Towards allele-level human leucocyte antigens genotyping - assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq

2015 ◽  
Vol 42 (5) ◽  
pp. 346-358 ◽  
Author(s):  
J. L. Duke ◽  
C. Lind ◽  
K. Mackiewicz ◽  
D. Ferriola ◽  
A. Papazoglou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Personal Genome ◽  
Ion Torrent ◽  
Next Generation ◽  
Personal Genome Machine ◽  
Human Leucocyte Antigens ◽  
Sequencing Platforms ◽  
Leucocyte Antigens ◽  
Generation Sequencing

scholarly journals A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 341 ◽  
Author(s):  
Michael Quail ◽  
Miriam E Smith ◽  
Paul Coupland ◽  
Thomas D Otto ◽  
Simon R Harris ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Ion Torrent ◽  
Next Generation ◽  
Pacific Biosciences ◽  
Sequencing Platforms ◽  
Generation Sequencing

scholarly journals A Comprehensive Assay for CFTR Mutational Analysis Using Next-Generation Sequencing

2013 ◽  
Vol 59 (10) ◽  
pp. 1481-1488 ◽  
Author(s):  
Ahmad N Abou Tayoun ◽  
Christopher D Tunkey ◽  
Trevor J Pugh ◽  
Tristen Ross ◽  
Minita Shah ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Next Generation Sequencing ◽  
Mutational Analysis ◽  
Genetic Disorder ◽  
Sequencing Error ◽  
Personal Genome ◽  
Ion Torrent ◽  
Next Generation ◽  
Cftr Mutations ◽  
Generation Sequencing

BACKGROUND Cystic fibrosis is a life-threatening genetic disorder that has been associated with mutations in the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene. Hundreds of CFTR mutations have been detected to date. Current CFTR genotyping assays target a subset of these mutations, particularly a mutation panel recommended by the American College of Medical Genetics for carrier screening of the general population. Fast sequencing of the entire coding sequence in a scalable manner could expand the detection of CFTR mutations and facilitate management of costs and turnaround times in the clinical laboratory. METHODS We describe a proof-of-concept CFTR assay that uses PCR target enrichment and next-generation sequencing on the Ion Torrent Personal Genome Machine™ (PGM™) platform. RESULTS The scalability of the assay was demonstrated, with an average mean depth of coverage ranging from 500× to 3500×, depending on the number of multiplexed patient samples and the Ion Torrent chip used. In a blinded study of 79 previously genotyped patient DNA samples and cell lines, our assay detected most of the mutations, including single-nucleotide variants, small insertions and deletions, and large copy-number variants. The reproducibility was 100% for detecting mutations in independent runs. Our assay demonstrated high specificity, with only 2 false-positive calls (at 2184delA) found in 2 samples caused by a sequencing error in a homopolymer stretch of sequence. The detection rate for variants of unknown significance was very low in the targeted region. CONCLUSIONS With continued optimization and system refinements, PGM sequencing promises to be a powerful, rapid, and scalable means of clinical diagnostic sequencing.

Detection of actionable oncogene drivers alterations in HER2-amplified gastric cancer by next generation sequencing.

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 67-67
Author(s):  
Carlos Gomez-Martin ◽  
Roberto A. Pazo Cid ◽  
Antonieta Salud ◽  
Paula J. Fonseca ◽  
Ana Leon ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Personal Genome ◽  
Ion Torrent ◽  
Next Generation ◽  
Sequencing Data ◽  
Sequencing Platform ◽  
Formalin Fixed Paraffin ◽  
Mutational Hotspots ◽  
Formalin Fixed Paraffin Embedded ◽  
Generation Sequencing

67 Background: HER2 amplified cases are the only subset of gastric carcinoma (GC) patients with an approved targeted therapy (≈20%). In GC it is still unknown if there is a mutually exclusive pattern of mutations in major driver oncogenes. We performed a systematic search for targetable oncogenes in a cohort of HER2 amplified GC patients. Methods: 53 Formalin-fixed paraffin embedded samples from HER2 amplified GC patients (43 tumor and 10 normal samples) were selected for next generation sequencing (NGS). Before DNA extraction a macrodissection procedure was performed to guarantee at least 30% tumor in all cases. DNA samples were sequenced using the Ion Torrent Personal Genome Machine (PGM) sequencing platform (Life Technologies, Carlsbad, CA, USA). The Ion AmpliSeq Cancer Hotspot Panel v2 was used. This panel encompasses more than 2800 mutational hotspots of 50 oncogenes and tumor suppressor genes. Data were processed using the Ion Torrent platform-specific pipeline software Torrent suite v4.2. Moreover, sequencing data were analyzed with Ion Reporter software 4.2 to detect any copy number alteration of the genes included in the panel. Results: We successfully sequenced all samples. We identified 89 mutations in 12 genes (range from 1 ~ 9). The most frequent significant mutations included TP53 mutations (30), PI3KCA (3), SMAD4 (3), CDKN2A (4), CTNNB1 (3) and MET (3). Other mutations were found in KRAS, NOTCH, APC, and VHL genes. We also detected potential amplifications in the KRAS (4), EGFR (9), PI3KCA (11), AKT (6), FGFR (6), CDKN2A (4) and CDH1(8) genes. Among 43 tumor specimens, 86% of specimens harbored at least one genetic alteration, most of them linked to actionable mutations or amplifications Conclusions: Within HER2 amplified GCs, there are additional subsets with a potentially targetable oncogene. Future testing for these targets will benefit from including HER2 amplified GC patients Supported by the Spanish Ministry of Health, Fondo de Investigaciones Sanitarias grant PI11/01005 and European FEDER (PN I+D+I 2008‐20011).

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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