- 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...
- Effect of crizotinib on overall survival in patients with advanced non-small-cell lung cancer harbouring ALK gene rearrangement: a retrospective analysis
Alice T Shaw
Massachusetts General Hospital Cancer Center, Boston, MA, USA
Lancet Oncol 12:1004-12. 2011
ALK gene rearrangement defines a new molecular subtype of non-small-cell lung cancer (NSCLC)...
- A microhomology-mediated break-induced replication model for the origin of human copy number variation
P J Hastings
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
PLoS Genet 5:e1000327. 2009
- Comprehensive histologic analysis of ALK-rearranged lung carcinomas
Pathology and Clinical Laboratory Division, National Cancer Center Hospital, Tokyo, Japan
Am J Surg Pathol 35:1226-34. 2011
..ALK-positive cancers commonly showed coexpression of thyroid transcription factor-1 and p63, and its significance is currently unclear...
- A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
Jennifer A Lee
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, 77030, USA
Cell 131:1235-47. 2007
..We propose that complex duplication and deletion rearrangements associated with PMD, and potentially other nonrecurrent rearrangements, may be explained by this replication-based mechanism...
- Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Wigard P Kloosterman
Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands
Genome Biol 12:R103. 2011
..The significance of these clusters for tumor development or metastatic spread is largely unclear...
- Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae)
Ocean Research Institute, University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
J Mol Evol 59:287-97. 2004
..the complete nucleotide sequence of the mitogenome for a parrotfish, Chlorurus sordidus, and found a gene rearrangement accompanied by a tRNA pseudogene...
- PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia
CNRS FRE 3144, Centre de Genetique Moleculaire, Gif sur Yvette F 91198 Cedex, France
Genes Dev 23:2478-83. 2009
..This is the first in vivo evidence suggesting an essential endonucleolytic function of a domesticated piggyBac transposase...
- Complex landscapes of somatic rearrangement in human breast cancer genomes
Philip J Stephens
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 462:1005-10. 2009
..The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development...
- Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species
Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita di Milano, Milano, Italy
Heredity (Edinb) 101:301-20. 2008
..Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups...
- Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements
Andrew J Holland
Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
Nat Med 18:1630-8. 2012
..Complex rearrangements are present in a broad spectrum of tumors and in individuals with congenital or developmental defects, highlighting the impact of chromoanagenesis on human disease...
- Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline
Wigard P Kloosterman
Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
Hum Mol Genet 20:1916-24. 2011
..We conclude that a similar mechanism may also drive the formation of de novo structural variation in the germline...
- EML4-ALK rearrangement in non-small cell lung cancer and non-tumor lung tissues
Maria Paola Martelli
Institute of Hematology, University of Perugia, Perugia, Italy
Am J Pathol 174:661-70. 2009
..The EML4-ALK transcript cannot be regarded as a specific diagnostic tool for NSCLC. Our results show therefore that the causal role and value of EML4-ALK as a therapeutic target remain to be defined...
- Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients
INSERM U892, Universite de Nantes, Nantes, France
Blood 118:675-8. 2011
..3% of samples. Moreover, this catastrophic event confers a poor outcome. Because chromothripsis appears to occur in a single crisis, our results suggest that high-risk MM patients use this novel way of cancer evolution...
- TMPRSS2-ERG gene fusion is not associated with outcome in patients treated by prostatectomy
Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
Cancer Res 69:1400-6. 2009
..We analyzed TMPRSS2-ERG gene rearrangement status by fluorescence in situ hybridization in 521 cases of clinically localized surgically treated ..
- Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar
Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Hiroshima, Japan
Mol Biol Evol 25:874-91. 2008
..be mediated by a replication fork barrier lying in the CR; 3) general recombination has a potential to cause gene rearrangement in upstream regions of multiple CRs as the results of gene conversion and unequal crossing over processes...
