Next generation sequencing with a semi-conductor technology (Ion Torrent PGM™) for HLA typing: overall workflow performance and debate

2016 ◽  
Vol 74 (4) ◽  
pp. 449-456 ◽  
Author(s):  
Virginie Moalic-Allain ◽  
Bernard Mercier ◽  
Paul Gueguen ◽  
Claude Ferec
Keyword(s):  
Next Generation Sequencing ◽  
Hla Typing ◽  
Ion Torrent ◽  
Next Generation ◽  
Ion Torrent Pgm ◽  
Generation Sequencing

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 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.

scholarly journals Next-Generation Sequencing Workflow for NSCLC Critical Samples Using a Targeted Sequencing Approach by Ion Torrent PGM™ Platform

2015 ◽  
Vol 16 (12) ◽  
pp. 28765-28782 ◽  
Author(s):  
Irene Vanni ◽  
Simona Coco ◽  
Anna Truini ◽  
Marta Rusmini ◽  
Maria Dal Bello ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Targeted Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Ion Torrent Pgm ◽  
Generation Sequencing

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

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