Nanopore sequencing

Nanopore sequencing is based on a support slide (more specifically flow cells, as used also by SGS such as Illumina) where a nanoscale array of holes (nanopores) embedded in a membrane is placed. Each nanopore is connected to an electrode and a sensor continuously measuring the current passing through the pore.

The single DNA molecule slides through the hole, one nucleotide at a time. This produces a unique alteration in the current, allowing for base calling and therefore sequencing (Figure 10).

Even though nanopore sequencing has significantly improved its performance over the past few years, recent studies (25, 26) show it still displays a higher error rate compared to Illumina SGS. 

However, it’s important to remember that the choice of a certain sequencing technique depends on the aim of the experiment: for instance, if we wanted to precisely identify SNP mutations in cancer patients, SGS would then be the preferred option; if instead if we are interested in bigger structural changes, as insertions or deletions, the longer sequences provided by TGS techniques such as nanopore would be an advantage.

It is also worth mentioning that nanopore technology was the first to make sequencing portable, thanks to the development of the MinION sequencer; MinION can be practically plugged into a computer to download the data as the sequencing is ongoing.

For more information about the history of nanopore sequencing and its applications, you can read these reviews:

• Deamer et al, “Three decades of nanopore sequencing”, 2016
• Wang et al, “Nanopore sequencing technology, bioinformatics, and application”, 2021