- Multiplex reverse transcription-PCR screening for EML4-ALK fusion transcripts
Division of Pathology, The Cancer Institute, Tokyo, Japan
Clin Cancer Res 14:6618-24. 2008
..To allow sensitive detection of EML4-ALK fusion transcripts, we have now developed a multiplex reverse transcription-PCR (RT-PCR) system that captures all in-frame fusions between the two genes...
- High-resolution characterization of a hepatocellular carcinoma genome
Division of Cancer Genomics, National Cancer Center Research Institute, Chuo Ku, Tokyo, Japan
Nat Genet 43:464-9. 2011
- The biology and treatment of EML4-ALK non-small cell lung cancer
Lowe Center for Thoracic Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
Eur J Cancer 46:1773-80. 2010
..This review will focus on the biology, clinical characteristics, diagnosis and treatment of EML4-ALK NSCLC...
- Update and analysis of the University College London low density lipoprotein receptor familial hypercholesterolemia database
S E A Leigh
Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, The Rayne Building, Royal Free and University College London Medical School, London WC1E 6JJ, UK
Ann Hum Genet 72:485-98. 2008
- Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders
Rachel Lockridge Mueller
Museum of Vertebrate Zoology, University of California, Berkeley, USA
Mol Biol Evol 22:2104-12. 2005
Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae)...
- The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
Nat Genet 41:849-53. 2009
..The FoSTeS/MMBIR mechanism can explain both the gene duplication-divergence hypothesis and exon shuffling, suggesting an important role in both genome and single-gene evolution...
- DNA elimination in ciliates: transposon domestication and genome surveillance
Douglas L Chalker
Department of Biology, Washington University, St Louis, Missouri 63130, USA
Annu Rev Genet 45:227-46. 2011
..This DNA elimination pathway in ciliates shares extensive similarity with piRNA-mediated silencing of metazoans and highlights the remarkable ability of homologous RNAs to shape developing genomes...
- Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates
Departement de Biochimie, Faculte de Medecine, Universite de Montreal, Quebec, Canada
J Mol Biol 212:599-634. 1990
..These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level...
- Correlation of IHC and FISH for ALK gene rearrangement in non-small cell lung carcinoma: IHC score algorithm for FISH
Eunhee S Yi
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
J Thorac Oncol 6:459-65. 2011
Accurate, cost-effective methods for testing anaplastic lymphoma kinase gene rearrangement (ALK+) are needed to select patients with non-small cell lung carcinoma for ALK-inhibitor therapy...
- Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Peter J Campbell
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nat Genet 40:722-9. 2008
..The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy...
- Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Axel M Hillmer
Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
Genome Res 21:665-75. 2011
- Screening of anaplastic lymphoma kinase rearrangement by immunohistochemistry in non-small cell lung cancer: correlation with fluorescence in situ hybridization
Jin Ho Paik
Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Gyeunggi do, South Korea
J Thorac Oncol 6:466-72. 2011
..There are no universally accepted, evidence-based guidelines on identifying patients with ALK-rearranged lung cancer using IHC...
- Complex human chromosomal and genomic rearrangements
Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children s Hospital, Houston, TX 77030, USA
Trends Genet 25:298-307. 2009
- Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss
Dennis V Lavrov
Department of Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 19:163-9. 2002
..The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons...
- Comparisons among two fertile and three male-sterile mitochondrial genomes of maize
James O Allen
Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
Genetics 177:1173-92. 2007
..This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C...
- A fluorescence in situ hybridization screen for E26 transformation-specific aberrations: identification of DDX5-ETV4 fusion protein in prostate cancer
Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
Cancer Res 68:7629-37. 2008
..Fourth, we identified a ubiquitously expressed, androgen-insensitive gene, DDX5, fused in frame with ETV4, leading to the expression of a DDX5-ETV4 fusion protein...
