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https://www.readbyqxmd.com/read/28207930/elevation-of-glycosaminoglycans-in-the-amniotic-fluid-of-a-fetus-with-mucopolysaccharidosis-vii
#1
Francyne Kubaski, Ana Carolina Brusius-Facchin, Robert W Mason, Pravin Patel, Maira G Burin, Kristiane Michelin-Tirelli, Rejane Gus Kessler, Fernanda Bender, Sandra Leistner-Segal, Carolina A Moreno, Denise P Cavalcanti, Roberto Giugliani, Shunji Tomatsu
OBJECTIVE: The aim of this study was to quantify GAGs in amniotic fluid (AF) from an MPS VII fetus compared with age-matched fetuses obtained from normal pregnancies. METHOD: Disaccharides were measured by liquid chromatography tandem mass spectrometry (LC/MS/MS), compared to age-matched controls. Enzyme assay was performed in AF supernatant or cultured amniocytes. GUSB was analyzed by next generation sequencing using Ion Torrent Personal Genome Machine with a customized panel...
February 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28192086/variant-call-concordance-between-two-laboratory-developed-solid-tumor-targeted-genomic-profiling-assays-using-distinct-workflows-and-sequencing-instruments
#2
Ken J Hampel, Francine B de Abreu, Nikoletta Sidiropoulos, Jason D Peterson, Gregory J Tsongalis
Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes...
February 10, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28188339/microbial-composition-and-diversity-are-associated-with-plant-performance-a-case-study-on-long-term-fertilization-effect-on-wheat-growth-in-an-ultisol
#3
Lihua Li, Fenliang Fan, Alin Song, Chang Yin, Peiyuan Cui, Zhaojun Li, Yongchao Liang
The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested...
February 10, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28178310/diversity-and-composition-of-vaginal-microbiota-of-pregnant-women-at-risk-for-transmitting-group-b-streptococcus-treated-with-intrapartum-penicillin
#4
Luiz Fernando Wurdig Roesch, Rita C Silveira, Andréa L Corso, Priscila Thiago Dobbler, Volker Mai, Bruna S Rojas, Álvaro M Laureano, Renato S Procianoy
BACKGROUND: Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers' microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. METHODS: Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls...
2017: PloS One
https://www.readbyqxmd.com/read/28163825/genomic-analysis-of-four-strains-of-corynebacterium-pseudotuberculosis-bv-equi-isolated-from-horses-showing-distinct-signs-of-infection
#5
Rafael A Baraúna, Rommel T J Ramos, Adonney A O Veras, Pablo H C G de Sá, Luís C Guimarães, Diego A das Graças, Adriana R Carneiro, Judy M Edman, Sharon J Spier, Vasco Azevedo, Artur Silva
The genomes of four strains (MB11, MB14, MB30, and MB66) of the species Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, completely assembled, and their gene content and structure were analyzed. The strains were isolated from horses with distinct signs of infection, including ulcerative lymphangitis, external abscesses on the chest, or internal abscesses on the liver, kidneys, and lungs. The average size of the genomes was 2.3 Mbp, with 2169 (Strain MB11) to 2235 (Strain MB14) predicted coding sequences (CDSs)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28161563/single-center-experience-with-a-targeted-next-generation-sequencing-assay-for-assessment-of-relevant-somatic-alterations-in-solid-tumors
#6
Aino Paasinen-Sohns, Viktor H Koelzer, Angela Frank, Julian Schafroth, Aline Gisler, Melanie Sachs, Anne Graber, Sacha I Rothschild, Andreas Wicki, Gieri Cathomas, Kirsten D Mertz
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material...
February 2, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28127742/performance-comparison-of-nextseq-and-ion-proton-platforms-for-molecular-diagnosis-of-clinical-oncology
#7
Fei Cao, Lianju Gao, Longgang Wei, Zhanni Chen, Yan Wang, Xia Ran, Xuehong Meng, Ji Tao
PURPOSE: Next-generation sequencing is a powerful approach to detect genetic mutations with which cancer diagnosis and treatment can be tailored to the individual patient in the era of personalized and precision medicine. Ion Torrent Systems Ion Proton and Illumina NextSeq are 2 major targeted sequencing platforms; however, not much work has been done to compare these platforms' performance for mutation detection in formalin-fixed paraffin-embedded (FFPE) materials. METHODS: We benchmarked the performance by using a collection of FFPE samples from 23 patients with different cancers for NextSeq and Ion Proton platforms...
