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Harvard Medical School

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Nucleic Acids Res., Oct 12 2023, gkad821 | https://doi.org/10.1093/nar/gkad821 The landscape of human SVA retrotransposons

Chong Chu ¹, Eric W Lin ^2,3, Antuan Tran ¹, Hu Jin ¹, Natalie I Ho ^2,3, Alexander Veit ¹, Isidro Cortes-Ciriano ⁴, Kathleen H Burns ⁵, David T Ting ^2,3, Peter J Park ¹

¹Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

²Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.

³Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA.

⁴European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

⁵Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.

To whom correspondence should be addressed. : Peter J Park

Abstract

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.

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형식Research article
게재일2023년 10월 (BRIC 등록일 2023-11-17)
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