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  • 1
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    Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-01-21
    Description: The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of approximately 3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A), JARID1C (also known as KDM5C) and SETD2 (ref. 2). These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030920/" 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/PMC3030920/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Varela, Ignacio -- Tarpey, Patrick -- Raine, Keiran -- Huang, Dachuan -- Ong, Choon Kiat -- Stephens, Philip -- Davies, Helen -- Jones, David -- Lin, Meng-Lay -- Teague, Jon -- Bignell, Graham -- Butler, Adam -- Cho, Juok -- Dalgliesh, Gillian L -- Galappaththige, Danushka -- Greenman, Chris -- Hardy, Claire -- Jia, Mingming -- Latimer, Calli -- Lau, King Wai -- Marshall, John -- McLaren, Stuart -- Menzies, Andrew -- Mudie, Laura -- Stebbings, Lucy -- Largaespada, David A -- Wessels, L F A -- Richard, Stephane -- Kahnoski, Richard J -- Anema, John -- Tuveson, David A -- Perez-Mancera, Pedro A -- Mustonen, Ville -- Fischer, Andrej -- Adams, David J -- Rust, Alistair -- Chan-on, Waraporn -- Subimerb, Chutima -- Dykema, Karl -- Furge, Kyle -- Campbell, Peter J -- Teh, Bin Tean -- Stratton, Michael R -- Futreal, P Andrew -- 077012/Wellcome Trust/United Kingdom -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- R01 CA113636/CA/NCI NIH HHS/ -- R01 CA134759/CA/NCI NIH HHS/ -- Cancer Research UK/United Kingdom -- England -- Nature. 2011 Jan 27;469(7331):539-42. doi: 10.1038/nature09639. Epub 2011 Jan 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21248752" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Carcinoma, Renal Cell/*genetics ; Cell Line, Tumor ; Disease Models, Animal ; Gene Expression Regulation ; Gene Knockdown Techniques ; Humans ; Kidney Neoplasms/*genetics ; Mice ; Mutation/*genetics ; Nuclear Proteins/*genetics/*metabolism ; Pancreatic Neoplasms/genetics ; Transcription Factors/*genetics/*metabolism
    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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    Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-01-08
    Description: Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820242/" 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/PMC2820242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalgliesh, Gillian L -- Furge, Kyle -- Greenman, Chris -- Chen, Lina -- Bignell, Graham -- Butler, Adam -- Davies, Helen -- Edkins, Sarah -- Hardy, Claire -- Latimer, Calli -- Teague, Jon -- Andrews, Jenny -- Barthorpe, Syd -- Beare, Dave -- Buck, Gemma -- Campbell, Peter J -- Forbes, Simon -- Jia, Mingming -- Jones, David -- Knott, Henry -- Kok, Chai Yin -- Lau, King Wai -- Leroy, Catherine -- Lin, Meng-Lay -- McBride, David J -- Maddison, Mark -- Maguire, Simon -- McLay, Kirsten -- Menzies, Andrew -- Mironenko, Tatiana -- Mulderrig, Lee -- Mudie, Laura -- O'Meara, Sarah -- Pleasance, Erin -- Rajasingham, Arjunan -- Shepherd, Rebecca -- Smith, Raffaella -- Stebbings, Lucy -- Stephens, Philip -- Tang, Gurpreet -- Tarpey, Patrick S -- Turrell, Kelly -- Dykema, Karl J -- Khoo, Sok Kean -- Petillo, David -- Wondergem, Bill -- Anema, John -- Kahnoski, Richard J -- Teh, Bin Tean -- Stratton, Michael R -- Futreal, P Andrew -- 077012/Wellcome Trust/United Kingdom -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 082359/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- England -- Nature. 2010 Jan 21;463(7279):360-3. doi: 10.1038/nature08672. Epub 2010 Jan 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054297" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinoma, Renal Cell/*genetics/pathology ; Cell Hypoxia/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Neoplastic ; *Genes, Neurofibromatosis 2 ; Histone Demethylases ; Histone-Lysine N-Methyltransferase/*genetics ; Histones/*metabolism ; Humans ; Kidney Neoplasms/*genetics/pathology ; Mutation/genetics ; Nuclear Proteins/*genetics ; Oxidoreductases, N-Demethylating/*genetics ; 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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  • 3
    Electronic Resource
    Electronic Resource
    Electrophoretic karyotype of the amylolytic yeast Lipomyces starkeyi and cloning, sequencing and chromosomal localization of its TRP1 gene (1996)
    Springer
    Current genetics 30 (1996), S. 83-88 
    Details
    ISSN: 1432-0983
    Keywords: Key wordsLipomyces starkeyi ; Electrophoretic karyotype ; CHEF ; TRP1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The genome of the amylolytic yeast strain Lipomyces starkeyi NCYC 1436 was analysed using contour-clamped homogeneous electric field gel electrophoresis (CHEF). The banding pattern under a variety of running conditions indicating the presence of 11 different chromosome-sized DNA molecules. The sizes of these chromosome bands were determined by comparison with chromosomes from standard strains of Schizosaccharomyces pombe and Saccharomyces cerevisiae. The chromosomal bands were estimated to be within the range 0.7–2.8 Mb, with the genome (excluding mitochondrial DNA) estimated at 15 Mb. The molecular cloning of the TRP1 gene, isolated from a genomic library of this strain, is also reported: the gene was present on a 6.5-kb Sau3A DNA fragment, and complemented the trpC gene of E. coli. The DNA sequence was determined (EMBL accession No. Z68292) and compared to other tryptophan biosynthetic genes encoding N-(5′-phosphoribosyl) anthranilate isomerase (PRAI) activity. The gene was also used as a probe in hybridization studies, and by this means, its chromosomal location was identified.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002940050104
