October 24, 2019

Nanopore sequencing

How does nanopore DNA sequencing work?

Nanopore sequencing is a unique, scalable technology that enables direct, real-time analysis of long DNA or RNA fragments. It works by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence. For more info click link:

https://nanoporetech.com/applications/dna-nanopore-sequencing

 

 

 

Applications

Massively parallel sequencing (MPS) has become an indispensable tool throughout all Life Sciences research field. Currently, long-read sequencing (LRS) will penetrate this field as it has clear advantages of short-read sequencers while costs have dropped to almost the same cost as short-read sequencers (depending on several factors):

  • Long reads are imperative in de novo genome assembly as these long reads can be used to contig and scaffold the data into more accurate genomes (certainly in repetitive regions) with fewer gaps.
  • Long reads allow phasing of genomic variants and allow untangling of (complex) structural variations.
  • As entire RNA transcripts can be sequenced in one read: detection and quantitative measurement of RNA isoforms, new long non-coding RNA, etc. becomes much easier than with short reads.
  • Individual DNA and RNA molecules can be sequenced directly without the need for a PCR reaction, avoiding PCR artefacts, representative bias and loss of the epigenetic modifications.
  • Epigenetic modifications can be determined directly on RNA and DNA.

Hence the new technology will have its application in whole genome sequencing, de novo assembly, scaffolding and finishing of genomes, variant analysis (structural variation, single-nucleotide variants, phasing), resequencing, targeted sequencing such as exome and cancer panels, long-amplicon 16S rRNA metagenomic analysis, RNA sequencing (splice variant analysis, transcriptome/gene expression, fusion transcript analysis, etc.), metagenomics (unbiased), epigenetics, non-coding RNA activity, etc.