Integrative annotation of variants from 1092 humans: application to cancer genomics. (Articolo in rivista)

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Label
  • Integrative annotation of variants from 1092 humans: application to cancer genomics. (Articolo in rivista) (literal)
Anno
  • 2013-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1126/science.1235587. (literal)
Alternative label
  • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, McVean GA. (2013)
    Integrative annotation of variants from 1092 humans: application to cancer genomics.
    in Science (N. Y., N.Y.)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, McVean GA. (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 342 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo
  • 6154 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK. Institute of Genetics and Biophysics, National Research Council (CNR), 80131 Naples, Italy. Center for Statistical Genetics, Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland. Institute for Precision Medicine and the Department of Pathology and Laboratory Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital, New York, NY 10065, USA. The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA. Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA. Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX 77030, USA. Department of Chemistry, Yale University, New Haven, CT 06520, USA. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Department of Biology, Boston College, Chestnut Hill, MA 02467, USA. Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA. Keck Biotechnology Resource Laboratory, Yale University, New Haven, CT 06511, USA. Pediatric Surgical Research Laboratories, MassGeneral Hospital for Children, Massachusetts General Hospital, Boston, MA 02114, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Harvard Medical School, Boston, MA 02115, USA. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. Center for Protein Research, University of Copenhagen, Copenhagen, Denmark. Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA. Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA. Division of Endocrinology and Center for Basic and Translational Obesity Research, Children's Hospital, Boston, MA 02115, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07101, USA. IST/High Performance and Research Computing, Rutgers University Newark, NJ 07101, USA. Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA. Child Study Center, Yale University, New Haven, CT 06520, USA. Department of Computer Science, Yale University, New Haven, CT 06520, USA. (literal)
Titolo
  • Integrative annotation of variants from 1092 humans: application to cancer genomics. (literal)
Abstract
  • Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations (\"ultrasensitive\") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, \"motif-breakers\"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers. (literal)
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