Workflow: Structural variationLiterature
Date: 10th November 2023
Resolving structural variants with long nanopore sequencing reads
Structural variants (SVs) — genomic aberrations >50 bp — have known causative effects in an extensive range of both normal and aberrant phenotypes. The need to comprehensively characterise SVs is becoming increasingly clear; however, they are difficult to detect using short-read sequencing as the DNA must be both fragmented and amplified, limiting detection according to their size, complexity, and position in the genome. Using PCR-free nanopore sequencing, there is no limit to read length — long nanopore reads can span entire SVs in a single read, including within repetitive or GC-rich regions. High-output PromethION devices enable accurate resolution of even highly complex variants in any genomic context.
Here, we present a simple workflow for an effective whole-genome SV survey from a human clinical research blood sample, using the PromethION sequencing device range.