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

The advent of next generation sequencing (NGS) has altered the face of genotyping the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, and research contexts. NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies. This has led to a broader and deeper profiling of the key genes in the human immunogenetic make-up. The rapid evolution of sequencing technologies is evidenced by the development of varied short-read sequencing platforms with differing read lengths and sequencing capacities to long-read sequencing platforms capable of profiling full genes without fragmentation. Concomitantly, there has been development of a diverse set of computational analyses and software tools developed to deal with the various strengths and limitations of the sequencing data generated by the different sequencing platforms. This review surveys the different modalities involved in generating NGS HLA profiling sequence data. It systematically describes various computational approaches that have been developed to achieve HLA genotyping to different degrees of resolution. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.

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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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Comparing fragment size with read-length and their effect on HLA genotyping by next-generation sequencing (NGS)

Human Immunology ◽

10.1016/j.humimm.2015.07.072 ◽

2015 ◽

Vol 76 ◽

pp. 52

Author(s):

Tracie Profaizer ◽

Eszter Lazar-Molnar ◽

Julio C. Delgado ◽

Attila Kumanovics

Keyword(s):

Next Generation Sequencing ◽

Fragment Size ◽

Read Length ◽

Next Generation ◽

Hla Genotyping ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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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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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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