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https://www.readbyqxmd.com/read/28068558/targeted-next-generation-sequencing-of-the-entire-vitamin-d-receptor-gene-reveals-polymorphisms-correlated-with-vitamin-d-deficiency-among-older-filipino-women-with-and-without-fragility-fracture
#1
Mark Pretzel Zumaraga, Paul Julius Medina, Juan Miguel Recto, Lauro Abrahan, Edelyn Azurin, Celeste C Tanchoco, Cecilia A Jimeno, Cynthia Palmes-Saloma
This study aimed to discover genetic variants in the entire 101 kB vitamin D receptor (VDR) gene for vitamin D deficiency in a group of postmenopausal Filipino women using targeted next generation sequencing (TNGS) approach in a case-control study design. A total of 50 women with and without osteoporotic fracture seen at the Philippine Orthopedic Center were included. Blood samples were collected for determination of serum vitamin D, calcium, phosphorus, glucose, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase and as primary source for targeted VDR gene sequencing using the Ion Torrent Personal Genome Machine...
December 21, 2016: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28056803/de-novo-transcriptome-and-expression-profile-analyses-of-the-asian-corn-borer-ostrinia-furnacalis-reveals-relevant-flubendiamide-response-genes
#2
Li Cui, Changhui Rui, Daibin Yang, Zhenying Wang, Huizhu Yuan
BACKGROUND: The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging insect pest of corn in Asia. However, the lack of genome or transcriptome information heavily hinders our further understanding of ACB in every aspect at a molecular level and on a genome-wide scale. Here, we used the Ion Torrent Personal Genome Machine (PGM) Sequencer to explore the ACB transcriptome and to identify relevant genes in response to flubendiamide, showing high selective activity against ACB...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28052134/assessment-of-common-and-emerging-bioinformatics-pipelines-for-targeted-metagenomics
#3
Léa Siegwald, Hélène Touzet, Yves Lemoine, David Hot, Christophe Audebert, Ségolène Caboche
Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results...
2017: PloS One
https://www.readbyqxmd.com/read/28049581/validation-of-a-next-generation-sequencing-panel-for-detection-of-hotspot-cancer-mutations-in-a-clinical-laboratory
#4
Reza Shahsiah, Jenefer DeKoning, Saeed Samie, Seyed Ziaeddin Latifzadeh, Zahra Mehdizadeh Kashi
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform...
December 16, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28012117/complete-genome-sequence-analysis-of-chicken-astrovirus-isolate-from-india
#5
Amrutlal K Patel, Ramesh J Pandit, Jalpa R Thakkar, Ankit T Hinsu, Vinod C Pandey, Joy K Pal, Kantilal S Prajapati, Subhash J Jakhesara, Chaitanya G Joshi
OBJECTIVE: Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and "white chicks" condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens. METHODS: Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein...
December 23, 2016: Veterinary Research Communications
https://www.readbyqxmd.com/read/28006002/unbiased-rna-shotgun-metagenomics-in-social-and-solitary-wild-bees-detects-associations-with-eukaryote-parasites-and-new-viruses
#6
Karel Schoonvaere, Lina De Smet, Guy Smagghe, Andy Vierstraete, Bart P Braeckman, Dirk C de Graaf
The diversity of eukaryote organisms and viruses associated with wild bees remains poorly characterized in contrast to the well-documented pathosphere of the western honey bee, Apis mellifera. Using a deliberate RNA shotgun metagenomic sequencing strategy in combination with a dedicated bioinformatics workflow, we identified the (micro-)organisms and viruses associated with two bumble bee hosts, Bombus terrestris and Bombus pascuorum, and two solitary bee hosts, Osmia cornuta and Andrena vaga. Ion Torrent semiconductor sequencing generated approximately 3...
2016: PloS One
https://www.readbyqxmd.com/read/28003022/the-variability-and-reproducibility-of-whole-genome-sequencing-technology-for-detecting-resistance-to-anti-tuberculous-drugs
#7
Jody Phelan, Denise M O'Sullivan, Diana Machado, Jorge Ramos, Alexandra S Whale, Justin O'Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F Huggett, Taane G Clark
BACKGROUND: The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles. METHODS: We investigated two sequencing platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor) using a well characterised reference strain (H37Rv) and clinical isolates from patients with tuberculosis resistant to up to 13 drugs...
