nanopore
Definition
Nanopore sequencing is a single-molecule sequencing technology that identifies nucleotides by measuring changes in electrical current as DNA or RNA molecules pass through a protein nanopore embedded in a membrane. Unlike traditional sequencing methods, nanopore technology reads nucleic acids in real-time without requiring amplification or chemical labeling, enabling ultra-long reads (>100 kb) and direct detection of base modifications like methylation. This approach offers significant advantages for resolving complex genomic regions, structural variants, and full-length transcript isoforms. The technology's portability, exemplified by Oxford Nanopore's MinION device, has democratized sequencing for field research and clinical applications, while its ability to sequence native molecules preserves epigenetic information critical for understanding gene regulation.
Visualize nanopore in Nodes Bio
Researchers can use Nodes Bio to integrate nanopore sequencing data with multi-omics networks, visualizing relationships between detected structural variants, gene expression patterns, and downstream phenotypic effects. Network graphs can map long-read isoform data to protein interaction networks, revealing how alternative splicing events identified through nanopore sequencing affect pathway connectivity and disease mechanisms.
Visualization Ideas:
- Structural variant impact networks showing genomic rearrangements connected to affected genes and pathways
- Isoform-protein interaction networks mapping alternative splice variants to functional protein complexes
- Methylation-gene regulation networks linking base modifications detected by nanopore to transcriptional control elements
Example Use Case
A cancer genomics team uses nanopore sequencing to identify complex structural rearrangements in tumor samples that short-read technologies missed. They detect a novel fusion gene involving a kinase domain. Using network visualization, they map this fusion protein's predicted interactions within signaling pathways, discovering unexpected connections to immune checkpoint regulators. This network analysis reveals potential combination therapy targets, as the fusion protein appears to bridge oncogenic and immunosuppressive pathways, explaining the tumor's aggressive phenotype and resistance to standard treatments.