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

Biology ◽  
2012 ◽  
Vol 1 (3) ◽  
pp. 895-905 ◽  
Author(s):  
Matthias Dodt ◽  
Johannes Roehr ◽  
Rina Ahmed ◽  
Christoph Dieterich
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Sequencing Platforms ◽  
Generation Sequencing

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

GigaScience ◽  
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.

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

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

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

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.

Next Generation Sequencing Platforms and its Applications in Genomics

2016 ◽  
Vol 9 (6) ◽  
pp. 947
Author(s):  
J.C. Bommesh ◽  
Kattula Nagaraju ◽  
M.K. Sunilkumar ◽  
Manjunatha D.C. Gowda ◽  
M. Mallik ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Sequencing Platforms ◽  
Generation Sequencing

scholarly journals The Genetic Germline Background of Single and Multiple Primary Melanomas

2021 ◽  
Vol 7 ◽  
Author(s):  
Simona De Summa ◽  
Antonia Lasorella ◽  
Sabino Strippoli ◽  
Giuseppe Giudice ◽  
Gabriella Guida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cell Cycle Control ◽  
Germline Mutations ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Multiple Genes ◽  
Multiple Primary ◽  
Small Cohort ◽  
Sequencing Platforms ◽  
Generation Sequencing

Background:Melanoma has a complex molecular background and multiple genes are involved in its development and progression. The advent of next generation sequencing platforms has enabled the evaluation of multiple genes at a time, thus unraveling new insights into the genetics of melanoma. We investigated a set of germline mutations able to discriminate the development of multiple primary melanomas (MPM) vs. single site primary melanomas (SPM) using a targeted next generation sequencing panel.Materials and Methods:A total of 39 patients, 20 with SPM and 19 with MPM, were enrolled in our study. Next generation analysis was carried out using a custom targeted sequencing panel that included 32 genes known to have a role in several carcinogenic pathways, such as those involved in DNA repair, pigmentation, regulation of kinases, cell cycle control and senescence.Results:We found a significant correlation between PIK3CA:p.I391M and MPMs, compared to SPMs,p= 0.031 and a trend for the association between CYP1B1: p.N453S and SPMs, compared to MPMs (p= 0.096). We also found that both subgroups shared a spectrum of 9 alterations in 8 genes (CYP1B1: p.N453S, BAP1: p.C39fs, PIK3CA: p.I391M, CDKAL1: c.1226_1227TG, POLE: p.V1161fs, OCA2: p.R419Q, OCA2: p.R305W, MC1R: p.V60L, MGMT: p.L115F), which suggested that these genes may play a role in melanoma development.Conclusions:In conclusion, despite the small cohort of patients, we found that germline mutations, such as those of PIK3CAand CYP1B1, might contribute to the differential development of SPM and MPM.

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