Workflow: characterising structural variants in FFPE cancer research samples
Formalin-fixed, paraffin-embedded (FFPE) sampling is a widely used, simple method to preserve important cancer research samples. Structural variation (SV) is a key mutational process in cancer, defined as genomic alterations >50 bp in length, and can impact whole genes or chromosomes. Formalin fixing damages DNA molecules and reduces their fragment length; however, sequences spanning several kilobases still remain. Oxford Nanopore has optimised a workflow specifically designed to extract and sequence DNA spanning several kilobases from FFPE samples, enabling accurate SV detection and analysis. With long nanopore sequencing reads, SVs can be comprehensively characterised across cancer genomes.
Here, we present a simple workflow for the analysis of SVs in DNA extracted from FFPE samples using a PromethION™ Flow Cell.