- Mitochondrial genomes of two Barklice, Psococerastis albimaculata and Longivalvus hyalospilus (Psocoptera: Psocomorpha): contrasting rates in mitochondrial gene rearrangement between major lineages of Psocodea
Department of Entomology, China Agricultural University, Beijing, China
PLoS ONE 8:e61685. 2013
..We conclude that mt gene rearrangement has been substantially faster in the lineage leading to the booklice and the parasitic lice than in the ..
- Recent segmental duplications in the human genome
Jeffrey A Bailey
Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
Science 297:1003-7. 2002
..Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity...
- Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Cell 110:689-99. 2002
..We propose that these small RNAs function to specify sequences to be eliminated by a mechanism similar to RNA-mediated gene silencing...
- Correlations between the percentage of tumor cells showing an anaplastic lymphoma kinase (ALK) gene rearrangement, ALK signal copy number, and response to crizotinib therapy in ALK fluorescence in situ hybridization-positive nonsmall cell lung cancer
D Ross Camidge
University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
Cancer 118:4486-94. 2012
..Increased copy numbers of fused and rearranged signals also occur. Here, correlations are explored between the percentage of ALK+ cells and signal copy number and their association with response to ALK inhibition...
- Inference and analysis of the relative stability of bacterial chromosomes
Eduardo P C Rocha
Unité Génétique des Génomes Bactériens, Institut Pasteur, Paris, France and Atelier de BioInformatique, Universite Pierre et Marie Curie Paris VI, Paris, France
Mol Biol Evol 23:513-22. 2006
..Hence, although this method has allowed uncovering some of mechanisms leading to rearrangements, we still ignore the forces that differentially shape selection upon genome stability in different species...
- ND6 gene "lost" and found: evolution of mitochondrial gene rearrangement in Antarctic notothenioids
Department of Animal Biology, University of Illinois at Urbana Champaign, IL, USA
Mol Biol Evol 27:1391-403. 2010
- Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): notable differences in gene arrangement
Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780 8520, Japan
Gene 476:27-37. 2011
..Our results support the validity of the morphological classification that separated the family Coralliidae into two genera, Corallium and Paracorallium...
- Sessile snails, dynamic genomes: gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs
Timothy A Rawlings
Cape Breton University, 1250 Grand Lake Road, Sydney, NS B1P 6L2, Canada
BMC Genomics 11:440. 2010
- Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)
Department of Zoology and Developmental Biology, Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
BMC Genomics 9:610. 2008
..genomes, but in the suborder Heteroptera (Insecta: Hemiptera), there was only one complete mitochondrial genome sequenced without gene rearrangement and the phylogeny of infraorder Pentatomomorpha in Heteroptera was still uncertain.
- Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia
Anne Le Mouël
Laboratoire de Genetique Moleculaire, CNRS UMR 8541, Ecole Normale Superieure, 75005 Paris, France
Eukaryot Cell 2:1076-90. 2003
- Evolutionary and biomedical insights from the rhesus macaque genome
Richard A Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 316:222-34. 2007
..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
- Detection of ALK gene rearrangement in non-small cell lung cancer: a comparison of fluorescence in situ hybridization and chromogenic in situ hybridization with correlation of ALK protein expression
Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
J Thorac Oncol 6:1359-66. 2011
..This study evaluates the concordance between ALK gene rearrangement in non-small cell lung cancer assessed by ALK FISH and a newly developed ALK chromogenic in situ ..
- Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila
Colin D Malone
Biology Department, Washington University, St Louis, MO 63130, USA
Mol Cell Biol 25:9151-64. 2005
- Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia
Ecole Normale Superieure, Laboratoire de Genetique Moleculaire, Centre 75005 Paris, France
Genes Dev 22:1501-12. 2008
- Efficient sorting of genomic permutations by translocation, inversion and block interchange
The Feinstein Institute for Medical Research North Shore LIJ Health System, Manhasset, NY 11030, USA
Bioinformatics 21:3340-6. 2005
..We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form...
- MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia
Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
Blood 119:2110-3. 2012
..This study underscores the importance of miR-650 in CLL biology and normal B-cell physiology...
- Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications
Institute of Evolutionary Biology and Ecology, Rheinische Friedrich Wilhelms Universitat Bonn, Bonn, Germany
Mol Phylogenet Evol 64:106-17. 2012
..In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context...
- Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)
Jan Y Poulsen
Natural History Collections, University Museum of Bergen, University of Bergen, Allegaten 41, P O Box 7800, Bergen N 5020, Norway
BMC Evol Biol 13:111. 2013
..This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements...
- Nowa1p and Nowa2p: novel putative RNA binding proteins involved in trans-nuclear crosstalk in Paramecium tetraurelia
Laboratoire de Genetique Moleculaire, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8541, Ecole Normale Superieure, 46 rue d Ulm, 75005 Paris, France
Curr Biol 15:1616-28. 2005
- Histologic and cytomorphologic features of ALK-rearranged lung adenocarcinomas
Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
Mod Pathol 25:1462-72. 2012
..However, morphologic screening alone will not detect a minority of ALK+ lung adenocarcinomas, and the routine use of ancillary studies may be warranted to identify all patients who may benefit from crizotinib treatment...
- The Bruton's tyrosine kinase gene is expressed throughout B cell differentiation, from early precursor B cell stages preceding immunoglobulin gene rearrangement up to mature B cell stages
M De Weers
Department of Immunohematology, University Hospital, The Netherlands
Eur J Immunol 23:3109-14. 1993
..from early precursor-B cell stages preceding Ig rearrangement up to mature B cells, supports the hypothesis that the XLA defect resides in a critical step of B cell development which is independent of the Ig gene recombination machinery...
- Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma
INSERM U830, Institut Curie, Centre de Recherche, Paris, France
Cancer Res 73:195-204. 2013
..These results indicate that genomic rearrangements constitute an alternative mechanism to ALK point mutations resulting in receptor activation...
- Identification of targetable FGFR gene fusions in diverse cancers
Yi Mi Wu
Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E Medical Center Drive 5316 CCGC, Ann Arbor, MI 48109 5940, USA
Cancer Discov 3:636-47. 2013
- Radiosensitive SCID patients with Artemis gene mutations show a complete B-cell differentiation arrest at the pre-B-cell receptor checkpoint in bone marrow
Jeroen G Noordzij
Department of Immunology, Erasmus MC University Medical Center Rotterdam, The Netherlands
Blood 101:1446-52. 2003
..The completeness of this arrest illustrates the importance of Artemis at this stage of lymphoid differentiation...
- Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer
Department of Medicine and Genome Sciences, University of Washington, Seattle, WA 98195 7720, USA
JAMA 295:1379-88. 2006
..Furthermore, other breast cancer genes generally are not evaluated...
- A functional role for transposases in a large eukaryotic genome
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
Science 324:935-8. 2009
..This study suggests a new important role in Oxytricha for this large portion of genomic DNA that was previously thought of as junk...
- Complete nucleotide sequence of the mitochondrial genome of Schlegel's tree frog Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements
Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
Genes Genet Syst 80:213-24. 2005
..schlegelii and B. buergeri. Based on parsimonious consideration and the basal phylogenetic position of B. buergeri, these genes seemed to have been rearranged in an ancestral lineage leading to Rh. schlegelii...
- Recovering genome rearrangements in the mammalian phylogeny
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore
Genome Res 19:934-42. 2009
..Together, this substantiates the model that regions of high sequence identity have been associated with rearrangement events throughout the mammalian phylogeny...
- Hsp-27 expression at diagnosis predicts poor clinical outcome in prostate cancer independent of ETS-gene rearrangement
C S Foster
Division of Cellular Pathology and Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
Br J Cancer 101:1137-44. 2009
..This study was performed to test the hypothesis that expression of small heat shock protein Hsp-27 is, at diagnosis, a reliable predictive biomarker of clinically aggressive prostate cancer...
