Portable nanopore-sequencing technology: Trends in development and applications

Abstract

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.

Beta‐cell death and dysfunction drives hyperglycaemia in organ donors

“…Newer technologies, such as the portable nanopore sequencing devices could overcome some of these issues and provide immediate data at the time of donation, which could ultimately guide decision making on use of donor organs. 22 We limited the reporting of our post-transplantation outcomes to the islet transplant cohort because (a) comprehensive assessment of beta-cell function using a mixed meal tolerance test is not performed routinely following pancreas transplantation, and (b) technical factors such as thrombosis, pancreatitis and bleeding are accountable for a significant proportion of early graft losses following pancreas transplantation. This study was not powered to detect a relationship between markers of donor beta-cell death and isolated islet failure following pancreas transplantation.…”

“…Such factors include the times between sample acquisition, centrifugation, storage on ice and storage at −70°C, with the latter being determined by the distance from the donor hospital to the central processing laboratory. Newer technologies, such as the portable nanopore sequencing devices could overcome some of these issues and provide immediate data at the time of donation, which could ultimately guide decision making on use of donor organs 22 …”

Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting

“…Nanopore sequencing is being used worldwide to quickly sequence and analyze SARS‐CoV‐2 viral genomes 24 . Rapid data sharing enables genomic epidemiological analysis, a key part of the global public health response to the COVID‐19 pandemic 25 . Nanopore technology has been used to rapidly sequence the emerging and reemerging pathogens including Zika, Ebola, and other pathogens in multiple outbreaks, where surveillance and genomic investigation capacities are limited 26–30 .…”

Nanopore sequencing technology and its applications

“…Translocation of nucleic acids too fast will increase the difficulty of clip identification. In early experiments in the development of nanopore sequencing, single‐stranded DNA passed through the nanopore at a rate of 1–10 bases per millisecond, making it difficult to detect the sequencing signal 10 . The unstable translocation rate also brings difficulties to subsequent data analysis.…”

“…The concept of nanopore sequencing, where singlestranded nucleic acids pass through a nanopore in a membrane under an electric field, was first proposed by David Deamer in the 1980s. 1 Despite initial skepticism, technological advances eventually made nanopore Technologies (ONT), founded in 2005 by Oxford professor Bayley and colleagues, 10 facilitated the commercialization of nanopore sequencing with the release of their MinION sequencer in 2014. 2 Currently, ONT has established a complete sequencing system process that includes advanced library preparation techniques combined with amplicon and other technologies, as well as numerous bioinformatics methods for analyzing and mining nanopore sequencing data.…”