December 22, 2016: Genome Medicine
https://www.readbyqxmd.com/read/28002797/targeted-exome-sequencing-reveals-distinct-pathogenic-variants-in-iranians-with-colorectal-cancer
#8
Hassan Ashktorab, Pooneh Mokarram, Hamed Azimi, Hasti Olumi, Sudhir Varma, Michael L Nickerson, Hassan Brim
PURPOSE: Next Generation Sequencing (NGS) is currently used to establish mutational profiles in many multigene diseases such as colorectal cancer (CRC), which is on the rise in many parts of the developing World including, Iran. Little is known about its genetic hallmarks in these populations. AIM: To identify variants in 15 CRC-associated genes in patients of Iranian descent. RESULTS: There were 51 validated variants distributed on 12 genes: 22% MSH3 (n = 11/51), 10% MSH6 (n = 5/51), 8% AMER1 (n = 4/51), 20% APC (n = 10/51), 2% BRAF (n = 1/51), 2% KRAS (n = 1/51), 12% PIK3CA (n = 6/51), 8% TGFβR2A (n = 4/51), 2% SMAD4 (n = 1/51), 4% SOX9 (n = 2/51), 6% TCF7L2 (n = 3/51), and 6% TP53 (n = 3/51)...
December 16, 2016: Oncotarget
https://www.readbyqxmd.com/read/27994184/complete-mitochondrial-genome-of-threatened-mahseer-tor-tor-hamilton-1822-and-its-phylogenetic-relationship-within-cyprinidae-family
#9
A Pavan-Kumar, Sudhanshu Raman, Prakash G Koringa, Namrata Patel, Tejas Shah, Rajeev K Singh, Gopal Krishna, C G Joshi, P Gireesh-Babu, Aparna Chaudhari
The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000 x...
December 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27986441/silent-genetic-alterations-identified-by-targeted-next-generation-sequencing-in-pheochromocytoma-paraganglioma-a-clinicopathological-correlations
#10
Suja Pillai, Vinod Gopalan, Chung Y Lo, Victor Liew, Robert A Smith, Alfred King Y Lam
AIMS: The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma. METHODS: Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer...
December 13, 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27981713/the-effect-of-inoculum-source-and-fluid-shear-force-on-the-development-of-in-vitro-oral-multi-species-biofilms
#11
Constanza E Fernández, Marcelo B Aspiras, Michael W Dodds, Carlos González-Cabezas, Alexander H Rickard
AIM: Saliva has been previously used as an inoculum for in-vitro oral biofilm studies. However, the microbial community profile of saliva is markedly different from hard and soft tissue-associated oral biofilms. Here, we investigated the changes in the biofilm architecture and microbial diversity of in-vitro oral biofilms developed from saliva, tongue or plaque-derived inocula under different salivary shear forces. METHODS AND RESULTS: Four inoculum-types (saliva, bacteria harvested from the tongue, toothbrush and curette-harvested plaque) were collected and pooled...
December 15, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27951431/developmental-validation-of-a-custom-panel-including-273-snps-for-forensic-application-using-ion-torrent-pgm
#12
Suhua Zhang, Yingnan Bian, Anqi Chen, Hancheng Zheng, Yuzhen Gao, Yiping Hou, Chengtao Li
Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM...
December 7, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27943208/small-rna-library-construction-for-exosomal-rna-from-biological-samples-for-the-ion-torrent-pgm%C3%A2-and-ion-s5%C3%A2-system
#13
Lesley Cheng, Andrew F Hill
Next-generation deep sequencing (NGS) technology represents a powerful and innovative approach to profile small RNA. Currently, there are a number of large-scale and benchtop sequencing platforms available on the market. Although each platform is relatively straightforward to operate, constructing cDNA libraries can be the most difficult part of the NGS workflow. Constructing quality libraries is essential to obtaining a successful sequencing run of high-quality reads and coverage. The quality and yield of RNA affect hybridization and ligation of sequencing adapters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27939319/ability-of-lactobacillus-kefiri-lkf01-dsm32079-to-colonize-the-intestinal-environment-and-modify-the-gut-microbiota-composition-of-healthy-individuals
#14
Marco Toscano, Roberta De Grandi, Vito Leonardo Miniello, Roberto Mattina, Lorenzo Drago
BACKGROUND: Probiotics have been observed to positively influence the host's health, but to date few data about the ability of probiotics to modify the gut microbiota composition exist. AIMS: To evaluate the ability of Lactobacillus kefiri LKF01 DSM32079 (LKEF) to colonize the intestinal environment of healthy subjects and modify the gut microbiota composition. METHODS: Twenty Italian healthy volunteers were randomized in pre-prandial and post-prandial groups...
