keyword
MENU ▼
Read by QxMD icon Read
search

ion torrent

keyword
https://www.readbyqxmd.com/read/29146836/complete-genome-sequences-of-bk-polyomavirus-strains-from-two-patients-with-urinary-tract-infection-sequenced-using-the-ion-torrent-platform
#1
Graham Rose, Kyriaki Ranellou, Raju Misra, Colin Crump, David Wooldridge, Surendra Parmar, Christopher Maddren, Saheer Gharbia, Hamid Jalal
BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29141311/-study-on-mosaicism-of-scn1a-gene-mutation-in-parents-of-children-with-dravet-syndrome
#2
A J Liu, X X Yang, X J Xu, Q X Wu, X J Tian, X L Yang, X R Wu, L P Wei, Y H Zhang
Objective: To investigate the clinical phenotypes and the mutant allele proportion of parents with SCN1A gene mutation mosaicism of Dravet syndrome (DS) children, thus to provide guidance for family reproduction and prenatal diagnosis. Method: The clinical data and peripheral blood DNA samples of DS patients with a SCN1A gene mutation proved by Sanger sequencing were collected prospectively from February 2005 to November 2016 in Department of Pediatrics, Peking University First Hospital. The same mutation was searched in parents and other available relatives...
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29140103/salmonella-gallinarum-field-isolates-and-its-relationship-to-vaccine-strain-sg9r
#3
P K V Koerich, B B Fonseca, E Balestrin, V Tagliari, P G Hoepers, C Ueira-Vieira, I Oldoni, R H Rauber, L Ruschel, V P Do Nascimento
1. The aim of the present study was to determine if the 9R-strain of the Salmonella gallinarum live vaccine was responsible for having fowl typhoid outbreaks in chicken flocks from both chicken and turkey breeders as well as to verify the antimicrobial resistance of the isolates from the outbreaks. 2. The triplex polymerase chain reaction (PCR), standard antimicrobial test, beta-lactamase genes identification and Ion Torrent PMG whole genome sequence were used in the field isolates and in the vaccine strain of S...
November 15, 2017: British Poultry Science
https://www.readbyqxmd.com/read/29134591/sequencing-assembling-and-finishing-complete-bacteriophage-genomes
#4
Daniel A Russell
Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29128545/massive-parallel-sequencing-of-mitochondrial-dna-genomes-from-mother-child-pairs-using-the-ion-torrent-personal-genome-machine-pgm
#5
Ke Ma, Xueying Zhao, Hui Li, Yu Cao, Wei Li, Jian Ouyang, Lu Xie, Wenbin Liu
Mitochondrial genome analysis is a potent tool in forensic practice and in the understanding of human phylogeny in the maternal lineage. With the development of molecular biology and bioinformatics techniques, high-throughput sequencing has enabled mtDNA analysis during whole genome sequencing, which provides more comprehensive information and raises the power of discrimination. In this study, peripheral blood samples were taken from 194 mother-offspring pairs and sequenced by Ion Torrent Personal Genome Machine and obtained high-coverage mitochondrial sequencing data, demonstrating the mutation levels at each position in the mitochondrial DNA (mtDNA) between maternally related pairs...
November 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29126106/airvf-a-filtering-toolbox-for-precise-variant-calling-in-ion-torrent-sequencing
#6
Sunguk Shin, Hanna Lee, Hyeonju Son, Soonmyung Paik, Sangwoo Kim
Summary: Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (<15%). Here, we developed a multi-step filtering toolbox AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29122352/microbial-community-response-to-silver-nanoparticles-and-ag-in-nitrifying-activated-sludge-revealed-by-ion-semiconductor-sequencing
#7
Carley A Gwin, Emilie Lefevre, Christina L Alito, Claudia K Gunsch
Silver nanoparticles (AgNPs), which are known to act as biocides, are incorporated into medical and consumer products including athletic clothing, stuffed animals, liquid dietary supplements, and more. The increasing use of AgNPs in these products is likely to lead to their entry into both natural and engineered systems, which has the potential to disrupt bacterial processes including those involved in nutrient cycling in wastewater treatment. In the present study, sequencing batch reactors (SBR) mimicking secondary wastewater treatment were operated to determine the effects of AgNPs on the microbial communities contained within activated sludge of wastewater treatment plants (WWTP)...
November 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29074089/application-of-next-generation-sequencing-to-detect-acyclovir-resistant-herpes-simplex-virus-type-1-variants-at-low-frequency-in-thymidine-kinase-gene-of-the-isolates-recovered-from-patients-with-hematopoietic-stem-cell-transplantation
#8
Hikaru Fujii, Satsuki Kakiuchi, Masanori Tsuji, Hidekazu Nishimura, Tomoki Yoshikawa, Souichi Yamada, Natsumi Omura, Takuya Inagaki, Miho Shibamura, Shizuko Harada, Shuichi Taniguchi, Masayuki Saijo
Ion Torrent next-generation sequencing (NGS) technology was applied to study the mode of emergence of acyclovir (ACV)-resistant (ACVr) herpes simplex virus type 1 (HSV-1) in patients with hematopoietic stem cell transplantation (HSCT) by quantitatively detecting mutations in the viral thymidine kinase (vTK) gene in the HSV-1 isolates recovered from HSCT patients. All of the mutations detected with the Sanger sequencing method in the vTK genes of HSV-1 isolates were also detected with the NGS assay. Furthermore, different mutations, which conferred ACV resistance and were not detected with the Sanger sequencing method, were also detected in a quantitative manner by using the NGS assay...
