Mikhail Kolmogorov from the National Cancer Institute, NIH, spoke at the Nanopore Community Meeting Houston about “Nanopore sequencing reveals structural heterogeneity in canine osteosarcoma.” Structural variants are any alterations greater than 50 bp. These events can affect one or multiple genes… or whole chromosomes! NCI has a comparative osteosarcoma (OS) program that recruits dogs nationwide. OS is most common in children, with 800 cases/year in the US and 70% long-term survival. In dogs, however, there are 10,000+ cases each year. Using Nanopore sequencing, the team sequenced two dog osteosarcomas with R10 flow cells. One dog, Oliver, had somatic SV mostly distributed in two chromosomes. The team also analyzed sample and haplotype-specific methylation patterns. The research team also analyzed chromosome-level variations and breakage-fusion-bridge amplification. Kolmogorov’s lab developed the Severus long-read somatic SV caller that produces haplotype-specific calls. The team sequenced several cell lines to benchmark Severus for analysis of cancer SVs.
