SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structu...

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Main Authors: Balachandran, P. (Author), Beck, C.R (Author), Danis, D. (Author), Haimel, M. (Author), Helbig, I. (Author), Jacobsen, J.O.B (Author), Lee, C. (Author), Lyon, G.J (Author), Mungall, C.J (Author), Reese, J. (Author), Robinson, P.N (Author), Smedley, D. (Author), Yilmaz, F. (Author), Zhu, Q. (Author)
Format: Article
Language:English
Published: BioMed Central Ltd 2022
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Online Access:View Fulltext in Publisher
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Summary:Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnna. © 2022, The Author(s).
ISBN:1756994X (ISSN)
DOI:10.1186/s13073-022-01046-6