- Identification and characterization of a novel MLH1 genomic rearrangement as the cause of HNPCC in a Tunisian family: evidence for a homologous Alu-mediated recombination
Sana Aissi-Ben Moussa
Laboratoire de Biochimie et Biologie Moleculaire, Faculte des Sciences de Tunis, Tunis, Tunisia
Fam Cancer 8:119-26. 2009
..This germline MLH1 rearrangement was associated to a severe phenotype in this family. This is the first report of a molecular analysis in a Tunisian family with HNPCC...
- Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families
Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 2nd Floor, Outpatient Centre, 1 Jalan SS12 1A, Subang Jaya, 47500, Selangor, Malaysia
Breast Cancer Res Treat 124:579-84. 2010
..In conclusion, this study in a multi-ethnic (Malay, Chinese, Indian) cohort suggests that large genomic rearrangements are present at a low frequency but should nonetheless be included in the routine testing for BRCA1 and BRCA2...
- Stability of related human and chicken Campylobacter jejuni genotypes after passage through chick intestine studied by pulsed-field gel electrophoresis
M L Hänninen
Department of Food and Environmental Hygiene, The Haartman Institute, 00231 Helsinki, Finland
Appl Environ Microbiol 65:2272-5. 1999
..Serotype 27 of strain BTI remained stable. Our study suggests that during intestinal colonization, genomic rearrangement, as demonstrated by changed PFGE and ribopatterns, may occur...
- Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat
Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA
BMC Genomics 9:S25. 2008
..Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction...
- The endless tale of non-homologous end-joining
Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center, 2201 Inwood Road, Dallas, TX 75390 9187, USA
Cell Res 18:114-24. 2008
..In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented...
- Dermatofibrosarcoma protuberans COL1A1-PDGFB fusion is identified in virtually all dermatofibrosarcoma protuberans cases when investigated by newly developed multiplex reverse transcription polymerase chain reaction and fluorescence in situ hybridization
Kayuri U Patel
Department of Pathology at Texas Children s Hospital and Baylor College of Medicine, Houston, TX 77030, USA
Hum Pathol 39:184-93. 2008
..Its detection may be particularly helpful in the differential diagnosis of atypical, fibrosarcomatous, and metastatic DFSP...
- ERG gene rearrangement status in prostate cancer detected by immunohistochemistry
Sara Moscovita Falzarano
Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
Virchows Arch 459:441-7. 2011
..Given the high yield and the easier task of performing immunohistochemistry vs. FISH, ERG assessment by immunohistochemistry may be useful for characterizing ERG status in prostate cancer...
- Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster
Department of Earth and Planetary Sciences, Nagoya University, Japan
Mol Biol Evol 13:1242-54. 1996
..The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs...
- The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences
CNRS UPR3404 Centre de Génétique Moléculaire, Gif sur Yvette, France
PLoS Genet 8:e1002984. 2012
- ALK-positive large B-cell lymphomas with cryptic SEC31A-ALK and NPM1-ALK fusions
Katrien Van Roosbroeck
Center for Human Genetics, K U Leuven, Gasthuisberg, Herestraat 49, Box 602, B 3000 Leuven, Belgium
Haematologica 95:509-13. 2010
- Insertion sequence-driven evolution of Escherichia coli in chemostats
Laboratoire Adaptation et Pathogenie des Microorganismes, Universite Joseph Fourier Grenoble 1, BP 170, 38042, Grenoble Cedex 9, France
J Mol Evol 72:398-412. 2011
..Therefore, IS elements strongly influenced the evolutionary processes in continuous E. coli cultures by providing a way to modify both the global regulatory network and the mutation rates of evolving cells...
- Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm
Pablo A Quijada
Plant Breeding and Plant Genetics Program, and Department of Agronomy, University of Wisconsin, Madison, WI 53706, USA
Theor Appl Genet 113:549-61. 2006
..napus and could account for a portion of the heterotic effects in hybrids...