December 6, 2016: Digestive and Liver Disease
https://www.readbyqxmd.com/read/27932081/draft-genome-sequence-of-a-ges-5-producing-serratia-marcescens-isolated-in-southern-brazil
#15
Carolina Silva Nodari, Marina Siebert, Ursula da Silveira Matte, Afonso Luís Barth
Serratia marcescens is a Gram-negative rod intrinsically resistant to polymyxins and usually associated with wound, respiratory and urinary tract infections. The whole genome of the first GES-5-producing S. marcescens isolated from a Brazilian patient was sequenced using Ion Torrent PGM System. Besides blaGES-5, we were able to identify genes encoding for other β-lactamases, for aminoglycoside modifying enzymes and for an efflux pump to tetracyclines.
November 23, 2016: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/27902415/inversion-of-correia-repeat-enclosed-elements-in-neisseria-gonorrhoeae
#16
Firat Elbeyioglu, Sabrina B Roberts, Russell Spencer-Smith, Madhuri Pulijala, Marta A Zelewska, Jean-Christophe Nebel, Lori As Snyder
Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Within the gonococcal genome are over 100 copies of the IS-like Correia Repeat Enclosed Element, which has been predicted to be mobile within the neisserial genomes. Although there is evidence of ancestral movement of these elements, no previous study has provided evidence for current mobilisation. The Correia Repeat Enclosed Element has the ability to alter gene expression and regulation in many ways: by insertional mutagenesis; by introducing promoter elements; by generating mRNA processing sites, and by association with ncRNAs...
November 16, 2016: Microbiology
https://www.readbyqxmd.com/read/27898681/common-lung-microbiome-identified-among-mechanically-ventilated-surgical-patients
#17
Ashley D Smith, Yan Zhang, Robert C Barber, Christian T Minshall, Ryan M Huebinger, Michael S Allen
The examination of the pulmonary microbiome in patients with non-chronic disease states has not been extensively examined. Traditional culture based screening methods are often unable to identify bacteria from bronchoalveolar lavage samples. The advancement of next-generation sequencing technologies allows for a culture-independent molecular based analysis to determine the microbial composition in the lung of this patient population. For this study, the Ion Torrent PGM system was used to assess the microbial complexity of culture negative bronchoalveolar lavage samples...
2016: PloS One
https://www.readbyqxmd.com/read/27894793/a-quick-reference-on-anion-gap-and-strong-ion-gap
#18
REVIEW
Carlos Torrente Artero
Metabolic acid-base disorders are common in emergency and critically ill patients. Clinicians may have difficulty recognizing their presence when multiple acid-base derangements are present in a single patient simultaneously. The anion gap and the strong ion gap concepts are useful calculations to identify the components of complex metabolic acid-base associated to the presence of unmeasured anions. This article presents their definition, normal values, indications, limitations, and guidelines for interpretation of changes in the clinical setting...
November 25, 2016: Veterinary Clinics of North America. Small Animal Practice
https://www.readbyqxmd.com/read/27884156/targeted-myocardial-gene-expression-in-failing-hearts-by-rna-sequencing
#19
Kajari Dhar, Alexandra M Moulton, Eric Rome, Fang Qiu, Jeff Kittrell, Eugenia Raichlin, Ronald Zolty, John Y Um, Michael J Moulton, Hesham Basma, Daniel R Anderson, James D Eudy, Brian D Lowes
BACKGROUND: Myocardial recovery with left ventricular assist device (LVAD) therapy is highly variable and difficult to predict. Next generation ribonucleic acid (RNA) sequencing is an innovative, rapid, and quantitative approach to gene expression profiling in small amounts of tissue. Our primary goal was to identify baseline transcriptional profiles in non-ischemic cardiomyopathies that predict myocardial recovery in response to LVAD therapy. We also sought to verify transcriptional differences between failing and non-failing human hearts...
November 25, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27875997/identification-of-the-transcripts-associated-with-spontaneous-hcv-clearance-in-individuals-co-infected-with-hiv-and-hcv
#20
Yue Chen, Chengli Shen, Debjani Guha, Ming Ding, Scott Kulich, Aiymkul Ashimkhanova, Charles Rinaldo, Eric Seaberg, Joseph B Margolick, Valentina Stosor, Otoniel Martínez-Maza, Phalguni Gupta
BACKGROUND: Infection with human immunodeficiency virus (HIV) influences the outcome and natural disease progression of hepatitis C virus (HCV) infection. While the majority of HCV mono-infected and HCV/HIV co-infected subjects develop chronic HCV infection, 20-46% of mono- and co-infected subjects spontaneously clear HCV infection. The mechanism underlying viral clearance is not clearly understood. Analysis of differential cellular gene expression (mRNA) between HIV-infected patients with persistent HCV infection or spontaneous clearance could provide a unique opportunity to decipher the mechanism of HCV clearance...
November 22, 2016: BMC Infectious Diseases
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