Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

Dna Fragmentation ◽

Microfluidic Chip ◽

Acoustic Streaming ◽

Next Generation ◽

Highly Efficient ◽

On Chip ◽

Sequencing Platforms ◽

We present a new bubble-enhanced microfluidic approach for highly efficient DNA fragmentation, suitable for next generation sequencing platforms. Improved on-chip performance arises from acoustic streaming generated by oscillating bubble interfaces.

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):

Short Tandem Repeats ◽

Tandem Repeats ◽

Next Generation ◽

Sequencing Platforms ◽

Generation Sequencing ◽

Short Tandem

Preparation of Next-Generation Sequencing Libraries Using Nextera™ Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition

Methods in Molecular Biology - High-Throughput Next Generation Sequencing ◽

10.1007/978-1-61779-089-8_17 ◽

2011 ◽

pp. 241-255 ◽

Cited By ~ 59

Author(s):

Nicholas Caruccio

Keyword(s):

Dna Fragmentation ◽

Next Generation ◽

Generation Sequencing ◽

In Vitro Transposition

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):

High Throughput Sequencing ◽

Data Generation ◽

Next Generation ◽

Sequencing Data ◽

Yield Data ◽

Chromosome Conformation ◽

Sequencing Platform ◽

Sequencing Platforms ◽

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.

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 Platforms ◽

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

Nucleic Acids Research ◽

10.1093/nar/gks754 ◽

2012 ◽

Vol 40 (22) ◽

pp. e171-e171 ◽

Cited By ~ 118

Author(s):

Daniel C. Jones ◽

Walter L. Ruzzo ◽

Xinxia Peng ◽

Michael G. Katze

Keyword(s):

De Novo Assembly ◽

De Novo ◽

Next Generation ◽

Highly Efficient ◽

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 ◽

Hla Genotyping ◽

Sequencing Platforms ◽

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 Platforms ◽

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):

High Performance ◽

Solid Tumours ◽

Next Generation ◽

Formalin Fixed Paraffin ◽

Ffpe Samples ◽

Thermo Fisher Scientific ◽

Formalin Fixed Paraffin Embedded ◽

Sequencing Platforms ◽

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.