Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics

Life, Journal Year: 2021, Volume and Issue: 12(1), P. 30 - 30

Published: Dec. 26, 2021

Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, introduction of novel set methodologies, presented by two platforms, Pacific Biosciences (PacBio) Oxford Nanopore Sequencing (ONT), gave birth third-generation (TGS). The innovative long-read technologies turn genome into an ease-of-handle procedure greatly reducing average time library construction workflows simplifying process de novo assembly due generation long reads. Long reads produced both TGS methodologies have already facilitated decipherment transcriptional profiling since they enable identification full-length transcripts without need for or use sophisticated bioinformatics tools. Long-read also provided new insights field epitranscriptomics, allowing direct detection RNA modifications on native molecules. This review highlights advantageous features newly introduced technologies, discusses their limitations provides in-depth comparison regarding scientific background available protocols as well potential utility in research clinical applications.

Language: Английский

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A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

BioMed Research International, Journal Year: 2022, Volume and Issue: 2022, P. 1 - 12

Published: Sept. 29, 2022

Background. Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement these has enhanced volume several billion nucleotides within a very short time low cost. During the last few years, usage of latest DNA platforms large number research projects helped improve technologies, thus enabling wide variety research/review publications applications technologies. Objective. The study is aimed at highlighting most fast accurate NGS instruments by various companies comparing output per hour, quality reads, maximum read length, reads run, their domains. This will help institutions biological/clinical laboratories choose instrument best suited environment. end users general overview about history developments, improvements made technologies till now. Results. study, based on previous studies manufacturers’ descriptions, highlighted that terms Nanopore PromethION outperformed all sequencers. BGI was second position, Illumina third position. Conclusion. investigated that, overall, fastest approach. can beat Illumina, which currently popular company. With respect quality, Ion Torrent are top list, DNB Secondly, memory- time-saving algorithms databases need be analyze data produced 3rd- 4th-generation methods. people adopt platform for work, diagnostic activities.

Language: Английский

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Long read sequencing on its way to the routine diagnostics of genetic diseases

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: March 6, 2024

The clinical application of technological progress in the identification DNA alterations has always led to improvements diagnostic yields genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects genomic microarrays detecting cryptic copy variants, at molecular level, Sanger method studying nucleotide sequence single genes high-throughput next-generation sequencing (NGS) technologies, resolution sensitivity progressively increased expanding considerably range detectable anomalies alongside Mendelian disorders with known causes. However, particular regions (i.e., repetitive GC-rich sequences) are inefficiently analyzed by standard tests, still relying on laborious, time-consuming low-sensitive approaches southern-blot for repeat expansion or long-PCR highly homologous pseudogenes), accounting least part patients undiagnosed disorders. Third generation sequencing, generating long reads improved mappability, is more suitable detection hardly accessible regions. Although recently implemented not yet clinically available, read (LRS) technologies have already shown their potential medicine research that might greatly impact yield reporting times, through translation settings. main investigated LRS concerns variants expansions, probably because evolved as rapidly those dedicated (SNV) identification: gold analyses karyotyping balanced unbalanced rearrangements, respectively, southern blot repeat-primed PCR amplification sizing expanded alleles, impaired limited been significantly advent NGS. Nevertheless, recently, accuracy provided latest product releases, tested also SNV detection, especially pseudogenes haplotype reconstruction assess parental origin alleles de novo pathogenic variants. We provide a review relevant recent scientific papers exploring diagnosis diseases its future applications routine testing.

Language: Английский

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Nanopore sequencing: flourishing in its teenage years

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

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Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing

Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11

Published: June 29, 2023

Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) susceptibility testing on slow growing bacteria like MTBC requires many weeks to months complete, whereas sequencing-based approaches can predict resistance (DR) reduced turnaround time. We sought develop a multiplexed, targeted next generation sequencing (tNGS) assay that DR be performed directly clinical respiratory specimens. A multiplex PCR was designed amplify group thirteen full-length genes promoter regions mutations known involved in first- second-line drugs. Long-read amplicon libraries were sequenced Oxford Nanopore Technologies platforms high-confidence identified real-time using an in-house developed bioinformatics pipeline. Sensitivity, specificity, reproducibility, accuracy the tNGS assessed part validation study. In total, 72 primary specimens 55 MTBC-positive cultures results compared whole genome (WGS) paired patient cultures. Complete or partial profiles generated from 82% smear positive by 100% concordant WGS. addition performing samples, this used sequence mixed other mycobacterial species would yield WGS results. The effectively implemented clinical/diagnostic laboratory two three day time and, even if batched weekly, available average 15 days earlier than culture-derived This study demonstrates reliably provide critical information timely manner for appropriate treatment patients tuberculosis.