January 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29051756/genomic-gc-content-affects-the-accuracy-of-16s-rrna-gene-sequencing-based-microbial-profiling-due-to-pcr-bias
#9
Martin F Laursen, Marlene D Dalgaard, Martin I Bahl
Profiling of microbial community composition is frequently performed by partial 16S rRNA gene sequencing on benchtop platforms following PCR amplification of specific hypervariable regions within this gene. Accuracy and reproducibility of this strategy are two key parameters to consider, which may be influenced during all processes from sample collection and storage, through DNA extraction and PCR based library preparation to the final sequencing. In order to evaluate both the reproducibility and accuracy of 16S rRNA gene based microbial profiling using the Ion Torrent PGM platform, we prepared libraries and performed sequencing of a well-defined and validated 20-member bacterial DNA mock community on five separate occasions and compared results with the expected even distribution...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29049006/the-dynamics-of-immunoglobulin-v-gene-usage-and-clonotype-expansion-in-mice-after-prime-and-boost-immunizations-as-analyzed-by-ngs
#10
Diego J Farfán-Arribas, Shuying Liu, Shixia Wang, Shan Lu
In the current study, an improved NGS approach was developed to study the B-cell repertoire evolution in a simple mouse immunization model including only two DNA immunizations. The combination of 5'RACE and Ion Torrent long reads enabled unbiased immunoglobulin repertoire analysis even from small amounts of peripheral mouse blood. The B-cell population expanded by the vaccine displayed a relatively strong clonality. Upon priming with the first vaccine dose, we observed a consistent pattern of V-segment gene and CDR3 usage (public specificities)...
October 19, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/29048639/phenotype-characterization-of-human-melanoma-cells-resistant-to-dabrafenib
#11
Fabiola Gilda Cordaro, Anna Lisa De Presbiteris, Rosa Camerlingo, Nicola Mozzillo, Giuseppe Pirozzi, Ernesta Cavalcanti, Antonella Manca, Giuseppe Palmieri, Antonio Cossu, Gennaro Ciliberto, Paolo A Ascierto, Salvatore Travali, Eduardo J Patriarca, Emilia Caputo
In the present study, the phenotype of melanoma cells resistant to dabrafenib (a B-RAF inhibitor) was investigated, to shed more light on melanoma resistance to B-RAF inhibition. Melanoma cells resistant to dabrafenib were generated using 3 different cell lines, A375, 397 and 624.38, all carrying B-RAFV600E, and they were characterized by cytofluorometric analysis, Ion Torrent technology, immunofluorescence and biochemistry. All dabrafenib-resistant cells showed, in addition to a re-activation of MAPK signaling, morphological changes compared to their sensitive counterparts, accompanied by an increase in CD90 (mesenchymal marker) expression and a decrease in E-cadherin (epithelial marker) expression, suggesting an epithelial-to-mesenchymal-like phenotypic transition...
September 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29045810/a-novel-next-generation-sequencing-assay-as-an-alternative-to-currently-available-methods-for-hepatitis-c-virus-genotyping
#12
G Dirani, E Paesini, E Mascetra, P Farabegoli, B Dalmo, B Bartolini, A R Garbuglia, M R Capobianchi, V Sambri
Chronic HCV infection is one of the leading causes of liver-related death and in many countries it is a primary reason for having a liver transplant. HCV genotype identification has long been used in the clinical practice, since different genotypes have different response rates and required different doses and durations of IFN/RBV treatment; moreover both the frequency and the pattern of resistance to different Direct-Acting Antivirals (DAAs) classes are subtype specific. Hence the necessity to make an accurate HCV subtyping becomes a fundamental tool to optimize current and future clinical management of HCV infected subjects...
January 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29019931/targeted-next-generation-sequencing-identification-of-mutations-in-disease-resistance-gene-analogs-rgas-in-wild-and-cultivated-beets
#13
Piergiorgio Stevanato, Chiara Broccanello, Luca Pajola, Filippo Biscarini, Chris Richards, Lee Panella, Mahdi Hassani, Elide Formentin, Claudia Chiodi, Giuseppe Concheri, Bahram Heidari
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples of ninety-six individuals from six sea beets (Beta vulgaris L. subsp. maritima) and six sugar beet pollinators (eight individuals each) were used for the discovery of single-nucleotide polymorphisms (SNPs). Target amplicons of about 200 bp in length were designed with the Ion AmpliSeq Designer system in order to cover the DNA sequences of the RGAs...
