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  • *Encyclopedias as Topic  (1)
  • Adult  (1)
  • Nature Publishing Group (NPG)  (2)
  • Oxford University Press
  • American Chemical Society (ACS)
  • 2010-2014  (2)
  • 1975-1979
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  • Nature Publishing Group (NPG)  (2)
  • Oxford University Press
  • American Chemical Society (ACS)
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  • 2010-2014  (2)
  • 1975-1979
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  • 1
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    De novo mutations in histone-modifying genes in congenital heart disease (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-05-15
    Description: Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes 'poised' promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706629/" 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/PMC3706629/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zaidi, Samir -- Choi, Murim -- Wakimoto, Hiroko -- Ma, Lijiang -- Jiang, Jianming -- Overton, John D -- Romano-Adesman, Angela -- Bjornson, Robert D -- Breitbart, Roger E -- Brown, Kerry K -- Carriero, Nicholas J -- Cheung, Yee Him -- Deanfield, John -- DePalma, Steve -- Fakhro, Khalid A -- Glessner, Joseph -- Hakonarson, Hakon -- Italia, Michael J -- Kaltman, Jonathan R -- Kaski, Juan -- Kim, Richard -- Kline, Jennie K -- Lee, Teresa -- Leipzig, Jeremy -- Lopez, Alexander -- Mane, Shrikant M -- Mitchell, Laura E -- Newburger, Jane W -- Parfenov, Michael -- Pe'er, Itsik -- Porter, George -- Roberts, Amy E -- Sachidanandam, Ravi -- Sanders, Stephan J -- Seiden, Howard S -- State, Mathew W -- Subramanian, Sailakshmi -- Tikhonova, Irina R -- Wang, Wei -- Warburton, Dorothy -- White, Peter S -- Williams, Ismee A -- Zhao, Hongyu -- Seidman, Jonathan G -- Brueckner, Martina -- Chung, Wendy K -- Gelb, Bruce D -- Goldmuntz, Elizabeth -- Seidman, Christine E -- Lifton, Richard P -- 5U54HG006504/HG/NHGRI NIH HHS/ -- F30 HL123238/HL/NHLBI NIH HHS/ -- P30 HD018655/HD/NICHD NIH HHS/ -- T32 GM007205/GM/NIGMS NIH HHS/ -- U01 HG006546/HG/NHGRI NIH HHS/ -- U01 HL098123/HL/NHLBI NIH HHS/ -- U01 HL098147/HL/NHLBI NIH HHS/ -- U01 HL098153/HL/NHLBI NIH HHS/ -- U01 HL098162/HL/NHLBI NIH HHS/ -- U01 HL098163/HL/NHLBI NIH HHS/ -- U01-HL098123/HL/NHLBI NIH HHS/ -- U01-HL098147/HL/NHLBI NIH HHS/ -- U01-HL098153/HL/NHLBI NIH HHS/ -- U01-HL098162/HL/NHLBI NIH HHS/ -- U01-HL098163/HL/NHLBI NIH HHS/ -- U01-HL098188/HL/NHLBI NIH HHS/ -- U54 HG006504/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jun 13;498(7453):220-3. doi: 10.1038/nature12141. Epub 2013 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23665959" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Case-Control Studies ; Child ; Chromatin/chemistry/metabolism ; DNA Mutational Analysis ; Enhancer Elements, Genetic/genetics ; Exome/genetics ; Female ; Genes, Developmental/genetics ; Heart Diseases/*congenital/*genetics/metabolism ; Histones/chemistry/*metabolism ; Humans ; Lysine/chemistry/metabolism ; Male ; Methylation ; Mutation ; Odds Ratio ; Promoter Regions, Genetic/genetics
    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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    The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-31
    Description: The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320027/" 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/PMC3320027/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barretina, Jordi -- Caponigro, Giordano -- Stransky, Nicolas -- Venkatesan, Kavitha -- Margolin, Adam A -- Kim, Sungjoon -- Wilson, Christopher J -- Lehar, Joseph -- Kryukov, Gregory V -- Sonkin, Dmitriy -- Reddy, Anupama -- Liu, Manway -- Murray, Lauren -- Berger, Michael F -- Monahan, John E -- Morais, Paula -- Meltzer, Jodi -- Korejwa, Adam -- Jane-Valbuena, Judit -- Mapa, Felipa A -- Thibault, Joseph -- Bric-Furlong, Eva -- Raman, Pichai -- Shipway, Aaron -- Engels, Ingo H -- Cheng, Jill -- Yu, Guoying K -- Yu, Jianjun -- Aspesi, Peter Jr -- de Silva, Melanie -- Jagtap, Kalpana -- Jones, Michael D -- Wang, Li -- Hatton, Charles -- Palescandolo, Emanuele -- Gupta, Supriya -- Mahan, Scott -- Sougnez, Carrie -- Onofrio, Robert C -- Liefeld, Ted -- MacConaill, Laura -- Winckler, Wendy -- Reich, Michael -- Li, Nanxin -- Mesirov, Jill P -- Gabriel, Stacey B -- Getz, Gad -- Ardlie, Kristin -- Chan, Vivien -- Myer, Vic E -- Weber, Barbara L -- Porter, Jeff -- Warmuth, Markus -- Finan, Peter -- Harris, Jennifer L -- Meyerson, Matthew -- Golub, Todd R -- Morrissey, Michael P -- Sellers, William R -- Schlegel, Robert -- Garraway, Levi A -- DP2 OD002750/OD/NIH HHS/ -- DP2 OD002750-01/OD/NIH HHS/ -- R33 CA126674/CA/NCI NIH HHS/ -- R33 CA126674-04/CA/NCI NIH HHS/ -- R33 CA155554/CA/NCI NIH HHS/ -- R33 CA155554-02/CA/NCI NIH HHS/ -- England -- Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460905" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Cell Lineage ; Chromosomes, Human/genetics ; Clinical Trials as Topic/methods ; *Databases, Factual ; Drug Screening Assays, Antitumor/*methods ; *Encyclopedias as Topic ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genes, ras/genetics ; Genome, Human/genetics ; Genomics ; Humans ; Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors/metabolism ; *Models, Biological ; Neoplasms/*drug therapy/genetics/metabolism/*pathology ; Pharmacogenetics ; Plasma Cells/cytology/drug effects/metabolism ; Precision Medicine/methods ; Receptor, IGF Type 1/antagonists & inhibitors/metabolism ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; Sequence Analysis, DNA ; Topoisomerase Inhibitors/pharmacology
    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)
    Location Call Number Expected Availability
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    PAPER CURRENT
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