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

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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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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Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform

GigaScience ◽

10.1093/gigascience/giaa087 ◽

2020 ◽

Vol 9 (8) ◽

Author(s):

Marcela Sandoval-Velasco ◽

Juan Antonio Rodríguez ◽

Cynthia Perez Estrada ◽

Guojie Zhang ◽

Erez Lieberman Aiden ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Throughput Sequencing ◽

Data Generation ◽

Next Generation ◽

Sequencing Data ◽

Yield Data ◽

Chromosome Conformation ◽

Sequencing Platform ◽

Sequencing Platforms ◽

Generation Sequencing

Abstract Background Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. Results We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. Conclusions Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.

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I.12-1 New Next Generation Sequencing Platforms (NGS) Versus Tailored Panels

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2019.09.108 ◽

2019 ◽

Vol 14 (11) ◽

pp. S1161

Author(s):

I. Wistuba

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing

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P139 False homozygosity observed for one sample’s HLA genotyping on two independent next generation sequencing platforms

Human Immunology ◽

10.1016/j.humimm.2016.07.204 ◽

2016 ◽

Vol 77 ◽

pp. 139

Author(s):

Zahra Kashi ◽

Meagan Barner ◽

Jenefer Dekoning ◽

Gabriel Caceres ◽

RaeAnna Neville ◽

...

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Hla Genotyping ◽

Sequencing Platforms ◽

Generation Sequencing

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FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

Biology ◽

10.3390/biology1030895 ◽

2012 ◽

Vol 1 (3) ◽

pp. 895-905 ◽

Cited By ~ 243

Author(s):

Matthias Dodt ◽

Johannes Roehr ◽

Rina Ahmed ◽

Christoph Dieterich

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing

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Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours

Journal of Clinical Pathology ◽

10.1136/jclinpath-2019-206422 ◽

2020 ◽

Vol 73 (9) ◽

pp. 602-604

Author(s):

Silvia Bessi ◽

Francesco Pepe ◽

Marco Ottaviantonio ◽

Pasquale Pisapia ◽

Umberto Malapelle ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Performance ◽

Solid Tumours ◽

Next Generation ◽

Formalin Fixed Paraffin ◽

Ffpe Samples ◽

Thermo Fisher Scientific ◽

Formalin Fixed Paraffin Embedded ◽

Sequencing Platforms ◽

Generation Sequencing

In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen’s kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson’s r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.

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