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  • 4
    Electronic Resource
    Electronic Resource
    Field assessment of thermal after-ripening time for dormancy release prediction in Lolium rigidum seeds (2003)
    Oxford, UK : Blackwell Science Ltd
    Weed research 43 (2003), S. 0 
    Details
    ISSN: 1365-3180
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Dormancy release was studied in four populations of annual ryegrass (Lolium rigidum) seeds to determine whether loss of dormancy in the field can be predicted from temperature alone or whether seed water content (WC) must also be considered. Freshly matured seeds were after-ripened at the northern and southern extremes of the Western Australian cereal cropping region and at constant 37°C. Seed WC was allowed to fluctuate with prevailing humidity, but full hydration was avoided by excluding rainfall. Dormancy was measured regularly during after-ripening by germinating seeds with 12-hourly light or in darkness. Germination was lower in darkness than in light/dark and dormancy release was slower when germination was tested in darkness. Seeds were consistently drier, and dormancy release was slower, during after-ripening at 37°C than under field conditions. However, within each population, the rate of dormancy release in the field (north and south) in terms of thermal time was unaffected by after-ripening site. While low seed WC slowed dormancy release in seeds held at 37°C, dormancy release in seeds after-ripened under Western Australian field conditions was adequately described by thermal after-ripening time, without the need to account for changes in WC elicited by fluctuating environmental humidity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.0043-1737.2003.00363.x
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  • 5
    Electronic Resource
    Electronic Resource
    Isolation of a DNA fragment which complements glutamine synthetase deficient strains ofS. pombe (1988)
    Springer
    Current genetics 13 (1988), S. 487-494 
    Details
    ISSN: 1432-0983
    Keywords: S. pombe ; Glutamine synthetase ; Gene cloning
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary From a gene bank ofS. pombe DNA, a 5.6 kb clone was isolated which complemented mutants defective in glutamine synthetase (GS) activity. Sub-cloning fragments of this 5.6 kb clone showed that the complementing activity was localised in a 1.6 kb HindIII-Aval fragment and a partial DNA sequence revealed an open reading frame preceded by TATA sequences and a TGACTA sequence. Plasmid constructs carrying up to 3.4 kb of DNA used to transformgln − strains gave transformants which showed a wide range of GS activity, in some cases 100 times the wild-type level. These constructs identify DNA sequences lying downstream from the putative coding sequence which have effects on the total amount of enzyme activity, but do not affect the control imposed by the nitrogen source on which the cells are grown.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02427754
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  • 6
    Electronic Resource
    Electronic Resource
    Localization of glucoamylase genes of Saccharomyces cerevisiae by pulsed field gel electrophoresis (1990)
    Springer
    Antonie van Leeuwenhoek 58 (1990), S. 49-55 
    Details
    ISSN: 1572-9699
    Keywords: glucoamylase ; STA ; PFGE ; CHEF
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The chromosomal locations of four glucoamylase-specifying genes in the yeastSaccharomyces cerevisiae have been determined. Chromosomes were separated by pulsed field gel electrophoresis and blots were probed with radiolabelledSTA2 and marker DNA from specific yeast chromosomes. The three genes encoding extracellular glucoamylases,STA1 (DEX2), STA2 (DEX1) andSTA3 (DEX3) are located on chromosomes IV, II and XIV, respectively.SGA, specifying the sporulation-specific glucoamylase, was positioned on chromosome IX.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02388079
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  • 7
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    A survey of homozygous deletions in human cancer genomes (2005)
    National Academy of Sciences
    Details
    Publication Date: 2005-03-10
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Single-cell paired-end genome sequencing reveals structural variation per cell cycle (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-28
    Description: The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Isolation of a DNA fragment which complements glutamine synthetase deficient strains ofS. pombe (1988)
    Springer
    Details
    Publication Date: 1988-06-01
    Print ISSN: 0172-8083
    Electronic ISSN: 1432-0983
    Topics: Biology
    Published by Springer
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  • 10
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    Electrophoretic karyotype of the amylolytic yeast Lipomyces starkeyi and cloning, sequencing and chromosomal localization of its TRP1 gene (1996)
    Springer
    Details
    Publication Date: 1996-06-24
    Print ISSN: 0172-8083
    Electronic ISSN: 1432-0983
    Topics: Biology
    Published by Springer
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