Characterizing structural variants in FFPE cancer research samples

Formalin-fixed, paraffin-embedded (FFPE) sampling is often used to preserve cancer research samples. However, formalin fixing damages DNA molecules and reduces their fragment length although sequences spanning several kilobases remain. 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.

This workflow, optimized by Oxford Nanopore, has been 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 characterized across cancer genomes.