Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals

Abstract

The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.

Towards the fully automated monitoring of ecological communities

“…behavioural, functional and morphological traits) is evaluated from 1 to 3 levels as follows: 1 bar corresponds to 'in corner-case situations only', 2 bars corresponds to 'in specific conditions and on specific organisms (for detecting, counting and classifying) or for a limited number of features (for measuring)', and 3 bars corresponds to 'in most cases and for most organisms (for detecting, counting and classifying) and for several features (for measuring)'. composed of portable nanopore sequencing devices such as the MinION and SmidgION (Ames et al, 2021;Jain et al, 2016) could allow them to achieve fully automated status in the future (Huo et al, 2021).…”

“…However, recent developments in miniaturised microfluidic technologies that automate the sampling and processing of eDNA samples (Dhar & Lee, 2018 ; Formel et al, 2021 ), and the advent of autonomous vehicles to carry such devices (Yamahara et al, 2019 ) have enabled the conception of environmental sample processors (ESPs) that can perform all these steps from sampling to DNA amplification and sample storage without human intervention (Hansen et al, 2020 ; Jacobsen, 2021 ) (Figure 2 ). While ESPs do not automate post‐sampling procedures such as DNA sequencing, equipping these devices with modules composed of portable nanopore sequencing devices such as the MinION and SmidgION (Ames et al, 2021 ; Jain et al, 2016 ) could allow them to achieve fully automated status in the future (Huo et al, 2021 ).…”

Large-scale nano-biosensing technologies

“…AI algorithms can deal with pattern association, recognition, classification, optimization, and prediction (Jin et al, 2020) tasks, addressing the challenges of big data; enabling fast realtime complex analysis and computations (Haick and Tang, 2021) and generalizing complex or unknown functions or data. For example bio-inspired AI paradigms based on evolutionary or genetic algorithms are implemented to provide solutions to optimization and search problems dealing with genomic diagnostics (Dias and Torkamani, 2019) and DNA sequencers (Huo et al, 2021). A label-free method for identification of respiratory viruses based on silicon nanopores and a machinelearning algorithm, trained on the changes in current as the viruses pass through the nanopores was reported build a working tool for accurate distinguishing and identifying multiple viral species (Arima et al, 2021).…”

Gold Ion Beam Milled Gold Zero-Mode Waveguides

“…The geometry and opacity of the ZMW enables measurements at physiological concentrations (∼1–100 μM) in SMS [ 30 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 ]. As a result, ZMWs have found wide application in studies of genomic sequencing [ 47 , 48 , 49 , 50 ], protein–protein interaction [ 51 , 52 , 53 , 54 ], ligand–receptor binding [ 55 , 56 , 57 , 58 , 59 , 60 , 61 ], membrane-bound diffusion events [ 62 , 63 ] and the study of membrane proteins [ 64 , 65 ]. ZMWs have also been used to manipulate exciton behavior in quantum dots [ 66 ], and ZMWs have been shown to extend Förster Resonance Energy Transfer (FRET) distances from 10 to 13.6 nm [ 67 ].…”