scholarly journals Next-Generation Sequencing: From Basic Research to Diagnostics

2009 ◽  
Vol 55 (4) ◽  
pp. 641-658 ◽  
Author(s):  
Karl V Voelkerding ◽  
Shale A Dames ◽  
Jacob D Durtschi
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Basic Research ◽  
Clinical Diagnostics ◽  
Massively Parallel ◽  
Next Generation ◽  
New Paradigm ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

Next Generation Sequencing Technology in Clinical Diagnostics

2020 ◽  
Vol 2 (7) ◽  
pp. 10-17
Author(s):  
Megha Agrawal ◽  
Keyword(s):  
Next Generation Sequencing ◽  
Basic Research ◽  
Cost Effective ◽  
Clinical Diagnostics ◽  
Library Preparation ◽  
Next Generation ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Diagnostic Applications ◽  
Generation Sequencing

The promise of next generation sequencing offers hope for the current DNA sequencing technology to evolve from the applications in basic research to transition to the clinical diagnostics. This advancement in the sequencing technology is happening in part due to the introduction of high throughput and benchtop instruments that offer fully automated cost-effective sequencing along with faster assay times. This development is believed to remove the bottleneck of the complex and cumbersome library preparation that include isolation of nucleic acids and the resulting amplified and barcoded DNA with sequencing adapters. Here, we present a brief overview of the principles of next generation sequencing and automation of library preparation along with the diagnostic applications of next generation sequencing in human immunogenetics. Finally, an outlook is presented.

scholarly journals Next generation sequencing technologies (NGST) development and applications

2011 ◽  
Vol 152 (2) ◽  
pp. 55-62 ◽  
Author(s):  
Zsuzsanna Mihály ◽  
Balázs Győrffy
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
New Technology ◽  
Objective Assessment ◽  
Basic Research ◽  
Next Generation ◽  
New Era ◽  
Sequencing Technologies ◽  
Meta Analyses ◽  
Generation Sequencing

In the past ten years the development of next generation sequencing technologies brought a new era in the field of quick and efficient DNA sequencing. In our study we give an overview of the methodological achievements from Sanger’s chain-termination sequencing in 1975 to those allowing real-time DNA sequencing today. Sequencing methods that utilize clonal amplicons for parallel multistrand sequencing comprise the basics of currently available next generation sequencing techniques. Nowadays next generation sequencing is mainly used for basic research in functional genomics, providing quintessential information in the meta-analyses of data from signal transduction pathways, onthologies, proteomics and metabolomics. Although next generation sequencing is yet sparsely used in clinical practice, cardiology, oncology and epidemiology already show an immense need for the additional knowledge obtained by this new technology. The main barrier of its spread is the lack of standardization of analysis evaluation methods, which obscure objective assessment of the results. Orv. Hetil., 2011, 152, 55–62.

scholarly journals The Impact of Next Generation Sequencing in Cancer Research

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2928
Author(s):  
Katia Nones ◽  
Ann-Marie Patch
Keyword(s):  
Cancer Research ◽  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing ◽  
Technical Revolution

Next generation sequencing (NGS) describes the technical revolution that enabled massively parallel sequencing of fragmented nucleic acids, thus making possible our current genomic understanding of cancers [...]

scholarly journals Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

2020 ◽  
Author(s):  
Jonathan Foox ◽  
Scott W. Tighe ◽  
Charles M. Nicolet ◽  
Justin M. Zook ◽  
Marta Byrska-Bishop ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Large Scale ◽  
Error Rates ◽  
Clinical Diagnostics ◽  
Small Scale ◽  
Next Generation ◽  
Oxford Nanopore ◽  
Sequencing Platforms ◽  
Generation Sequencing

AbstractMassively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Phase II Study to measure quality and reproducibility of DNA sequencing. Replicates of human and bacterial reference DNA samples were generated across multiple sequencing platforms, including well-established technologies such as Illumina, ThermoFisher Ion Torrent, and Pacific Biosciences, as well as emerging technologies such as BGI, Genapsys, and Oxford Nanopore. A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection of small-scale polymorphisms and large-scale structural variants. This study provides a comprehensive baseline resource for continual benchmarking as chemistries, methods, and platforms evolve for DNA sequencing.

scholarly journals Suitability of Bronchoscopic Biopsy Tissue Samples for Next-Generation Sequencing

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 391
Author(s):  
Shuji Murakami ◽  
Tomoyuki Yokose ◽  
Daiji Nemoto ◽  
Masaki Suzuki ◽  
Ryou Usui ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Success Rate ◽  
Rna Sequencing ◽  
Surface Area ◽  
Endobronchial Ultrasound ◽  
Next Generation ◽  
Endobronchial Ultrasonography ◽  
Tissue Surface ◽  
The Impact ◽  
Generation Sequencing

A sufficiently large tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥1 mm2) and tumor content rate (≥30%) on the success rate of the Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

scholarly journals Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

2017 ◽  
Vol 36 (7) ◽  
pp. 1339-1342
Author(s):  
K. G. Joensen ◽  
A. L. Ø. Engsbro ◽  
O. Lukjancenko ◽  
R. S. Kaas ◽  
O. Lund ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Diarrhoeal Disease ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Generation Sequencing
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