Tonight I watched the London Calling 2023 session entitled “The potential application of nanopore sequencing for liquid biopsy analysis in children with cancer.” The second speaker was Carolin Sauer, a public research fellow at EMBL-EBI in the UK. Sauer focused on pediatric cancers and noted that they are the leading cause of death in the western world, and there are 400,000 new diagnoses each year worldwide. Sauer wanted to address the question: can we use long-read sequencing (Nanopore) to develop multi-modal liquid biopsy test for cancer screening and monitoring? For multi-modal, they were focusing on copy number, SVs/SNVs, methylation, and fragmentomics. What is fragmentomics? Sauer noted the challenges of obtaining enough tissue for genomics. Sauer is part of the Stratified Medicine Pediatrics program in the UK. They shared a plot of cfDNA detection and copy number differences. Their approach with methylation also includes the potential of deconvoluting tumor signals: different methylation patterns can be classified as different tumors. In this short session, Sauer explained that in their proposed multimodal biopsy test, they use computational tools for cfDNA analysis, classify the disease based on methylation, and then monitor relapse and treatment with a combination of nanopore and Illumina approaches. Their approach incorporates Nanopore sequencing of cell-free (cf) DNA from liquid biopsies to detect fragmentation size profiles, copy number aberrations, and methylation signals for cancer screening and monitoring. Sauer also concluded by mentioning their study to recruit and sequencing longitudinal pediatric cf DNA samples and expanding to other patient cohorts. Sauer’s session was brief and nevertheless introduced multiple uses for cell free DNA from pediatric liquid biopsies.
