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ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data.
Ford, Michael K B; Hari, Ananth; Rodriguez, Oscar; Xu, Junyan; Lack, Justin; Oguz, Cihan; Zhang, Yu; Weber, Sarah; Magliocco, Mary; Barnett, Jason; Xirasagar, Sandhya; Samuel, Smilee; Imberti, Luisa; Bonfanti, Paolo; Biondi, Andrea; Dalgard, Clifton L; Chanock, Stephen; Rosen, Lindsey; Holland, Steven; Su, Helen; Notarangelo, Luigi; Vishkin, Uzi; Watson, Corey T; Sahinalp, S Cenk.
  • Ford MKB; National Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: mike.ford@nih.gov.
  • Hari A; National Cancer Institute, NIH, Bethesda, MD, USA; Department of Electrical Engineering, University of Maryland, College Park, MD, USA.
  • Rodriguez O; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
  • Xu J; National Cancer Institute, NIH, Bethesda, MD, USA.
  • Lack J; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Oguz C; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Zhang Y; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Weber S; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Magliocco M; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Barnett J; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Xirasagar S; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Samuel S; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Imberti L; Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy.
  • Bonfanti P; University of Milano-Bicocca, Fondazione MBBM, Monza, Italy.
  • Biondi A; University of Milano-Bicocca, Fondazione MBBM, Monza, Italy.
  • Dalgard CL; Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
  • Chanock S; National Cancer Institute, NIH, Bethesda, MD, USA.
  • Rosen L; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Holland S; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Su H; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Notarangelo L; National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
  • Vishkin U; Department of Electrical Engineering, University of Maryland, College Park, MD, USA.
  • Watson CT; Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA.
  • Sahinalp SC; National Cancer Institute, NIH, Bethesda, MD, USA. Electronic address: cenk.sahinalp@nih.gov.
Cell Syst ; 13(10): 808-816.e5, 2022 Oct 19.
Article in English | MEDLINE | ID: covidwho-2075982
ABSTRACT
Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which are critical for the structure of antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype when using standard short-read sequencing technologies. Here, we introduce ImmunoTyper-SR, an algorithmic tool for the genotyping and CNV analysis of the germline IGHV genes on Illumina whole-genome sequencing (WGS) data using a combinatorial optimization formulation that resolves ambiguous read mappings. We have validated ImmunoTyper-SR on 12 individuals, whose IGHV allele composition had been independently validated, as well as concordance between WGS replicates from nine individuals. We then applied ImmunoTyper-SR on 585 COVID patients to investigate the associations between IGHV alleles and anti-type I IFN autoantibodies, which were previously associated with COVID-19 severity.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Immunoglobulin Variable Region / COVID-19 Type of study: Prognostic study Limits: Humans Language: English Journal: Cell Syst Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Immunoglobulin Variable Region / COVID-19 Type of study: Prognostic study Limits: Humans Language: English Journal: Cell Syst Year: 2022 Document Type: Article