- Molecular and clinical analysis of locally advanced dermatofibrosarcoma protuberans treated with imatinib: Imatinib Target Exploration Consortium Study B2225
Grant A McArthur
Peter MacCallum Cancer Centre, East Melbourne, Australia
J Clin Oncol 23:866-73. 2005
..The purpose of this study was to evaluate molecular, cytogenetic, and kinase activation profiles in a series of DFSPs and to determine whether these biologic parameters are correlated with the clinical responses of DFSP to imatinib...
- Activity of IPI-504, a novel heat-shock protein 90 inhibitor, in patients with molecularly defined non-small-cell lung cancer
Lecia V Sequist
Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
J Clin Oncol 28:4953-60. 2010
..We studied the activity of IPI-504 after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) therapy in patients with advanced, molecularly defined non-small-cell lung cancer (NSCLC)...
- Selection upon genome architecture: conservation of functional neighborhoods with changing genes
Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe CIPF, Valencia, Spain
PLoS Comput Biol 6:e1000953. 2010
..The picture arising from this study is a dynamic genomic landscape with a high level of functional organization...
- Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
Genome Res 18:1814-28. 2008
..Alignments from our pipeline are publicly available within the Ensembl genome browser...
- Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution
Children s Hospital and Research Center Oakland, Oakland, California, United States of America
PLoS Genet 5:e1000538. 2009
..The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution...
- Defining regions and rearrangements of the Silene latifolia Y chromosome
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, United Kingdom
Genetics 178:2045-53. 2008
..Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes...
- Large genomic rearrangements of the BRCA1 and BRCA2 genes: review of the literature and report of a novel BRCA1 mutation
Michelle D Sluiter
Department of Genetics, University of Pretoria, Pretoria, 0001, South Africa
Breast Cancer Res Treat 125:325-49. 2011
..Furthermore, we have clarified some of the previously misunderstood rules of nomenclature, which will make uniform reporting of BRCA1/2 easier in the future...
- T-cell receptor excision circle and T-cell dynamics after allogeneic stem cell transplantation are related to clinical events
Mette D Hazenberg
Department of Clinical Viro Immunology, CLB Sanquin, Amsterdam, The Netherlands
Blood 99:3449-53. 2002
- Breakpoint graphs and ancestral genome reconstructions
Max A Alekseyev
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0404, USA
Genome Res 19:943-57. 2009
..MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown...
- EWSR1-POU5F1 fusion in soft tissue myoepithelial tumors. A molecular analysis of sixty-six cases, including soft tissue, bone, and visceral lesions, showing common involvement of the EWSR1 gene
Cristina R Antonescu
Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York City, NY 10021, USA
Genes Chromosomes Cancer 49:1114-24. 2010
..A few reports have indicated EWSR1 gene rearrangement in soft tissue ME tumors, and, in one case each, the fusion partner was identified as either PBX1 or ZNF444...
- Genetic variation: molecular mechanisms and impact on microbial evolution
Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056, Basel, Switzerland
FEMS Microbiol Rev 24:1-7. 2000
..Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction...
- ALK-positive diffuse large B-cell lymphoma is associated with Clathrin-ALK rearrangements: report of 6 cases
Randy D Gascoyne
Department of Oncogeneiss and Signaling in Hematopoietic Cells, Instiut National de la Santé et de la Recherche Médicale U 563, Centre de Physiopatholgie de Toulouse Purpan, France
Blood 102:2568-73. 2003
- Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome
Jonathan L Gordon
Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
PLoS Genet 5:e1000485. 2009
..Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources...
- Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication
Jeong Hwan Mun
Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin ro, Gwonseon gu, Suwon 441 707, Korea
Genome Biol 10:R111. 2009
..rapa, which is a strong challenge of structural and comparative crop genomics...
- Genome dynamics of Campylobacter jejuni in response to bacteriophage predation
Andrew E Scott
Division of Food Sciences, University of Nottingham, Loughborough, United Kingdom
PLoS Pathog 3:e119. 2007
..jejuni exists in vivo as families of related meta-genomes generated to survive local environmental pressures...
