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Vijayalakshmi Padmanabhan, Heather B Steinmetz, Elizabeth J Rizzo, Amber J Erskine, Tamara L Fairbank, Francine B de Abreu, Gregory J Tsongalis, Laura J Tafe
CONTEXT: -At our medical center, cytopathologists perform rapid on-site evaluation for specimen adequacy of fine-needle aspiration and touch imprint of needle core biopsy lung cancer samples. Two years ago the molecular diagnostics laboratory at our institution changed to next-generation sequencing using the Ion Torrent PGM and the 50-gene AmpliSeq Cancer Hotspot Panel v2 for analyzing mutations in a 50-gene cancer hot spot panel. This was associated with in a dramatic fall in adequacy rate (68%)...
October 20, 2016: Archives of Pathology & Laboratory Medicine
Nana Zhang, Guanjun Yue, Yan Zhang, Jiangfeng You, Hua Wang
[This corrects the article DOI: 10.1371/journal.pone.0153546.].
2016: PloS One
Dario Kringel, Jörn Lötsch
BACKGROUND: The opioid system is involved in the control of pain, reward, addictive behaviors and vegetative effects. Opioids exert their pharmacological actions through the agonistic binding at opioid receptors and variation in the coding genes has been found to modulate opioid receptor expression or signaling. However, a limited selection of functional opioid receptor variants is perceived as insufficient in providing a genetic diagnosis of clinical phenotypes and therefore, unrestricted access to opioid receptor genetics is required...
October 8, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
A D Samarajeewa, J R Velicogna, J I Princz, R M Subasinghe, R P Scroggins, L A Beaudette
Silver nano-particles (AgNPs) are widely used in a range of consumer products as a result of their antimicrobial properties. Given the broad spectrum of uses, AgNPs have the potential for being released to the environment. As a result, environmental risks associated with AgNPs need to be assessed to aid in the development of regulatory guidelines. Research was performed to assess the effects of AgNPs on soil microbial activity and diversity in a sandy loam soil with an emphasis on using a battery of microbial tests involving multiple endpoints...
October 4, 2016: Environmental Pollution
Matthias Christgen, Jana L van Luttikhuizen, Mieke Raap, Peter Braubach, Lars Schmidt, Danny Jonigk, Friedrich Feuerhake, Ulrich Lehmann, Brigitte Schlegelberger, Hans H Kreipe, Doris Steinemann
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott)...
October 3, 2016: Oncotarget
T Aykanat, M Lindqvist, V L Pritchard, C R Primmer
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%)...
October 6, 2016: Journal of Fish Biology
Jovana Bavaresco, Jessé R Fink, Maria Lucia K Rodrigues, Clesio Gianello, Vidal Barrón, José Torrent
Prolonged use of biosolids with high metal content may result in diffuse pollution across large regions, especially if such ions can move freely through the soil profile and reach underground water sources. The objective of this study was to verify whether Cr added to the soil surface in the form of hydrolysed leather or a soluble salt would migrate over significant distances in four subtropical soils differing in physical, chemical and mineralogical properties. Horizontal and vertical mobility were assessed in Petri dishes and small pots, respectively, using low (12 mg kg(-1) soil) and high Cr levels (150 mg kg(-1) soil) added to the soil surface...
October 4, 2016: Bulletin of Environmental Contamination and Toxicology
Philippe Lebel, Ann Letellier, Jessie Longpré, Benoit Laplante, Etienne Yergeau, Philippe Fravalo
AIMS: The object of this study was to determine the impact of only modifying the processing and/or particle size of pig feed on Salmonella shedding and faecal microbiota. METHODS AND RESULTS: Pigs were fed a diet that varied only by their processing (pellet or mash) and their particle size (500, 750 or 1250 μm) for 21 days. Salmonella detection in faeces and seroconversion were determined. Faecal microbiota was assessed by Ion Torrent amplicon sequencing and real-time PCR...
September 29, 2016: Journal of Applied Microbiology
Maciej Pietrzak, Audrey Papp, Amanda Curtis, Samuel K Handelman, Maria Kataki, Douglas W Scharre, Grzegorz Rempala, Wolfgang Sadee
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing...
October 28, 2016: Biochemical and Biophysical Research Communications
Lorena Lazo de la Vega, Daniel H Hovelson, Andi K Cani, Chia-Jen Liu, Jonathan B McHugh, David R Lucas, Dafydd G Thomas, Rajiv M Patel, Scott A Tomlins
Gene fusions between CIC and DUX4 define a rare class of soft tissue sarcomas poorly understood at the molecular level. Previous karyotyping and fluorescence in situ hybridization studies support trisomy chromosome 8 as a recurrent alteration, however other driving alterations are largely unknown. Thus, we analyzed eleven formalin fixed paraffin embedded CIC-DUX4 sarcoma tissue samples (including three sample pairs) using targeted Ion Torrent based multiplexed polymerase chain reaction (PCR) next generation sequencing to characterize potential somatic driver alterations in 409 genes...
September 21, 2016: Human Pathology
Stacie Tardif, Étienne Yergeau, Julien Tremblay, Pierre Legendre, Lyle G Whyte, Charles W Greer
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv...
