scholarly journals In Phase HLA Genotyping by Next Generation Sequencing — A Comparison Between Two Massively Parallel Sequencing Bench-Top Systems, the Roche GS Junior and Ion Torrent PGM

10.5772/57556 ◽  
2014 ◽  
Author(s):  
Jerzy K. ◽  
Shingo Suzuki ◽  
Yuki Ozaki ◽  
Shigeki Mitsunaga ◽  
Hidetoshi Inoko ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Ion Torrent ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Ion Torrent Pgm ◽  
Hla Genotyping ◽  
Generation Sequencing

scholarly journals The Impact of Next Generation Sequencing in Cancer Research

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2928
Author(s):  
Katia Nones ◽  
Ann-Marie Patch
Keyword(s):  
Cancer Research ◽  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing ◽  
Technical Revolution

Next generation sequencing (NGS) describes the technical revolution that enabled massively parallel sequencing of fragmented nucleic acids, thus making possible our current genomic understanding of cancers [...]

scholarly journals Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6661 ◽  
Author(s):  
Arianna Nicolussi ◽  
Francesca Belardinilli ◽  
Yasaman Mahdavian ◽  
Valeria Colicchia ◽  
Sonia D’Inzeo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Germline Mutations ◽  
Ion Torrent ◽  
Next Generation ◽  
Training Set ◽  
Brca1 And Brca2 ◽  
Ion Torrent Pgm ◽  
Validation Set ◽  
Generation Sequencing

Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.

scholarly journals Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

2010 ◽  
Vol 76 (12) ◽  
pp. 3863-3868 ◽  
Author(s):  
J. Kirk Harris ◽  
Jason W. Sahl ◽  
Todd A. Castoe ◽  
Brandie D. Wagner ◽  
David D. Pollock ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Massively Parallel Sequencing ◽  
Sequence Data ◽  
Cost Savings ◽  
Massively Parallel ◽  
Next Generation ◽  
Normalization Methods ◽  
The Cost ◽  
Generation Sequencing

ABSTRACT Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where ≤1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel.

scholarly journals Comparison of Next-Generation Sequencing Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Lin Liu ◽  
Yinhu Li ◽  
Siliang Li ◽  
Ni Hu ◽  
Yimin He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Sequence Information ◽  
Ion Torrent ◽  
Next Generation ◽  
Extensive Experience ◽  
Ion Torrent Pgm ◽  
Fast Development ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world’s biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

The Next Generation Sequencing Techniques and Application in Drug Discovery and Development

2019 ◽  
pp. 240-259
Author(s):  
Afzal Hussain
Keyword(s):  
Next Generation Sequencing ◽  
Rna Sequencing ◽  
Expression Profiling ◽  
Massively Parallel Sequencing ◽  
Life Sciences ◽  
Rna Seq ◽  
Next Generation ◽  
Parallel Sequencing ◽  
Short Period ◽  
Generation Sequencing

Next-generation sequencing or massively parallel sequencing describe DNA sequencing, RNA sequencing, or methylation sequencing, which shows its great impact on the life sciences. The recent advances of these parallel sequencing for the generation of huge amounts of data in a very short period of time as well as reducing the computing cost for the same. It plays a major role in the gene expression profiling, chromosome counting, finding out the epigenetic changes, and enabling the future of personalized medicine. Here the authors describe the NGS technologies and its application as well as applying different tools such as TopHat, Bowtie, Cufflinks, Cuffmerge, Cuffdiff for analyzing the high throughput RNA sequencing (RNA-Seq) data.

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