Language: Английский

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Nanopore sequencing technology and its applications

MedComm, Journal Year: 2023, Volume and Issue: 4(4)

Published: July 10, 2023

Abstract Since the development of Sanger sequencing in 1977, technology has played a pivotal role molecular biology research by enabling interpretation biological genetic codes. Today, nanopore is one leading third‐generation technologies. With its long reads, portability, and low cost, widely used various scientific fields including epidemic prevention control, disease diagnosis, animal plant breeding. Despite initial concerns about high error rates, continuous innovation platforms algorithm analysis effectively addressed accuracy. During coronavirus (COVID‐19) pandemic, critical detecting severe acute respiratory syndrome coronavirus‐2 virus genome containing pandemic. However, lack understanding this may limit popularization application. Nanopore poised to become mainstream choice for preventing controlling COVID‐19 future epidemics while creating value other such as oncology botany. This work introduces contributions during pandemic promote public use emerging outbreaks worldwide. We discuss application microbial detection, cancer genomes, genomes summarize strategies improve

Language: Английский

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Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Antibiotics, Journal Year: 2023, Volume and Issue: 12(11), P. 1580 - 1580

Published: Oct. 30, 2023

Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.

Language: Английский

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Comparing the accuracy and efficiency of third generation sequencing technologies, Oxford Nanopore Technologies, and Pacific Biosciences, for DNA barcode sequencing applications

Ecological Genetics and Genomics, Journal Year: 2023, Volume and Issue: 28, P. 100181 - 100181

Published: May 31, 2023

New genomic technologies, such as third generation sequencing (TGS), have enabled for high-throughput, rapid, and cost-effective data of non-model organisms, accelerating taxonomic identification studies contributing to conservation applications. Here, we present the first comparison two leading TGS providers, Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT), purpose DNA barcoding, using morphological Sanger reference. We demonstrate that highest numbers successfully sequenced samples were achieved with ONT R10 & Q20+ chemistry combination. In terms library preparation time, protocols quickest. Compared sequencing, estimate third-generation platforms become more when a study requires barcoding than 61 (Flongle), 183 (MinION), or 356 samples. Although both tested are suitable had limitations, applicability different studies. The pipeline developed, which goes from whole specimens final barcode sequences, can aid planning budgeting biodiversity studies, maximising number in one run speeding up sample processing time.

Language: Английский

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Carbon-Based Fluorescent Nano-Biosensors for the Detection of Cell-Free Circulating MicroRNAs

Biosensors, Journal Year: 2023, Volume and Issue: 13(2), P. 226 - 226

Published: Feb. 4, 2023

Currently, non-communicable diseases (NCDs) have emerged as potential risks for humans due to adopting a sedentary lifestyle and inaccurate diagnoses. The early detection of NCDs using point-of-care technologies significantly decreases the burden will be poised transform clinical intervention healthcare provision. An imbalance in levels circulating cell-free microRNAs (ccf-miRNA) has manifested NCDs, which are passively released into bloodstream or actively produced from cells, improving efficacy disease screening providing enormous sensing potential. effective ccf-miRNA continues significant technical challenge, even though sophisticated equipment is needed analyze readouts expression patterns. Nanomaterials come light solution they provide advantages over other widely used diagnostic techniques measure miRNAs. Particularly, CNDs-based fluorescence nano-biosensors great interest. Owing excellent characteristics CNDs, developing such sensors ccf-microRNAs been much more accessible. Here, we critically examined recent advancements fluorescence-based CNDs biosensors, including tools manufacturing these biosensors. Green synthesis methods scaling up high-quality, fluorescent natural source discussed. various surface modifications that help attach biomolecules utilizing covalent conjugation multiple applications, self-assembly, sensing, imaging, analyzed. current review particular interest researchers interested materials chemistry, nanomedicine, related fields, focus on ccf-miRNAs applications medical field.

Language: Английский

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An update on pathogenesis and clinical scenario for Parkinson’s disease: diagnosis and treatment

3 Biotech, Journal Year: 2023, Volume and Issue: 13(5)

Published: April 27, 2023

Language: Английский

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