London Calling 2023: Genomics England long-read cancer whole-genome sequencing pilot

Genomics England are currently running a pilot study to investigate the use of Oxford Nanopore sequencing in large-scale, clinical, whole-genome analysis in cancer. This pilot is being run in conjunction with NHS England. Sequencing will be started at two pathfinder translational sites at Genomic Laboratory hubs located in Leeds and the Royal Marsden, London, before being rolled out to five other sites nationally. In the run up to this pilot, Genomics England has been sequencing large research cohorts of samples at the GEL Sequencing R&D lab. This has led to the optimisation of large-scale sequencing protocols for whole-genome sequencing on the PromethION 48 sequencer, as well as optimisation of data transfer from the machine to enable centralised storage and analysis. Structural variant calling has been optimised following the benchmarking of several algorithms. Significant process has been made with copy number variant calling, methylation calling, and small variant calling. Several case studies have been made of complex variants not called by short-read sequencing but which are able to be resolved using long-read sequencing.