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bioRxiv · 10.1101/2020.07.22.214262

Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv

Shiraishi, Y.·Koya, J.·Chiba, K.·Saito, Y.·Okada, A.·Kataoka, K.
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Abstract

We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5 truncations, internal inversions, as well as source sites for 3 transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.

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Shiraishi, Y., Koya, J., Chiba, K., Saito, Y., Okada, A., Kataoka, K.. 2020-07-23. Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv. https://doi.org/10.1101/2020.07.22.214262

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