2016: Frontiers in Microbiology
Shreya Srivastava, Basdeo Kushwaha, Jyoti Prakash, Ravindra Kumar, N S Nagpure, Suyash Agarwal, Manmohan Pandey, P Das, C G Joshi, J K Jena
Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde+4acde ver. 3.1 categories by the IUCN (2015) due to decreasing population trend. Microsatellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present study, 31,814 SSRs of C. batrachus (magur) were identified using microsatellite identification tool programme from the next generation sequencing data generated on Roche 454 and Ion Torrent platforms. A bioinformatics pipeline, with stringent criteria resulted in selection of 1672 microsatellite loci falling in the genic region...
September 2016: Journal of Genetics
Laura J Tafe, Kirsten J Pierce, Jason D Peterson, Francine de Abreu, Vincent A Memoli, Candice C Black, Jason R Pettus, Jonathan D Marotti, Edward J Gutmann, Xiaoying Liu, Keisuke Shirai, Konstantin H Dragnev, Christopher I Amos, Gregory J Tsongalis
Detection of somatic mutations in non-small cell lung cancers (NSCLCs), especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM) and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips)...
September 2016: Neoplasia: An International Journal for Oncology Research
G Hoarau, P K Mukherjee, C Gower-Rousseau, C Hager, J Chandra, M A Retuerto, C Neut, S Vermeire, J Clemente, J F Colombel, H Fujioka, D Poulain, B Sendid, M A Ghannoum
UNLABELLED: Crohn's disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their nondiseased first-degree relatives (NCDR) in 9 familial clusters living in northern France-Belgium and in healthy individuals from 4 families living in the same area (non-CD unrelated [NCDU])...
2016: MBio
Nadezda P Velizheva, Markus P Rechsteiner, Christine E Wong, Qing Zhong, Matthias Rössle, Beata Bode, Holger Moch, Alex Soltermann, Peter J Wild, Verena Tischler
BACKGROUND: Molecular testing of lung adenocarcinomas (ADCs) is crucial for therapy stratification of patients. Because of the often limited diagnostic material, the authors aimed to explore the suitability of cytology smears for next-generation sequencing (NGS) and compared the results with concurrent histological specimens or cell blocks. METHODS: A total of 16 formalin-fixed paraffin-embedded (FFPE) ADCs with known genetic alterations were used as the first cohort for targeted DNA and RNA sequencing...
September 16, 2016: Cancer Cytopathology
Gian Matteo Rigolin, Elena Saccenti, Cristian Bassi, Laura Lupini, Francesca Maria Quaglia, Maurizio Cavallari, Sara Martinelli, Luca Formigaro, Enrico Lista, Maria Antonella Bardi, Eleonora Volta, Elisa Tammiso, Aurora Melandri, Antonio Urso, Francesco Cavazzini, Massimo Negrini, Antonio Cuneo
BACKGROUND: In chronic lymphocytic leukemia (CLL), next-generation sequencing (NGS) analysis represents a sensitive, reproducible, and resource-efficient technique for routine screening of gene mutations. METHODS: We performed an extensive biologic characterization of newly diagnosed CLL, including NGS analysis of 20 genes frequently mutated in CLL and karyotype analysis to assess whether NGS and karyotype results could be of clinical relevance in the refinement of prognosis and assessment of risk of progression...
September 15, 2016: Journal of Hematology & Oncology
Nadia Marascio, Grazia Pavia, Alessio Strazzulla, Tim Dierckx, Lize Cuypers, Bram Vrancken, Giorgio Settimo Barreca, Teresa Mirante, Donatella Malanga, Duarte Mendes Oliveira, Anne-Mieke Vandamme, Carlo Torti, Maria Carla Liberto, Alfredo Focà, The Sinergie-Umg Study Group
Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1b genome from serum samples of DAA-naïve patients in the context of the SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology, 2014) project. We deep-sequenced the NS3/4A protease region of the viral population using the Ion Torrent Personal Genome Machine, and patient-specific majority rule consensus sequence summaries were constructed with a combination of freely available next generation sequencing data analysis software...
2016: International Journal of Molecular Sciences
Sintia Almeida, Dan Loureiro, Ricardo W Portela, Diego C B Mariano, Thiago J Sousa, Felipe L Pereira, Fernanda A Dorella, Alex F Carvalho, Lilia F Moura-Costa, Carlos A G Leal, Henrique C Figueiredo, Roberto Meyer, Vasco Azevedo
We present here the genome sequence of the attenuated Corynebacterium pseudotuberculosis strain T1. The sequencing was performed with an Ion Torrent Personal Genome Machine platform. The genome is a circular chromosome of 2,337,201 bp, with a G+C content of 52.85% and a total of 2,125 coding sequences (CDSs), 12 rRNAs, 49 tRNAs, and 24 pseudogenes.
2016: Genome Announcements
Andy S Alic, Ignacio Blanquer
Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis...
September 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Sarah Beasley, Phillip J Buckhaults, Nancy G Pedigo, Christopher L Farrell
Recent cancer studies have suggested that the faciogenital dysplasia 1 (FGD1) gene may play a role in the development of tumor cells. Somatic alterations in the FGD1 gene and increased Fgd1 protein expression have been observed in many breast tumor cases. The present study sequenced the FGD1 gene in tumor DNA from 46 breast cancer patients using Ion Torrent sequencing. Three synonymous polymorphisms and one missense polymorphism were detected with next-generation sequencing; however, no somatic mutations were observed...
September 2016: Oncology Letters
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