- S locus genes and the evolution of self-fertility in Arabidopsis thaliana
Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
Plant Cell 19:94-106. 2007
..Furthermore, analysis of SRK and SCR polymorphisms in these accessions argues against the occurrence of a selective sweep of a particular allele of SCR, as previously proposed...
- Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491
The Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nature 404:502-6. 2000
..Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen...
- Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros
Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
Nat Immunol 9:927-36. 2008
..Thus, Ikaros is an obligate component of a network that regulates B cell fate commitment and immunoglobulin heavy-chain gene recombination...
- Remembrance of things past retrieved from the Paramecium genome
Centre de Genetique Moleculaire, CNRS UPR3404, Avenue de la Terrasse, 91198 Gif sur Yvette, France
Res Microbiol 162:587-97. 2011
- Dual IHC and FISH testing for ALK gene rearrangement in lung adenocarcinomas in a routine practice: a French study
Plateforme hospitalière de Génétique Moléculaire des Cancers, Department of Hematology, Onco Genetics and Immunology, Päle de Biologie et de Pathologie, CHU A Michallon, Grenoble, France
J Thorac Oncol 7:348-54. 2012
- Alternative mutations of BRAF, RET and NTRK1 are associated with similar but distinct gene expression patterns in papillary thyroid cancer
Department of Pathology, Experimental Molecular Pathology, Istituto Nazionale Tumori, Milan, Italy
Oncogene 23:7436-40. 2004
..However, a supervised analysis of the obtained data identified a subset of genes differentially expressed in tumors carrying BRAF mutation or RTK rearrangement...
- Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda
Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
Genome Biol Evol 2:425-40. 2010
..The same analyses also recover monophyly of traditionally recognized arthropod lineages such as Arachnida and of the highly debated clade Mandibulata...
- A novel method for interpretation of T-cell receptor gamma gene rearrangement assay by capillary gel electrophoresis based on normal distribution
Frank C Kuo
Department of Pathology, Brigham and Women s Hospital, 75 Francis Street, Boston, MA 02115, USA
J Mol Diagn 9:12-9. 2007
T-cell receptor gamma (TRG) gene rearrangement status is useful for the differential diagnosis of T-cell lesions...
- Multichromosomal median and halving problems under different genomic distances
INRIA Rhone Alpes, Inovallée, Montbonnot, Saint Ismier Cedex, France
BMC Bioinformatics 10:120. 2009
- Recurrent chromosomal rearrangements at bands 8q24 and 11q13 in gastric cancer as detected by multicolor spectral karyotyping
Department of Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, Kawaramachi Hirokoji, Kamigyo ku, Kyoto 602 8566, Japan
World J Gastroenterol 11:5129-35. 2005
..To identify chromosomal translocations specific to gastric cancer (GC), spectral karyotyping (SKY) analysis was performed on established cell lines and cancerous ascitic fluids...
- Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome
Centre Rene Huguenin, Laboratoire d oncogénétique, Institut Nationale de la Santé et de la Recherche Médicale INSERM U735, Saint Cloud, France
Hum Mutat 30:867-75. 2009
..In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided...
- Favorable response to crizotinib in three patients with echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase fusion-type oncogene-positive non-small cell lung cancer
Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, Osaka, Japan
Cancer Sci 102:1602-4. 2011
..In the present study, we report on three cases harboring EML4-ALK rearrangement who were enrolled in the trial (A8081001, NCT00585195). All three patients showed favorable responses to the ALK-specific tyrosine kinase inhibitor...
- The evolution of adaptive immune systems
Max D Cooper
Division of Developmental and Clinical Immunology, Departments of Medicine, Microbiology, Pediatrics, and Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Cell 124:815-22. 2006
..The convergent evolution of these remarkably different adaptive immune systems involved innovative genetic modification of innate-immune-system components...