Kieran O’Neill from Canada’s Michael Smith Genome Sciences Center (GSC), BC Cancer, Canada presented at London Calling 2022 on “Nanopore sequencing shows potential for personalised oncogenomics.” O’Neill spoke about the GSC’s work on genome research and sequencing. They have a Personalized Oncogenomics Program (POG) that consists of taking a biopsy, whole genome transcriptome analysis, reporting, and clinical interventions. They have used Illumina sequencing and asked what can Nanopore bring to POG. They used Nanopore sequencing to improve germline structural variant resolution. The GSC POG sequenced 13 cases, resolving some ambiguities from Illumina with Nanopore sequencing. Using a PromethION, they also sequenced blood to determine susceptibility variants. The group has also used “Long POG” for epigenomic dysregulation studies. They have used long-read epigenetic analyses to phager Illumina POG cases. They are also working on adapting MAVIS: merging, annotation, validation, and illustration of SVs workflow for Nanopore. O’Neill also described worked using Nanopore sequencing to identify HPV16 integration sites. O’Neill concluded that Nanopore sequencing has potential for personalized oncogenomics, including…
- calling 5-mc and using that to detect and confirm epigenomic dysregulation phenotypes,
- using phased methylation to detect oncogenic aberrations in imprinting,
- confirming structural variants, and
- detecting oncoviral integration sites.
O’Neill explained that future work at the GSC will work to improve workflows and extend the use of Nanopore sequencing. I think it is useful to learn what tools and applications groups are using for clinical work.
