Small RNA Library Construction for Exosomal RNA from Biological Samples for the Ion Torrent PGM™ and Ion S5™ System

2016 ◽  
pp. 71-90 ◽  
Author(s):  
Lesley Cheng ◽  
Andrew F. Hill
Keyword(s):  
Small Rna ◽  
Biological Samples ◽  
Ion Torrent ◽  
Library Construction ◽  
Ion Torrent Pgm ◽  
Small Rna Library

scholarly journals Small RNA Library Construction from Minute Biological Samples

2013 ◽  
pp. 123-136 ◽  
Author(s):  
Jessica A. Matts ◽  
Yuliya Sytnikova ◽  
Gung-wei Chirn ◽  
Gabor L. Igloi ◽  
Nelson C. Lau
Keyword(s):  
Small Rna ◽  
Biological Samples ◽  
Library Construction ◽  
Small Rna Library

scholarly journals Ligation bias is a major contributor to nonstoichiometric abundances of secondary siRNAs and impacts analyses of microRNAs

2020 ◽  
Author(s):  
Patricia Baldrich ◽  
Saleh Tamim ◽  
Sandra Mathioni ◽  
Blake Meyers
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Library Construction ◽  
Construction Methods ◽  
Wide Range ◽  
Secondary Sirnas ◽  
Two Stages ◽  
Material Library ◽  
Small Rna Library

ABSTRACTPlant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. High-throughput sequencing is used for the discovery and quantification of small RNAs. However, several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two stages of maize anthers to evaluate the performance of seven commercially-available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phasiRNAs, or tRNA-derived fragment. We also observed that ligation bias occurs at both ends of miRNAs and phasiRNAs, suggesting that the biased compositions observed in small RNA populations, including nonstoichiometric levels of phasiRNAs within a locus, may reflect a combination of biological and technical influences.

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.

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