SVFX: a machine learning framework to quantify the pathogenicity of structural variants

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Abstract

There is a lack of approaches for identifying pathogenic genomic structural variants (SVs) although they play a crucial role in many diseases. We present a mechanism-agnostic machine learning-based workflow, called SVFX, to assign pathogenicity scores to somatic and germline SVs. In particular, we generate somatic and germline training models, which include genomic, epigenomic, and conservation-based features, for SV call sets in diseased and healthy individuals. We then apply SVFX to SVs in cancer and other diseases; SVFX achieves high accuracy in identifying pathogenic SVs. Predicted pathogenic SVs in cancer cohorts are enriched among known cancer genes and many cancer-related pathways.

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Kumar, S., Harmanci, A., Vytheeswaran, J., & Gerstein, M. B. (2020). SVFX: a machine learning framework to quantify the pathogenicity of structural variants. Genome Biology, 21(1), 274. https://doi.org/10.1186/s13059-020-02178-x

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