Read by QxMD icon Read

ion torrent

Yan Hao, Dawei Chen, Zhiguo Zhang, Ping Zhou, Yunxia Cao, Zhaolian Wei, Xiaofeng Xu, Beili Chen, Weiwei Zou, Mingrong Lv, Dongmei Ji, Xiaojin He
Hearing loss may place a heavy burden on the patient and patient's family. Given the high incidence of hearing loss among newborns and the huge cost of treatment and care (including cochlear implantation), prenatal diagnosis is strongly recommended. Termination of the fetus may be considered as an extreme outcome to the discovery of a potential deaf fetus, and therefore preimplantation genetic diagnosis has become an important option for avoiding the birth of affected children without facing the risk of abortion following prenatal diagnosis...
April 2018: Oncology Letters
Ioana Onuț-Brännström, Mitchell Benjamin, Douglas G Scofield, Starri Heiðmarsson, Martin G I Andersson, Eva S Lindström, Hanna Johannesson
In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10-18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations...
March 13, 2018: Scientific Reports
Rebecca C Arend, Angelina I Londono, Allison M Montgomery, Haller J Smith, Zachary C Dobbin, Ashwini A Katre, Alba Martinez, Eddy S Yang, Ronald D Alvarez, Warner K Huh, Kerri S Bevis, J Michael Straughn, Jacob M Estes, Lea Novak, David K Crossman, Sara J Cooper, Charles N Landen, Charles A Leath
While high-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants (by DNA next-generation sequencing [NGS] using a 50 gene Ion Torrent panel) and gene expression (using the NanoString® PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT)...
March 9, 2018: Molecular Cancer Research: MCR
Sandrine Baron, Laetitia Le Devendec, Fabrice Touzain, Eric Jouy, Pierrick Lucas, Claire de Boisséson, Emeline Larvor, Isabelle Kempf
Resistance to extended-spectrum cephalosporins (ESCs) is mostly borne by conjugative plasmids. The aim of the present study was to evaluate the characteristics and diversity of ESC resistance plasmids in Escherichia coli from different free-range broiler flocks in France, and their persistence in flocks during rearing. Two hatcheries were selected. Faecal samples from 11 flocks were collected from before their arrival on the broiler production farm up to their slaughter at the end of the rearing period. A selection of 25 E...
March 2018: Veterinary Microbiology
Lisa F Stinson, Jeffrey A Keelan, Matthew S Payne
The establishment of human gut microbiota commences initially in utero . Meconium-the first fecal material passed after birth-can be used to study fetal gut contents; however, processing meconium samples for microbiome studies presents significant technical challenges. Meconium hosts a low biomass microbiome, is tar-like in texture and contains high concentrations of PCR inhibitors. This study aimed to evaluate four different DNA extraction methods to elucidate the most effective method for bacterial DNA recovery and sequencing analysis from first-pass meconium...
2018: Frontiers in Microbiology
Andrey S Glotov, Sergey V Kazakov, Elena S Vashukova, Vladimir S Pakin, Maria M Danilova, Yulia A Nasykhova, Aleksey E Masharsky, Elena V Mozgovaya, Dina R Eremeeva, Marina S Zainullina, Vladislav S Baranov
BACKGROUND: Preeclampsia (PE) is the most common complication of pregnancy that remains to be a major cause of maternal and fetal mortality. Prediction and early diagnosis of PE would allow for timely initiation of preventive therapy. According to recent studies of ACVR2A gene polymorphism is associated with PE, but it is still unclear whether these findings reflect specific pathogenetic mechanisms of this disease. METHODS: We performed targeted next-generation sequencing (NGS) sequencing of ACVR2A gene by means of Ion Torrent Personal Genome machine (PGM) Sequencer...
