scholarly journals Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e520 ◽  
Author(s):  
Yan Wei Lim ◽  
Daniel A. Cuevas ◽  
Genivaldo Gueiros Z. Silva ◽  
Kristen Aguinaldo ◽  
Elizabeth A. Dinsdale ◽  
...  
Keyword(s):  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Line Islands

scholarly journals Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

2014 ◽  
Author(s):  
Yan Wei Lim ◽  
Daniel A Cuevas ◽  
Genivaldo Gueiros Z. Silva ◽  
Kristen Aguinaldo ◽  
Elizabeth Dinsdale ◽  
...  
Keyword(s):  
Ion Torrent ◽  
Microbial Genomes ◽  
Ion Torrent Pgm ◽  
Remote Locations ◽  
Microbial Ecosystems ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Line Islands ◽  
Generation Sequencing

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phospohonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

scholarly journals Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

2014 ◽  
Author(s):  
Yan Wei Lim ◽  
Daniel A Cuevas ◽  
Genivaldo Gueiros Z. Silva ◽  
Kristen Aguinaldo ◽  
Elizabeth Dinsdale ◽  
...  
Keyword(s):  
Ion Torrent ◽  
Microbial Genomes ◽  
Ion Torrent Pgm ◽  
Remote Locations ◽  
Microbial Ecosystems ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Line Islands ◽  
Generation Sequencing

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phospohonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

An SNP panel for the analysis of paternally inherited alleles in maternal plasma using ion Torrent PGM

2017 ◽  
Vol 132 (2) ◽  
pp. 343-352 ◽  
Author(s):  
Donggui Yang ◽  
Hao Liang ◽  
Shaobin Lin ◽  
Qing Li ◽  
Xiaoyan Ma ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Snp Panel

scholarly journals A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines

2020 ◽  
Vol 43 (2) ◽  
Author(s):  
Gabriela Pereira Branco ◽  
Renan Valieris ◽  
Lucas Venezian Povoa ◽  
Luiza Ferreira de Araújo ◽  
Gustavo Ribeiro Fernandes ◽  
...  
Keyword(s):  
Cell Lines ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Breast Cell Lines ◽  
Mirna Expression Profiles

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.

Abstract 4222: Ion AmpliSeq Panel for the DNA sequencing of BRCA1 and BRCA2 genes on Ion Torrent PGM.

2013 ◽  
Author(s):  
Jose L. Costa ◽  
Arjen Mensenkamp ◽  
Alain Rico ◽  
Guoying Liu ◽  
Rosella Petraroli ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Ion Torrent ◽  
Brca1 And Brca2 ◽  
Ion Torrent Pgm ◽  
Brca1 And Brca2 Genes

scholarly journals Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

2020 ◽  
Vol 280 ◽  
pp. 113865 ◽  
Author(s):  
Rachel L. Marine ◽  
Laura C. Magaña ◽  
Christina J. Castro ◽  
Kun Zhao ◽  
Anna M. Montmayeur ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Ion Torrent ◽  
Ion Torrent Pgm
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