The landscape of human SVA retrotransposons.
The landscape of human SVA retrotransposons.
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DOI：
10.1093/nar/gkad821
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发表时间：
2023-11-27
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
--
作者：
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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影响因子：
3.3
作者：
Carbone L;Harris RA;Mootnick AR;Milosavljevic A;Martin DI;Rocchi M;Capozzi O;Archidiacono N;Konkel MK;Walker JA;Batzer MA;de Jong PJ
通讯作者：
de Jong PJ
影响因子：
7
作者：
Gardner EJ;Lam VK;Harris DN;Chuang NT;Scott EC;Pittard WS;Mills RE;1000 Genomes Project Consortium;Devine SE
通讯作者：
Devine SE
影响因子：
14.5
作者：
Hancks DC;Kazazian HH Jr
通讯作者：
Kazazian HH Jr
影响因子：
2.8
作者：
Bantysh, O. B.;Buzdin, A. A.
通讯作者：
Buzdin, A. A.
影响因子：
5.6
作者：
Gianfrancesco, Olympia;Geary, Bethany;Quinn, John P.
通讯作者：
Quinn, John P.