Detection of structural variants in the human genome using nanopore sequencing

Silva, Catarina; Vieira, Luís

http://hdl.handle.net/10400.18/6795

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Authors

Silva, Catarina

Vieira, Luís

Abstract(s)

Nanopore sequencing is a recent technology that allows direct real-time sequencing of DNA/RNA molecules with read lengths as long as the size of the original fragments. The characteristics of nanopore sequencing make it well suited for whole genome sequencing and as a preferential tool to identify structural variants (SV), namely those associated with tumours. In this work, we present a complete workflow to detect SV in tumour samples using nanopore sequencing. We used a tumour sample to prepare DNA libraries using the Rapid Sequencing kit (Oxford Nanopore Technologies-ONT), sequenced those on the MinION device (ONT) and implemented a pipeline for SV detection using multiple bioinformatics tools. The MinION generated a total of 2.34 Gb of sequence. Overall, 87.8% of reads had a quality (Q) value >7 (quality threshold). The longest read obtained had 74369 bases and the mean read length was of 4508 bases. A total of 3470 SV were identified, including deletions, duplications, translocations, insertions and inversions. Nanopore sequencing is a fast and sensitive approach of great potential for human genomics research, namely in the detection of SV in the human genome.