Mashiat Mimosa from the University of Toronto, Canada, spoke about “Optimization and validation of a nanopore-based sequencing method for potential molecular testing of CNS tumours.” Mimosa explained that brain tumors are the leading cause of cancer-related deaths worldwide, and glioma brain tumors account for >80% of all malignant tumors! Glioma diagnostic algorithm is very complex and depends on the identification of a mutation in one gene. In Mimosa’s lab, they set out to develop a new assay using Nanopore sequencing. They analytically validated the test using guidelines by professional societies including the Association for Molecular Pathology and the College of American Pathologists. They determined concordance/accuracy, sensitivity, precision, limit of blank, and limit of detection. All IDH mutants and wild types were detected accurately with their approach. Precision and reproducibility were also calculated and deemed appropriate, with a coefficient of variation between 0.9-2.7%. They analyzed the limit of blank and detection at 500x sequencing depth. Mimosa explained that they determined the assay cost and turnaround for six and thirty sample runs. The cost went down from $134 Canadian dollars per sample for a six sample multiplex to $50 Canadian dollars for a thirty sample run. The time for six samples is about nine hours with five of those being “hands-on.” For thirty samples, Mimosa noted that it took them fifteen hours with eight of those being hands-on. With these data, they concluded that they analytically validated a nanopore sequencing assay for IDH SNV detection on FFPE tissue with excellent reproducibility, low cost per sample, and in less than two days. I was intrigued by their software use: Mimosa mentioned they used the Nanopolish software. I wonder what changes, if any, they made…