March 5, 2018: Journal of Maternal-fetal & Neonatal Medicine
Simon A Fox, Sean S Currie, Andrew J Dalley, Camile S Farah
BACKGROUND: The role of alcohol-containing mouthwash as a risk factor for the development of oral cancer is a subject of conflicting epidemiological evidence in the literature despite alcohol being a recognised carcinogen. The aim of this study was to use in vitro models to investigate mechanistic and global gene expression effects of exposure to alcohol-containing mouthwash. METHODS: Two brands of alcohol-containing mouthwash and their alcohol-free counterparts were used to treat two oral cell lines derived from normal (OKF6-TERT) and dysplastic (DOK) tissues...
March 5, 2018: Journal of Oral Pathology & Medicine
Yuan Liang, Qi Peng, Kangwei Wang, Pengyuan Zhu, Chunqiu Wu, Chunbao Rao, Jiang Chang, Siping Li, Xiaomei Lu
OBJECTIVES: To identity the genetic causes of hearing loss in a Han Chinese family with enlarged vestibular aqueduct syndrome. METHODS: Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to search for pathogenic mutations. A group of 1500 ethnically-matched normal hearing subjects screened for mutations in deafness-related genes using the same method in previously studied were included as a control. RESULTS: The proband and his little sister suffered from typical features of sensorineural hearing loss with enlarged vestibular aqueduct (EVA)...
April 2018: International Journal of Pediatric Otorhinolaryngology
Lan Yao, Zhen Xu, Hemiao Zhao, Zheng Tu, Zhifang Liu, Wanshui Li, Lan Hu, Lihua Wan
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons...
February 27, 2018: Legal Medicine
Alberto Ferrarini, Claudio Forcato, Genny Buson, Paola Tononi, Valentina Del Monaco, Mario Terracciano, Chiara Bolognesi, Francesca Fontana, Gianni Medoro, Rui Neves, Birte Möhlendick, Karim Rihawi, Andrea Ardizzoni, Semini Sumanasuriya, Penny Flohr, Maryou Lambros, Johann de Bono, Nikolas H Stoecklein, Nicolò Manaresi
Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications...
2018: PloS One
Angelamaria Becorpi, Giuseppina Campisciano, Nunzia Zanotta, Zelinda Tredici, Secondo Guaschino, Felice Petraglia, Annalisa Pieralli, Giovanni Sisti, Francesco De Seta, Manola Comar
The composition of vaginal microbiome in menopause and cancer survivor women changes dramatically leading to genitourinary syndrome of menopause (GSM) in up to 7% of patients. Recent reports suggest that laser therapy may be valuable as a not hormonal therapeutic modality. The aim of the present study was to evaluate the effects of fractional CO2 laser treatment on the vaginal secretory pathway of a large panel of immune mediators, usually implicated in tissue remodeling and inflammation, and on microbiome composition in postmenopausal breast cancer survivors...
March 1, 2018: Lasers in Medical Science
Flavio Guidi, Laura Pezzolesi, Silvana Vanucci
Algal-bacterial interactions play a major role in shaping diversity of algal associated bacterial communities. Temporal variation in bacterial phylogenetic composition reflects changes of these complex interactions which occur during the algal growth cycle as well as throughout the lifetime of algal blooms. Viruses are also known to cause shifts in bacterial community diversity which could affect algal bloom phases. This study investigated on changes of bacterial and viral abundances, bacterial physiological status, and on bacterial successional pattern associated with the harmful benthic dinoflagellate Ostreopsis cf...
February 27, 2018: MicrobiologyOpen
S M B Duarte, J T Stefano, L Miele, F R Ponziani, M Souza-Basqueira, L S R R Okada, F G de Barros Costa, K Toda, D F C Mazo, E C Sabino, F J Carrilho, A Gasbarrini, C P Oliveira
BACKGROUND AND AIM: The aim of the study was to compare the gut microbiomes from obese and lean patients with or without NASH to outline phenotypic differences. METHODS AND RESULTS: We performed a cross-sectional pilot study comprising biopsy-proven NASH patients grouped according to BMI. Microbiome DNA was extracted from stool samples, and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion PGM Torrent platform, and data were analyzed using QIIME software...