January 25, 2017: Tumori
https://www.readbyqxmd.com/read/28125655/assessing-the-genotypic-differences-between-strains-of-corynebacterium-pseudotuberculosis-biovar-equi-through-comparative-genomics
#8
Rafael A Baraúna, Rommel T J Ramos, Adonney A O Veras, Kenny C Pinheiro, Leandro J Benevides, Marcus V C Viana, Luís C Guimarães, Judy M Edman, Sharon J Spier, Vasco Azevedo, Artur Silva
Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny...
2017: PloS One
https://www.readbyqxmd.com/read/28116522/molecular-characterization-of-cd44-cd24-ck-cd45-cells-in-benign-and-malignant-breast-lesions
#9
Arnaud Da Cruz Paula, Catarina Leitão, Oriana Marques, Ana Margarida Rosa, Ana Helena Santos, Alexandra Rêma, Maria de Fátima Faria, Ana Rocha, José Luís Costa, Margarida Lima, Carlos Lopes
Breast cancer epithelial cells with the CD44(+)/CD24(-/low) phenotype possess tumor-initiating cells and epithelial-mesenchymal transition (EMT) capacity. Massive parallel sequencing can be an interesting approach to deepen the molecular characterization of these cells. We characterized CD44(+)/CD24(-)/cytokeratin(Ck)(+)/CD45(-) cells isolated through flow cytometry from 43 biopsy and 6 mastectomy samples harboring different benign and malignant breast lesions. The Ion Torrent Ampliseq Cancer Hotspot panel v2 (CHPv2) was used for the identification of somatic mutations in the DNA extracted from isolated CD44(+)/CD24(-)/Ck(+)/CD45(-) cells...
January 23, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28105921/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology
#10
Diego C B Mariano, Felipe L Pereira, Edgar L Aguiar, Letícia C Oliveira, Leandro Benevides, Luís C Guimarães, Edson L Folador, Thiago J Sousa, Preetam Ghosh, Debmalya Barh, Henrique C P Figueiredo, Artur Silva, Rommel T J Ramos, Vasco A C Azevedo
BACKGROUND: The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103826/tracking-the-origin-of-simultaneous-endometrial-and-ovarian-cancer-by-next-generation-sequencing-a-case-report
#11
Nadejda Valtcheva, Franziska M Lang, Aurelia Noske, Eleftherios P Samartzis, Anna-Maria Schmidt, Elisa Bellini, Daniel Fink, Holger Moch, Markus Rechsteiner, Konstantin J Dedes, Peter J Wild
BACKGROUND: Endometrioid adenocarcinoma of the uterus and ovarian endometrioid carcinoma share many morphological and molecular features. Differentiation between simultaneous primary carcinomas and ovarian metastases of an endometrial cancer may be very challenging but is essential for prognostic and therapeutic considerations. CASE PRESENTATION: In the present case study of a 33 year-old patient we used targeted amplicon next-generation re-sequencing for clarifying the origin of synchronous endometrioid cancer of the corpus uteri and the left ovary...
January 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28098358/subclinical-alteration-of-the-cervical-vaginal-microbiome-in-women-with-idiopathic-infertility
#12
Giuseppina Campisciano, Fiorella Florian, Angela D'Eustacchio, David Stanković, Giuseppe Ricci, Manola Comar
Biomarkers have a wide application in research and clinic, they help to choose the correct treatment for diseases. Recent studies, addressing the vaginal microbiome using next generation sequencing (NGS), reported the involvement of bacterial species in infertility. We compared the vaginal microbiome of idiopathic infertility diagnosed women with that of healthy, non-idiopathic infertile and bacterial vaginosis affected women, to identify bacterial species suitable as biomarkers. Information on microorganisms was obtained from the V3-16S rDNA sequencing of cervical-vaginal fluids of 96 women using the Ion Torrent platform...
January 18, 2017: Journal of Cellular Physiology
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
#13
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
#14
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
#15
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
#16
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
#17
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...
March 2017: 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
#18
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
#19
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
#20
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)...
January 31, 2017: Oncotarget
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