Molecular diagnostics for personal medicine using a nanopore

Mirsaidov, Utkur; Wang, Deqiang; Timp, Winston; Timp, G.

doi:10.1002/wnan.86

Cited by 19 publications

(13 citation statements)

References 69 publications

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“…Currently, RT-PCR is the most common mainstay technique for pathogen testing and is considered the "gold standard" for clinical diagnostics of RNA viruses due to its high reliability [4], [5]. For the detection of RNA viruses such as SARS-CoV-2, the RNA first needs to be reverse transcribed into complementary DNA (cDNA), and then amplified and detected via fluorescent probes (Figure 1a).…”

Section: Advantages Of Nanopore Sequencing Viral Pathogen Detection Imentioning

confidence: 99%

“…Nanopore sequencing relies on measuring characteristic electric and/or optical (spectroscopic) signals that are unique to each nucleotide [4]. To date, empirically demonstrated nanopore sequencing can be generalized into three general categories based on their fundamental operating mechanisms: (i) trans-pore/membrane ionic current modulation (TCIM), (ii) transverse (in-plane) current sequencing (TCS), and (iii) spectral analysis.…”

Section: Introductionmentioning

confidence: 99%

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Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

et al. 2020

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State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.

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Section: Advantages Of Nanopore Sequencing Viral Pathogen Detection Imentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

et al. 2020

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“…Molecular analysis of clinical samples will become increasingly important if the health benefits of the plethora of newer high throughput, system-wide data generating approaches are to have the maximum patient impact. Methods such as second and third generation sequencing, 14,15 dynamic array PCR along with the increasing use of microfluidics, 16 result in much more information being obtained from a sample than has been possible with established techniques. Concomitantly, as the importance of collecting the correct demographics and ensuring ethical sampling becomes better established, 17,18 it is likely that the use of large, well characterized biobanks will become a more common and valuable resource for such methodologies.…”

Section: Discussionmentioning

confidence: 99%

Quality Assessment of Biobanked Nucleic Acid Extracts for Downstream Molecular Analysis

Wahlberg¹,

Huggett²,

Sanders³

et al. 2012

Biopreservation and Biobanking

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Sample quality is of major importance when conducting molecular analysis of nucleic acids, and factors such as degradation, presence of impurities, and enzymatic inhibitors may have a significant impact on the quality of data. Issues of quality assessment become more important as the increased use of biobanking means that whole blood samples are being stored for longer periods. A range of commercially available kits/methods have been specifically developed for extraction of high quality nucleic acids from a variety of clinical samples, including blood, but there is limited information on how best to quality assess the extracts to determine their fitness for purpose in specific downstream applications. In this study, we have performed nucleic acid extractions from stored blood using a number of different methods. The resulting extracts were analyzed by a panel of quantity and quality metrics including UV spectrophotometry, PicoGreen fluorescence, electrophoresis, and a PCR approach. To evaluate the relevance of different metrics, DNA samples were subsequently assessed for their performance in real time PCR and microarray experiments. Our findings demonstrate that the most suitable extraction technique and quality assessment approach depends on the required downstream analytical method.

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“…In recent decades, progress has been made to quantitatively determine DNAm profiles by methods based on bisulfite modification of DNA, amplification and sequencing. The laborious nature of these techniques prompted the quest for alternative methods, one example being nanopore-based sequencing of single, native DNA molecules with no need for any chemical modification or amplification [31]. Recently, two articles described significant advances in the field.…”

Section: Search For Hematic Epigenetic Markers Of Atherosclerosismentioning

confidence: 99%