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  • Oligonucleotide Array Sequence Analysis  (2)
  • *Chromosome Aberrations  (1)
  • 1
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    Complex landscapes of somatic rearrangement in human breast cancer genomes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-25
    Description: Multiple somatic rearrangements are often found in cancer genomes; however, the underlying processes of rearrangement and their contribution to cancer development are poorly characterized. Here we use a paired-end sequencing strategy to identify somatic rearrangements in breast cancer genomes. There are more rearrangements in some breast cancers than previously appreciated. Rearrangements are more frequent over gene footprints and most are intrachromosomal. Multiple rearrangement architectures are present, but tandem duplications are particularly common in some cancers, perhaps reflecting a specific defect in DNA maintenance. Short overlapping sequences at most rearrangement junctions indicate that these have been mediated by non-homologous end-joining DNA repair, although varying sequence patterns indicate that multiple processes of this type are operative. Several expressed in-frame fusion genes were identified but none was recurrent. The study provides a new perspective on cancer genomes, highlighting the diversity of somatic rearrangements and their potential contribution to cancer development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398135/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398135/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stephens, Philip J -- McBride, David J -- Lin, Meng-Lay -- Varela, Ignacio -- Pleasance, Erin D -- Simpson, Jared T -- Stebbings, Lucy A -- Leroy, Catherine -- Edkins, Sarah -- Mudie, Laura J -- Greenman, Chris D -- Jia, Mingming -- Latimer, Calli -- Teague, Jon W -- Lau, King Wai -- Burton, John -- Quail, Michael A -- Swerdlow, Harold -- Churcher, Carol -- Natrajan, Rachael -- Sieuwerts, Anieta M -- Martens, John W M -- Silver, Daniel P -- Langerod, Anita -- Russnes, Hege E G -- Foekens, John A -- Reis-Filho, Jorge S -- van 't Veer, Laura -- Richardson, Andrea L -- Borresen-Dale, Anne-Lise -- Campbell, Peter J -- Futreal, P Andrew -- Stratton, Michael R -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- CA089393/CA/NCI NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1005-10. doi: 10.1038/nature08645.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033038" target="_blank"〉PubMed〈/a〉
    Keywords: Breast Neoplasms/*genetics ; Cell Line, Tumor ; Cells, Cultured ; *Chromosome Aberrations ; DNA Breaks ; Female ; Gene Rearrangement/*genetics ; Genome, Human/*genetics ; Genomic Library ; Humans ; Sequence Analysis, DNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Complete genome sequence and lytic phase transcription profile of a Coccolithovirus (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-08-16
    Description: The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Among the 472 predicted genes of the 407,339-base pair genome are a variety of unexpected genes, most notably those involved in biosynthesis of ceramide, a sphingolipid known to induce apoptosis. Uniquely for algal viruses, it also contains six RNA polymerase subunits and a novel promoter, suggesting this virus encodes its own transcription machinery. Microarray transcriptomic analysis reveals that 65% of the predicted virus-encoded genes are expressed during lytic infection of E. huxleyi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, William H -- Schroeder, Declan C -- Allen, Michael J -- Holden, Matthew T G -- Parkhill, Julian -- Barrell, Bart G -- Churcher, Carol -- Hamlin, Nancy -- Mungall, Karen -- Norbertczak, Halina -- Quail, Michael A -- Price, Claire -- Rabbinowitsch, Ester -- Walker, Danielle -- Craigon, Marie -- Roy, Douglas -- Ghazal, Peter -- New York, N.Y. -- Science. 2005 Aug 12;309(5737):1090-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. whw@pml.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16099989" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis ; Base Composition ; Ceramides/biosynthesis ; Computational Biology ; DNA, Viral/chemistry/genetics ; DNA-Directed RNA Polymerases/genetics ; Eukaryota/virology ; Gene Expression ; Gene Expression Profiling ; Genes, Viral ; *Genome, Viral ; Oligonucleotide Array Sequence Analysis ; Peptide Hydrolases/genetics ; Phycodnaviridae/classification/*genetics/*physiology ; Promoter Regions, Genetic ; Protein Subunits ; *Sequence Analysis, DNA ; Sphingolipids/biosynthesis ; *Transcription, Genetic ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-08
    Description: Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hall, Neil -- Karras, Marianna -- Raine, J Dale -- Carlton, Jane M -- Kooij, Taco W A -- Berriman, Matthew -- Florens, Laurence -- Janssen, Christoph S -- Pain, Arnab -- Christophides, Georges K -- James, Keith -- Rutherford, Kim -- Harris, Barbara -- Harris, David -- Churcher, Carol -- Quail, Michael A -- Ormond, Doug -- Doggett, Jon -- Trueman, Holly E -- Mendoza, Jacqui -- Bidwell, Shelby L -- Rajandream, Marie-Adele -- Carucci, Daniel J -- Yates, John R 3rd -- Kafatos, Fotis C -- Janse, Chris J -- Barrell, Bart -- Turner, C Michael R -- Waters, Andrew P -- Sinden, Robert E -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):82-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK. nhall@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637271" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Anopheles/parasitology ; Computational Biology ; Evolution, Molecular ; Gene Expression Profiling ; Gene Silencing ; Genes, Protozoan ; *Genome, Protozoan ; *Life Cycle Stages ; Malaria/parasitology ; Oligonucleotide Array Sequence Analysis ; Plasmodium/*genetics/*growth & development/metabolism ; Plasmodium berghei/genetics/growth & development/metabolism ; Plasmodium chabaudi/genetics/growth & development/metabolism ; Plasmodium falciparum/genetics/growth & development/metabolism ; Plasmodium yoelii/genetics/growth & development/metabolism ; Proteome/*analysis ; Proteomics ; Protozoan Proteins/analysis ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; Selection, Genetic ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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