DNA sequencing

The emergence of eDNA analysis is tightly linked to the development of next-generation sequencing. Chapter 7 “DNA sequencing” gives an overview of the characteristics and limitations of the main next-generation sequencing platforms. It focuses particularly on the Illumina platform, which is the only technology currently suitable for large-scale analysis with hundreds to thousands of samples. More specifically, Chapter 7 describes the Illumina library preparation process, the generation of sequencing clusters by bridge PCR on the flow cell, and the sequencing reaction itself, based on sequencing by synthesis. Finally, detailed information is provided on the meaning and coding of quality scores of the sequencing reads.

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

10.1101/2020.07.23.218602 ◽

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.

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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Nature Biotechnology ◽

10.1038/s41587-021-01049-5 ◽

2021 ◽

Vol 39 (9) ◽

pp. 1129-1140

Author(s):

Jonathan Foox ◽

Scott W. Tighe ◽

Charles M. Nicolet ◽

Justin M. Zook ◽

Marta Byrska-Bishop ◽

...

Keyword(s):

Next Generation Sequencing ◽

Dna Sequencing ◽

Performance Assessment ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing

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Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Nature Biotechnology ◽

10.1038/s41587-021-01122-z ◽

2021 ◽

Author(s):

Jonathan Foox ◽

Scott W. Tighe ◽

Charles M. Nicolet ◽

Justin M. Zook ◽

Marta Byrska-Bishop ◽

...

Keyword(s):

Next Generation Sequencing ◽

Dna Sequencing ◽

Performance Assessment ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing

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SNP Discovery through Next-Generation Sequencing and Its Applications

International Journal of Plant Genomics ◽

10.1155/2012/831460 ◽

2012 ◽

Vol 2012 ◽

pp. 1-15 ◽

Cited By ~ 87

Author(s):

Santosh Kumar ◽

Travis W. Banks ◽

Sylvie Cloutier

Keyword(s):

Next Generation Sequencing ◽

Large Scale ◽

Easy Access ◽

Next Generation ◽

Snp Discovery ◽

Genetic Studies ◽

Research Areas ◽

Wide Availability ◽

Sequencing Platforms ◽

Generation Sequencing

The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.

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Next-Generation Sequencing: An Emerging Tool for Drug Designing

Current Pharmaceutical Design ◽

10.2174/1381612825666190911155508 ◽

2019 ◽

Vol 25 (31) ◽

pp. 3350-3357 ◽

Cited By ~ 1

Author(s):

Pooja Tripathi ◽

Jyotsna Singh ◽

Jonathan A. Lal ◽

Vijay Tripathi

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Large Scale ◽

Massively Parallel Sequencing ◽

Genomic Research ◽

Biological Research ◽

Next Generation ◽

Human Welfare ◽

Drug Designing ◽

Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

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The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms

PLoS ONE ◽

10.1371/journal.pone.0113862 ◽

2014 ◽

Vol 9 (12) ◽

pp. e113862 ◽

Cited By ~ 15

Author(s):

Monika Zavodna ◽

Andrew Bagshaw ◽

Rudiger Brauning ◽

Neil J. Gemmell

Keyword(s):

Next Generation Sequencing ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing ◽

Short Tandem

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Next-Generation Sequencing: From Basic Research to Diagnostics

Clinical Chemistry ◽

10.1373/clinchem.2008.112789 ◽

2009 ◽

Vol 55 (4) ◽

pp. 641-658 ◽

Cited By ~ 459

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.

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Resolving Differential Diagnostic Problems in von Willebrand Disease, in Fibrinogen Disorders, in Prekallikrein Deficiency and in Hereditary Hemorrhagic Telangiectasia by Next-Generation Sequencing

Life ◽

10.3390/life11030202 ◽

2021 ◽

Vol 11 (3) ◽

pp. 202

Author(s):

Réka Gindele ◽

Adrienne Kerényi ◽

Judit Kállai ◽

György Pfliegler ◽

Ágota Schlammadinger ◽

...

Keyword(s):

Next Generation Sequencing ◽

Hereditary Hemorrhagic Telangiectasia ◽

Von Willebrand Disease ◽

Differential Diagnostics ◽

Bleeding Disorders ◽

Next Generation ◽

Illumina Platform ◽

Clinical Patient ◽

Von Willebrand ◽

Generation Sequencing

Diagnosis of rare bleeding disorders is challenging and there are several differential diagnostics issues. Next-generation sequencing (NGS) is a useful tool to overcome these problems. The aim of this study was to demonstrate the usefulness of molecular genetic investigations by summarizing the diagnostic work on cases with certain bleeding disorders. Here we report only those, in whom NGS was indicated due to uncertainty of diagnosis or if genetic confirmation of initial diagnosis was required. Based on clinical and/or laboratory suspicion of von Willebrand disease (vWD, n = 63), hypo-or dysfibrinogenemia (n = 27), hereditary hemorrhagic telangiectasia (HHT, n = 10) and unexplained activated partial thromboplastin time (APTT) prolongation (n = 1), NGS using Illumina platform was performed. Gene panel covered 14 genes (ACVRL1, ENG, MADH4, GDF2, RASA1, F5, F8, FGA, FGB, FGG, KLKB1, ADAMTS13, GP1BA and VWF) selected on the basis of laboratory results. We identified forty-seven mutations, n = 29 (6 novel) in vWD, n = 4 mutations leading to hemophilia A, n = 10 (2 novel) in fibrinogen disorders, n = 2 novel mutations in HHT phenotype and two mutations (1 novel) leading to prekallikrein deficiency. By reporting well-characterized cases using standardized, advanced laboratory methods we add new pieces of data to the continuously developing “bleeding disorders databases”, which are excellent supports for clinical patient management.

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