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The landscape of human SVA retrotransposons.
Chu, Chong; Lin, Eric W; Tran, Antuan; Jin, Hu; Ho, Natalie I; Veit, Alexander; Cortes-Ciriano, Isidro; Burns, Kathleen H; Ting, David T; Park, Peter J.
Afiliação
  • Chu C; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
  • Lin EW; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.
  • Tran A; Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA.
  • Jin H; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
  • Ho NI; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
  • Veit A; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.
  • Cortes-Ciriano I; Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA.
  • Burns KH; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
  • Ting DT; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
  • Park PJ; Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
Nucleic Acids Res ; 51(21): 11453-11465, 2023 Nov 27.
Article em En | MEDLINE | ID: mdl-37823611
SINE-VNTR-Alu (SVA) retrotransposons are evolutionarily young and still-active transposable elements (TEs) in the human genome. Several pathogenic SVA insertions have been identified that directly mutate host genes to cause neurodegenerative and other types of diseases. However, due to their sequence heterogeneity and complex structures as well as limitations in sequencing techniques and analysis, SVA insertions have been less well studied compared to other mobile element insertions. Here, we identified polymorphic SVA insertions from 3646 whole-genome sequencing (WGS) samples of >150 diverse populations and constructed a polymorphic SVA insertion reference catalog. Using 20 long-read samples, we also assembled reference and polymorphic SVA sequences and characterized the internal hexamer/variable-number-tandem-repeat (VNTR) expansions as well as differing SVA activity for SVA subfamilies and human populations. In addition, we developed a module to annotate both reference and polymorphic SVA copies. By characterizing the landscape of both reference and polymorphic SVA retrotransposons, our study enables more accurate genotyping of these elements and facilitate the discovery of pathogenic SVA insertions.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Retroelementos Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Genoma Humano / Retroelementos Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos