Next-Generation Sequencing (NGS) Platforms: An Exciting Era of Genome Sequence Analysis

Krishna, B. Meera; Khan, Munawwar Ali; Khan, Shams Tabrez

doi:10.1007/978-981-32-9860-6_6

Cited by 26 publications

(18 citation statements)

References 114 publications

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“…RNA-seq possesses a number of advantages compared to microarrays including the detection of novel sequences, broad dynamic range, high specificity, and sensitivity capable of picking up low abundance transcripts. 9,10 The first high-throughput sequencing platform appeared in 2005 11 and was followed by multiple NGS platforms, the most common of which is the Illumina-based sequencing technology. Rapid growth in NGS use was prompted by its application in the wholegenome sequencing project (WGS) and continued to grow as an essential tool due to its biomedical applications, its use in epidemiological studies of infectious diseases, surveillance of foodborne illnesses, and viral diversity studies.…”

Section: E Volution Of Rna-s Equen Cingmentioning

confidence: 99%

What sequencing technologies can teach us about innate immunity*

Salih

Carpenter

2021

Immunological Reviews

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For years, we have taken a reductionist approach to understanding gene regulation through the study of one gene in one cell at a time. While this approach has been fruitful it is laborious and fails to provide a global picture of what is occurring in complex situations involving tightly coordinated immune responses. The emergence of wholegenome techniques provides a system-level view of a response and can provide a plethora of information on events occurring in a cell from gene expression changes to splicing changes and chemical modifications. As with any technology, this often results in more questions than answers, but this wealth of knowledge is providing us with an unprecedented view of what occurs inside our cells during an immune response. In this review, we will discuss the current RNA-sequencing technologies and what they are helping us learn about the innate immune system.

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Section: E Volution Of Rna-s Equen Cingmentioning

confidence: 99%

What sequencing technologies can teach us about innate immunity*

Salih

Carpenter

2021

Immunological Reviews

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“…Since their introduction in 2005, many HTS sequencing platforms have been developed including Pyrosequencing, Ion Torrent technology, Illumina/Solexa, and Sequencing by Oligonucleotide Ligation and Detection. Further optimization has led to innovative third- and fourth-generation platforms such as single-molecule real-time sequencing by PacBio and Nanopore sequencing [ 26 ]. These platforms differ substantially in terms of their preparatory procedures, sequencing chemistry or technology, nucleotide incorporation technology, read type, length, accuracy, the size of generated data and price.…”

Section: Integration Of Hts In Plant Virology In Africamentioning

confidence: 99%

“…These platforms differ substantially in terms of their preparatory procedures, sequencing chemistry or technology, nucleotide incorporation technology, read type, length, accuracy, the size of generated data and price. More elaborate information on HTS can be found from previous reviews [ 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”

Section: Integration Of Hts In Plant Virology In Africamentioning

confidence: 99%

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Ibaba

Gubba

2020

Plants

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High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

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“…Individual nucleotides can be detected optically by combining them with fluorescent materials. For instance, solid-phase amplification is a representative DNA sequencer product that currently occupies more than 90% of the global genomic sequencing markets [4]. However, PCR-based sequencing methods can only support sequencing in short read lengths (100-150 bp) and require complex DNA sample preparation and processing procedures, all of which result in analyses that have high costs and low speeds.…”

Section: Introductionmentioning

confidence: 99%

Low-Area Four-Channel Controlled Dielectric Breakdown System Design for Point-of-Care Applications

Hong

Choi

et al. 2022

Sensors

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In this study, we propose a low-area multi-channel controlled dielectric breakdown (CDB) system that simultaneously produces several nanopore sensors. Conventionally, solid-state nanopores are prepared by etching or drilling openings in a silicon nitride (SiNx) substrate, which is expensive and requires a long processing time. To address these challenges, a CDB technique was introduced and used to fabricate nanopore channels in SiNx membranes. However, the nanopore sensors produced by the CDB result in a severe pore-to-pore diameter variation as a result of different fabrication conditions and processing times. Accordingly, it is indispensable to simultaneously fabricate nanopore sensors in the same environment to reduce the deleterious effects of pore-to-pore variation. In this study, we propose a four-channel CDB system that comprises an amplifier that boosts the command voltage, a 1-to-4 multiplexer, a level shifter, a low-noise transimpedance amplifier and a data acquisition device. To prove our design concept, we used the CDB system to fabricate four nanopore sensors with diameters of <10 nm, and its in vitro performance was verified using λ-DNA samples.

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Next-Generation Sequencing (NGS) Platforms: An Exciting Era of Genome Sequence Analysis

Cited by 26 publications

References 114 publications

What sequencing technologies can teach us about innate immunity*

What sequencing technologies can teach us about innate immunity*

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later

Low-Area Four-Channel Controlled Dielectric Breakdown System Design for Point-of-Care Applications

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