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Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.
Sahajpal, Nikhil Shri; Jill Lai, Chi-Yu; Hastie, Alex; Mondal, Ashis K; Dehkordi, Siavash Raeisi; van der Made, Caspar I; Fedrigo, Olivier; Al-Ajli, Farooq; Jalnapurkar, Sawan; Byrska-Bishop, Marta; Kanagal-Shamanna, Rashmi; Levy, Brynn; Schieck, Maximilian; Illig, Thomas; Bacanu, Silviu-Alin; Chou, Janet S; Randolph, Adrienne G; Rojiani, Amyn M; Zody, Michael C; Brownstein, Catherine A; Beggs, Alan H; Bafna, Vineet; Jarvis, Erich D; Hoischen, Alexander; Chaubey, Alka; Kolhe, Ravindra.
  • Sahajpal NS; Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
  • Jill Lai CY; Bionano Genomics, Inc., San Diego, CA 92121, USA.
  • Hastie A; Bionano Genomics, Inc., San Diego, CA 92121, USA.
  • Mondal AK; Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
  • Dehkordi SR; Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA.
  • van der Made CI; Department of Human Genetics, Radboud University Medical Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, 6525 Nijmegen, the
  • Fedrigo O; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
  • Al-Ajli F; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
  • Jalnapurkar S; Department of Medicine, Medical College of Georgia, Augusta University, GA 30912, USA.
  • Byrska-Bishop M; New York Genome Center, New York, NY 10013, USA.
  • Kanagal-Shamanna R; Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston 77030, USA.
  • Levy B; Department of Pathology and Cell Biology, Columbia University Medical Center, New York 10032, USA.
  • Schieck M; Department of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany.
  • Illig T; Department of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany.
  • Bacanu SA; Hannover Unified Biobank (HUB), Hannover 30625, Germany.
  • Chou JS; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23284, USA.
  • Randolph AG; Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA.
  • Rojiani AM; Department of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
  • Zody MC; Departments of Anesthesia and Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
  • Brownstein CA; Department of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
  • Beggs AH; New York Genome Center, New York, NY 10013, USA.
  • Bafna V; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • Jarvis ED; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • Hoischen A; Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA.
  • Chaubey A; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
  • Kolhe R; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
iScience ; 25(2): 103760, 2022 Feb 18.
Article in English | MEDLINE | ID: covidwho-1683208
ABSTRACT
Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs), which account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely ill COVID-19 patients to identify rare/unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways innate immunity and inflammatory response, and viral replication and spread in nine patients, of which SVs in STK26 and DPP4 genes are the most intriguing candidates. This study is the first to systematically assess the potential role of SVs in the pathogenesis of COVID-19 severity and highlights the need to evaluate SVs along with sequencing variants to comprehensively associate genomic information with interindividual variability in COVID-19 phenotypes.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Variants Language: English Journal: IScience Year: 2022 Document Type: Article Affiliation country: J.isci.2022.103760

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Topics: Variants Language: English Journal: IScience Year: 2022 Document Type: Article Affiliation country: J.isci.2022.103760