Tonight I watched a session from the Nanopore Community Meeting in Singapore entitled “Investigating structural variations and complex cancer genomes using Oxford Nanopore sequencing” presented by Marjan Naeini from the Garvan Institute of Medical Research in Australia. Naeini described the primary classes of structural variations (SVs) as deletions, duplications, inversions, insertions, and translocations. They studied complex structural variations in cancer. The approach used long-read Nanopore sequencing to identify variations including rearrangements. The workflow does a consensus SV call, which is more involved. There is an optional step to use short-read data to confirm SVs. In one case study, the team analyzed complex SVs in chromosome 2. In a second case, anaplastic ganglioglioma DNA was de novo assembled. In summary, the team established a consensus somatic SV calling workflow to identify and classify complex SVs and applied the workflow to several cancer types. They are continuing to test and improve workflow. I am curious about how this workflow establishes a “consensus.”
