Tasos Gogakos from Arena BioWorks and Massachusetts General Hospital spoke at the ONT Biopharma Day. The title of the session was “Nanopore sequencing at the intersection between the clinic and biotech.”Gogakos is a clinical pathologist who recently started at Arena BioWorks. Gogakos began by sharing two clinical cases. The patient had lung cancer and molecular testing at a commercial lab. Some reads matched to two parts of the genome. Hybrid capture and short-read sequencing were used. A possible rearrangement was detected, and phasing of an allele was necessary to confirm possible treatments. However, the short-read data was unable to verify this. The second case was of a fifty-six-year-old woman with ambiguous supporting read mapping. Gogakos began drawing possible variants and had to perform orthogonal testing, but it could still be ambiguous. Gogakos noted that Oxford Nanopore Technologies is a viable and realistic alternative test. Gogakos is interested in Cas9-directed cuts and enrichment of sequences of interest. The v14 chemistry and base calling updates provided improvements. Gogakos believes that ONT should “enable transition from alignment-based to assembly-based personalized diagnostics.”
