Luis Paulin from the Baylor College of Medicine presented at London Calling 2023 a short session entitled “The long and short of structural variants using Oxford Nanopore Sequencing.” Paulin described how genomic variation caused structural variants (SV) and copy number variants (CNV). Using long-read technology allows for access to difficult to sequence genomic regions, thus improving identification of structural variants. Using Sniffles 2.2. and Spectre, SV and CNV can be detected. Spectre can be used to assess mega-base and extreme chromosomal abnormalities. Paulin compared different tools for SV assessment. Paulin also described improvements to Sniffles 2 Population, a variant of Sniffles 2. The population tool was applied to the GREGoR consortium samples to evaluate disease-relevant SVs in the MECP2-gene locus.The team is developing a Sniffles 2 cancer pipeline for germline and mosaic. The combination of Sniffles and Spectre allows for evaluation of a broad range of structural variants. While I don’t think I will use these tools now, they could be useful for larger genomes we analyze.
