I am at the Gordon Research Conference in Maine. This is my first GRC! I was able to rest a little this afternoon and watched the London Calling 2023 session entitled “Genomics England long-read cancer whole -genome sequencing pilot” presented by Helen Webb from Genomics England, UK. Genomics England is also called GEL. Webb disclosed they have a genetic disorder that causes visual issues. Genomics England has the goal to deliver 100,000 genomes and started in 2013. In 2019, they reached the goal of sequencing 100,000 rare disease and cancer genomes in conjunction with the National Health Service (NHS). In 2020, they delivered the “first whole genome analysis in the NIHS Genomics Medicine Service” that I am curious to learn more about. Genomics England provides a service to the NHS England. The project was not just about sequencing genomes. More than 6,000 patients received diagnosis. Genomics England started a long-read sequencing program with the objectives of faster diagnosis and more comprehensive data with methylation information. The program also wanted to increase equitable access to cancer diagnosis approaches using long-read sequencing. They have two PromethIONs in clinical settings. Webb noted that they are getting good yields and sequence lengths. This is encouraging as they DNA was extracted for other applications. They have recently transitioned from R9.4 to R10.4.1 flow cells. Genomics England has also used several structural variant callers including Sniffles v2, SAVANA, and NanomanSV for benchmarking. Webb noted in several examples how variations can be detected with long-read sequencing. Genomics England has also used Nanopore devices to learn about promoter methylation states. The team also worked with developers and tested several CNV callers for benchmarking. Webb concluded that WGS using ONT sequencing is clinically promising, though it is not clear if it will be “the right technology for all cancer types.” The team also wants to add in transcriptomics in the future. This session showed the impressive amount of sequencing Genomics England has performed and how they have explored different software to improve detection of cancers.
