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.

Mutational landscape of AKT1/2/3 in Chinese patients with solid tumors.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15566-e15566
Author(s):  
Hui Kong ◽  
Weijia Fang ◽  
Haibo Mou ◽  
Feng Xiao Chen ◽  
Lingxiang Liu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Chinese Patients ◽  
Great Promise ◽  
Central Component ◽  
Next Generation ◽  
Gene Panel Testing ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e15566 Background: As a central component of PI3K/AKT pathway, AKT serves as an attractive target of anti-cancer strategy with various AKT inhibitors, which show great promise in phase I/II clinical trials. This study aimed to investigate AKT1/2/3 status in different types of cancers by using next generation sequencing (NGS). Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were collected from 10,010 Chinese patients with solid tumors and subjected to next-generation sequencing (NGS)-based 450 gene panel testing carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Genomic alterations, tumor mutational burden (TMB) values, and microsatellite instability (MSI) status were assessed with a mean coverage of 1000X, including single base substitutions, short and long insertion/deletions, copy number variations, gene fusions, and rearrangements. Genomic data and immune checkpoint inhibitors (ICIs) treatment outcome of a cohort of 1610 patients with solid tumors were derived from cBioPortal (MSKCC, Nat Genet. 2019). Results: AKT1/2/3 were found to be mutually exclusive with each other and accounted for 3.4% in this cohort. The frequencies of AKT1/2/3 variations were 1.1%, 1.6%, and 0.8%, respectively. The most common co-altered genes associated with AKT1/2/3 variations were TP53 (69.4%), PIK3CA (19.3%), KRAS (19%), CCNE1 (18.4%), CDKN2A (16.6%), and 11q13 (6.5%). AKT1/2/3 variations were significantly associated with higher TMB, and independent of MSI status. Outcome data from the MSKCC cohort showed that patients with AKT1/2/3 variations had a remarkable clinical benefit to ICIs treatment compared to patients with wild-type AKT1/2/3 in overall survival (OS) (NA vs 18 months, p = 0.009). Furthermore, AKT1/2/3 variations were independent risk factors of OS (HR: 0.55, 95%CI: 0.34-0.87, p = 0.012). Conclusions: The prevalence of AKT1/2/3 somatic alterations across different types of solid tumors in China was 3.4%. AKT1/2/3 variations were associated with an increased TMB and favorable response to ICIs, suggesting that A KT1/2/3 variations may be biomarkers for guiding anti-AKT agents and ICI treatment.

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.

Diagnostik der Sepsis – Teil 2: Erregeridentifikation

2019 ◽  
Vol 54 (01) ◽  
pp. 38-48 ◽  
Author(s):  
Daniel Richter ◽  
Alexandra Heininger ◽  
Karsten Schmidt ◽  
Thomas Schmoch ◽  
Michael Bernhard ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Chain Reaction ◽  
Antimikrobielle Therapie ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Kritisch Kranker

ZusammenfassungIm Rahmen der Sepsis und des septischen Schocks spielen, trotz der zunehmenden Verbreitung von neuen molekularbiologischen Verfahren, der kulturelle Erregernachweis und die Resistenztestung weiterhin die entscheidende Rolle in der antimikrobiellen Therapie auf der Intensivstation. Hierbei kann der Erregernachweis für die antimikrobielle Therapie einerseits direkt aus dem Patientenblut, andererseits aber auch aus diversen anderen Probenmaterialien (respiratorische Sekrete, Punktat, intraoperative Abstriche etc.) geführt werden. Ein Nachteil konventioneller kultureller Verfahren im Kontext kritisch kranker Patienten ist die zeitliche Latenz bis zum Erregernachweis bzw. zum Ergebnis der Resistenztestung. Molekularbiologische Verfahren wie Techniken der Erregerdiagnostik und Resistenztestung, die auf Polymerase Chain Reaction (PCR) oder vor allem Next-Generation Sequencing (NGS) basieren, versprechen hier zwar kürzere Umlaufzeiten, sind aber aktuell noch kein klinischer Standard. Trotzdem besitzen diese Verfahren das Potenzial, einen Paradigmenwechsel in der Erregerdiagnostik herbeizuführen.

scholarly journals Discovery of Negative-Sense RNA Viruses in Trees Infected with Apple Rubbery Wood Disease by Next-Generation Sequencing

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1254-1263 ◽  
Author(s):  
Michael E. Rott ◽  
Prasad Kesanakurti ◽  
Constanze Berwarth ◽  
Heidi Rast ◽  
Ian Boyes ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
New Genus ◽  
Fruit Trees ◽  
Next Generation ◽  
Chain Reaction ◽  
The Family ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Negative Sense ◽  
Generation Sequencing

Apple rubbery wood is a disease of apple found around the world, often associated with Apple flat limb disease, and regulated in many countries. Despite its long history in apple cultivation, the disease’s causal agent has remained elusive. In this study, next-generation sequencing (NGS) was used to identify and characterize several related novel viral agents from apple rubbery wood-infected plants, which have been named Apple rubbery wood virus (ARWV) 1 and 2. Additional specimens with apple rubbery wood disease tested positive by polymerase chain reaction with primers designed to ARWV 1 and 2 genomic RNA segments. In an NGS-based screening of over 100 Malus and 100 Prunus specimens from a collection of virus-infected trees, only one Malus specimen was found to be infected with ARWV not known to be infected with the disease, which strongly suggests that ARWV is not commonly found in Malus spp. or other fruit trees. The two viruses are most closely related to members of the order Bunyavirales. Three RNA segments (large, medium, and small) were characterized and the viruses likely represent a new genus under the family Phenuiviridae, with a suggested name of Rubodvirus (Rubbery wood virus).