October 26, 2017: Nutrition, Metabolism, and Cardiovascular Diseases: NMCD
Timothy J Divoll, Veronica A Brown, Jeff Kinne, Gary F McCracken, Joy M O'Keefe
Different second-generation sequencing technologies may have taxon-specific biases when DNA metabarcoding prey in predator feces. Our major objective was to examine differences in prey recovery from bat guano across two different sequencing workflows using the same fecal DNA extracts. We compared results between the Ion Torrent PGM and the Illumina MiSeq with similar library preparations and the same analysis pipeline. We focus on repeatability and provide an R Notebook in an effort toward transparency for future methodological improvements...
February 17, 2018: Molecular Ecology Resources
Urška Sivka, Nataša Toplak, Simon Koren, Jernej Jakše
Lithophaga lithophaga is a rock-boring bivalve with an ability to dissolve carbonate substrata with its siphonal and pallial gland secretions. However, the molecular mechanism that enables this species to bore into calcareous rocks is not yet known. In order to identify genes potentially involved in chemical boring we performed transcriptome sequencing of pallial-gland tissue samples of L. lithophaga. Transcriptome sequencing using an Ion Torrent platform generated 60.563 million clean reads with an average read length of 96 bp...
February 6, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
S Ingold, G Dørum, E Hanson, A Berti, W Branicki, P Brito, P Elsmore, K B Gettings, F Giangasparo, T E Gross, S Hansen, E N Hanssen, M-L Kampmann, M Kayser, F-X Laurent, N Morling, A Mosquera-Miguel, W Parson, C Phillips, M J Porto, E Pośpiech, A D Roeder, P M Schneider, K Schulze Johann, C R Steffen, D Syndercombe-Court, M Trautmann, M van den Berge, K J van der Gaag, J Vannier, V Verdoliva, A Vidaki, C Xavier, J Ballantyne, C Haas
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols...
January 31, 2018: Forensic Science International. Genetics
Geert Cremers, Lavinia Gambelli, Theo van Alen, Laura van Niftrik, Huub J M Op den Camp
With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology...
2018: PeerJ
Silje L Rekdal, Jarl Andreas Anmarkrud, Arild Johnsen, Jan T Lifjeld
Genotyping of classical major histocompatibility complex (MHC) genes is challenging when they are hypervariable and occur in multiple copies. In this study, we used several different approaches to genotype the moderately variable MHC class I exon 3 (MHCIe3) and the highly polymorphic MHC class II exon 2 (MHCIIβe2) in the bluethroat (Luscinia svecica). Two family groups (eight individuals) were sequenced in replicates at both markers using Ion Torrent technology with both a single- and a dual-indexed primer structure...
February 2018: Ecology and Evolution
Zhen-Wen Wang, Shi-Wen Jiang, Bao-Cheng Zhou
Phenylketonuria (PKU) is a common autosomal recessive disorder of phenylalanine metabolism and mainly results a deficiency of phenylalanine hydroxylase gene (PAH). The incidence of various PAH mutations have race and ethnicity differences. We report a spectrum of PAH mutations complied from 35 PKU children who are all Chinese Han population from north Jiangsu in this study. All 13 exons and their flanking intron sequences of PAH were determined by Ion Torrent PGM™ sequencing. The relationship of genotype and phenotype was analyzed based on the sum of the arbitrary value (AV) values of the two alleles...
February 2018: Kaohsiung Journal of Medical Sciences
Saranya Vijayakumar, Baby Abirami S, Kalaiyarasi Kanthan, Balaji Veeraraghavan
OBJECTIVES: Acinetobacter baumannii is a nosocomial pathogen responsible for various infections, including bloodstream infections, meningitis and ventilator-associated pneumonia. It is resistant to most antimicrobial agents, including colistin, and the development of colistin-resistant A. baumannii is of serious concern in the hospital setting. In this study, the whole-genome shotgun sequences of seven colistin-resistant A. baumannii isolates from bloodstream infections were characterised...
February 12, 2018: Journal of Global Antimicrobial Resistance
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"