Nanopore Sequencing

Overview

The quantity and wealth of information that can be gathered from sequencing data has increased tremendously from Sanger sequencing to Next Generation Sequencing (NGS), with a corresponding precipitous drop in the cost of sequencing1. Several new sequencing technologies have been developed in recent years, some of which enable the sequencing of single DNA molecules. Sequencing using nanopores, tiny apertures on the cell membrane, offers several advantages over existing technologies that use optical or pH change methods to detect DNA sequences.

 

Why nanopore technology?

Nanopore technology offers several benefits:

  • Flexibility and versatility
  • Single molecule sequencing
  • Both short and long read lengths
  • Real-time data generation and analysis
  • Cost-effectiveness

How does nanopore technology work?

Nanopore-based sequencing technology detects the unique electrical signals of different molecules as they pass through the nanopore with a semiconductor-based electronic detection system. This technology makes for a high throughput, cost effective sequencing solution. At the heart of the technology is the biological nanopore, a protein pore embedded in a membrane, while the brains of the technology lie in the electronics of a semiconductor integrated circuit and proprietary chemistries. The electronic sensor technology embedded in the chip enables automatic membrane assembly and nanopore insertion, while allowing for active control of individual sensors on the circuit. 

Different sequencing chemistries can be paired with the nanopore and electronic sensor technology to enable high throughput, high accuracy sequencing with faster time-to-data. The main challenge with nanopore-based sequencing is to ensure accurate single molecule base calls, which remains an inherent limitation of current nanopore systems.

Sequencing By eXpansion (SBXTM )

Stratos Genomics, a Roche company, has developed a novel chemistry called Sequencing by eXpansion (SBX) to significantly improve the accuracy and throughput of nanopore sequencing. This chemistry translates the sequence of DNA into a simple to measure surrogate molecule called an Xpandomer. Much like with polymerase chain reaction (PCR), Xpandomer synthesis is based on the natural function of DNA replication where expandable nucleoside triphosphates (X-NTPs) act as substrates for template-dependent, polymerase-based replication.

Xpandomer synthesis is based on four easily differentiated X-NTPs (also called High Signal-to-Noise Reporters), one for each DNA base. Engineered polymerases incorporate these modified nucleotides into Xpandomers, exactly copying the target nucleic acid template from the library. As the Xpandomer molecule transits through the nanopore, the distinct electrical signal of each base reporter is easily identifiable to enable highly accurate and high throughput nanopore-based nucleic acid sequencing.

Improving nanopore sequencing accuracy  

As the Xpandomer passes through the nanopore, the distinct electrical signal of each base reporter is identified. This results in accurate base calling for downstream analysis. The sequencing data below demonstrates the clear separation of the four bases, enabled by SBX chemistry coupled with CMOS nanopore detection.

  1. Park S and Kim J, 2016. Int Neurourol J. Trends in next-generation sequencing and a new era for whole genome sequencing.

Product in development, not commercially available.