Next generation sequencing, insect microbiomes, and the confounding effect of Wolbachia: a case study using Drosophila suzukii Matsumura (Diptera: Drosophilidae)

2021 ◽  
Author(s):  
Diana Wilches ◽  
Paul Coghlin ◽  
Kevin Floate
Keyword(s):  
Next Generation Sequencing ◽  
Newfoundland And Labrador ◽  
Confounding Factor ◽  
Next Generation ◽  
Drosophila Suzukii ◽  
Arthropod Species ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next generation sequencing (NGS) increasingly is being used to characterize the gut microbiome of insects to provide insights into the ecology and biology of the host, but results may be confounded by co-occurring infections of Wolbachia bacteria in the cells of the host. We illustrate this issue using spotted winged drosophila (SWD), Drosophila suzukii Matsumura, 1931 (Diptera: Drosophilidae) as an example. With a polymerase chain reaction based assay, we detected Wolbachia in 20 percent of flies collected from sites in British Columbia, Alberta, and Newfoundland and Labrador, Canada. With NGS, we determined that the total microbiome of infected flies was dominated by Wolbachia (ave. of 98.8%) with average values of bacterial richness and diversity 1.4- and 22-fold lower than that of co-occurring, uninfected flies (ave. of 0.6% Wolbachia). We review options available to address the confounding factor of Wolbachia, which vary with the presence of infections in the population, the prevalence of infected individuals in the population, and the titre of Wolbachia in infected individuals. Understanding this issue and how it can be resolved is of broad importance, given that an estimated 40 percent of terrestrial arthropod species harbour Wolbachia infections.

scholarly journals An interlaboratory study of complex variant detection

2017 ◽  
Author(s):  
Stephen E Lincoln ◽  
Justin M Zook ◽  
Shimul Chowdhury ◽  
Shazia Mahamdallie ◽  
Andrew Fellowes ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Validation Studies ◽  
Cost Effective ◽  
Interlaboratory Study ◽  
Next Generation ◽  
Variant Detection ◽  
Synthetic Controls ◽  
Next Generation Sequencing Ngs ◽  
Uniform Assessment ◽  
Generation Sequencing

ABSTRACTNext-generation sequencing (NGS) is widely used and cost-effective. Depending on the specific methods, NGS can have limitations detecting certain technically challenging variant types even though they are both prevalent in patients and medically important. These types are underrepresented in validation studies, hindering the uniform assessment of test methodologies by laboratory directors and clinicians. Specimens containing such variants can be difficult to obtain; thus, we evaluated a novel solution to this problem in which a diverse set of technically challenging variants was synthesized and introduced into a known genomic background. This specimen was sequenced by 7 laboratories using 10 different NGS workflows. The specimen was compatible with all 10 workflows and presented biochemical and bioinformatic challenges similar to those of patient specimens. Only 10 of 22 challenging variants were correctly identified by all 10 workflows, and only 3 workflows detected all 22. Many, but not all, of the sensitivity limitations were bioinformatic in nature. We conclude that Synthetic controls can provide an efficient and informative mechanism to augment studies with technically challenging variants that are difficult to obtain otherwise. Data from such specimens can facilitate inter-laboratory methodologic comparisons and can help establish standards that improve communication between clinicians and laboratories.

scholarly journals Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area

2020 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Alireza Tafazoli ◽  
Natalia Wawrusiewicz-Kurylonek ◽  
Renata Posmyk ◽  
Wojciech Miltyk
Keyword(s):  
Next Generation Sequencing ◽  
Personalized Medicine ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Clinical Practices ◽  
Clinical Investigations ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Pharmacogenomics (PGx) is the knowledge of diverse drug responses and effects in people, based on their genomic profiles. Such information is considered as one of the main directions to reach personalized medicine in future clinical practices. Since the start of applying next generation sequencing (NGS) methods in drug related clinical investigations, many common medicines found their genetic data for the related metabolizing/shipping proteins in the human body. Yet, the employing of technology is accompanied by big obtained data, which most of them have no clear guidelines for consideration in routine treatment decisions for patients. This review article talks about different types of NGS derived PGx variants in clinical studies and try to display the current and newly developed approaches to deal with pharmacogenetic data with/without clear guidelines for considering in clinical settings.

Sign in / Sign up

Export Citation Format

Share Document