolution of human amylase gene copy number variationGeorge 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... - Genome assembly comparison identifies structural variants in the human genomeRazi 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...
Research Grants
- Copy number variation in the human genomeCharles 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. ..
- Molecular Cytogenetic Tools for the ZebrafishCharles 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. ..
- Characterization and Evolution of Copy Number Variation Among PrimatesCharles 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. ..