October 11, 2017: Genes
https://www.readbyqxmd.com/read/29018424/sample-preservation-dna-or-rna-extraction-and-data-analysis-for-high-throughput-phytoplankton-community-sequencing
#14
Anita Mäki, Pauliina Salmi, Anu Mikkonen, Anke Kremp, Marja Tiirola
Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affected the results of the NGS analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28991373/novel-enriched-pathways-in-superficial-malignant-peripheral-nerve-sheath-tumors-mpnst-and-spindle-desmoplastic-melanomas-sdm
#15
George Jour, Nicole K Andeen, Rami Al -Rohil, Phyu P Aung, Meenakshi Mehrotra, Dzifa Duose, Benjamin Hoch, Zolt Argenyi, Rajyalakshmi Luthra, Ignacio I Wistuba, Victor G Prieto
Superficial malignant peripheral nerve sheath tumor (MPNST) is a rare, soft tissue neoplasm that shares morphological features and some molecular events with spindle and desmoplastic melanoma (SDM). Herein we sought to identify molecular targets for therapy using targeted RNA/DNA sequencing and gene expression of key immunological players. DNA and RNA from formalin-fixed, paraffin-embedded (FFPE) tissue were extracted and processed. Massive high-throughput deep parallel sequencing was performed using the Oncomine comprehensive panel enabling detection of relevant SNVs, CNVs, gene fusions, and indels from 143 unique genes on the Ion torrent sequencer for clinical trial research programs...
October 9, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28977035/indigenous-species-barcode-database-improves-the-identification-of-zooplankton
#16
Jianghua Yang, Xiaowei Zhang, Wanwan Zhang, Jingying Sun, Yuwei Xie, Yimin Zhang, G Allen Burton, Hongxia Yu
Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14...
2017: PloS One
https://www.readbyqxmd.com/read/28968423/advances-in-the-analysis-of-complex-food-matrices-species-identification-in-surimi-based-products-using-next-generation-sequencing-technologies
#17
Alice Giusti, Andrea Armani, Carmen G Sotelo
The Next Generation Sequencing (NGS) technologies represent a turning point in the food inspection field, particularly for species identification in matrices composed of a blend of two or more species. In this study NGS technologies were applied by testing the usefulness of the Ion Torrent Personal Genome Machine (PGM) in seafood traceability. Sixteen commercial surimi samples produced both in EU and non-EU countries were analysed. Libraries were prepared using a universal primer pair able to amplify a short 16SrRNA fragment from a wide range of fish and cephalopod species...
2017: PloS One
https://www.readbyqxmd.com/read/28960408/residual-disease-detection-using-targeted-parallel-sequencing-predicts-relapse-in-cytogenetically-normal-acute-myeloid-leukemia
#18
Lukas Gaksch, Karl Kashofer, Ellen Heitzer, Franz Quehenberger, Shruti Daga, Sybille Hofer, Iris Halbwedl, Ricarda Graf, Nina Krisper, Gerald Hoefler, Armin Zebisch, Heinz Sill, Albert Wölfler
Despite achieving complete remission after intensive therapy, most patients with cytogenetically normal (CN) AML relapse due to the persistence of submicroscopic residual disease. In this pilot study, we hypothesized that detection of leukemia-specific mutations following consolidation treatment using a targeted parallel sequencing approach predicts relapse. We included 34 AML patients of whom diagnostic material and remission bone marrow slides after at least one cycle of consolidation were available. Isolated DNA was screened for mutations in 19 genes using an Ion Torrent sequencing platform...
September 29, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28959181/bacterial-biota-of-women-with-bacterial-vaginosis-treated-with-lactoferrin-an-open-prospective-randomized-trial
#19
Alessandra Pino, Giuliana Giunta, Cinzia L Randazzo, Salvatore Caruso, Cinzia Caggia, Antonio Cianci
Background: Bacterial vaginosis is the most frequent condition associated to the vaginal microbiota imbalance, affecting about the 40-50% of women in the world. Even if antibiotics are effcetive for bacterial vaginosis treatment a long-term recurrence rates, higher than 70%, is recorded. Lactoferrin is an iron-binding glycoprotein with bacteriostatic and bactericidal properties. It owns the ability to protect the host against infection, by binding and regulating the iron needed for the bacterial proliferation...
2017: Microbial Ecology in Health and Disease
https://www.readbyqxmd.com/read/28952802/novel-tenascin-c-haplotype-modifies-the-risk-for-a-failure-to-heal-after-rotator-cuff-repair
#20
Rainer Kluger, Klaus R Huber, Philipp G Seely, Christian E Berger, Florian Frommlet
BACKGROUND: Several single-nucleotide polymorphisms (SNPs) in the TNC gene have recently been found to be associated with degenerative rotator cuff tears. HYPOTHESIS: Exonic SNPs in the TNC gene are related to the risk for a failure to heal after rotator cuff repair. STUDY DESIGN: Case-control study; Level of evidence, 3. METHODS: A total of 302 patients from the Vienna area and European Caucasian ancestry underwent mini-open rotator cuff repair for a full-thickness superior or posterosuperior tear and were assessed for the integrity of the repair 1 year postoperatively with a real-time 7...
November 2017: American Journal of Sports Medicine
keyword
keyword
45523
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"