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.
This Workflow explains:
- A process for the analysis of SVs in DNA extracted from FFPE samples using a PromethION™ Flow Cell.
- Recommendations for the extraction, library preparation, sequencing and analysis of SVs
- How Oxford Nanopore’s technology aids in the detection and analysis of SV
And much more!
Looking for more content?
- On-demand webinar: Introducing cancer genomics with long reads
- Learn more about other applications of nanopore sequencing in cancer research
This content was provided by Oxford Nanopore Technologies
