Tonight I watched the London Calling 2023 session by Kieran O’Neil from Canada’s Michael Smith Genome Sciences Centre at BC Cancer, Canada. The session title is “The potential of nanopore sequencing for personalised genomics.” They have been supporting a Personalized OncoGenomics Program (POG) that has focused on short-read whole genomes and interested in long-read sequencing of a POG cohort of 186 diverse tumors. They were primarily interested in structural variants. Their read N50s were about 40Kb! They did not shear their DNA. They did use a panel of structural variant detection software. They were able to detect all variants. They detected variants with only 20x coverage. They also detected DNA methylation (5-mC). Methylation clusters by tumor type according to preliminary results. O’Neil also spoke about assessment of phasing with Nanopore technologies. They are excited because of the two-hit hypothesis: tumor suppressor genes must be inactivated on both alleles to drive oncogenesis. Now, their approach with long-read sequencing, they can determine phasing information.Their plan is to release their data and use it as a resource for long-read cancer analysis.
