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https://www.readbyqxmd.com/read/28929273/complete-genome-sequence-of-a-novel-lytic-bacteriophage-isolated-from-ralstonia-solanacearum
#1
Jingfang Su, Hongwei Sun, Junjie Liu, Zhaokui Guo, Guoquan Fan, Gang Gu, Guanghua Wang
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively...
September 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28929202/intestinal-microbiota-of-white-shrimp-penaeus-vannamei-under-intensive-cultivation-conditions-in-ecuador
#2
Oreste Gainza, Carolina Ramírez, Alfredo Salinas Ramos, Jaime Romero
The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition...
September 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28903732/a-comparison-of-sequencing-platforms-and-bioinformatics-pipelines-for-compositional-analysis-of-the-gut-microbiome
#3
Imane Allali, Jason W Arnold, Jeffrey Roach, Maria Belen Cadenas, Natasha Butz, Hosni M Hassan, Matthew Koci, Anne Ballou, Mary Mendoza, Rizwana Ali, M Andrea Azcarate-Peril
BACKGROUND: Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines...
September 13, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28885040/validation-of-next-generation-sequencer-for-24-chromosome-aneuploidy-screening-in-human-embryos
#4
Kabir Sachdeva, Richard Discutido, Firas Albuz, Rawan Almekosh, Braulio Peramo
BACKGROUND: Next-Generation Sequencing (NGS) is the latest approach for preimplantation genetic diagnoses (PGD). AIM: The purpose of this study was to standardize and validate an NGS method for comprehensive chromosome screening and to investigate its applicability to PGD. METHODS: Embryo biopsy, whole-genome amplification, array comparative genomic hybridization (aCGH), and semiconductor sequencing were employed. RESULTS: A total of 204 whole-genome-amplified products were tested with an NGS-based protocol, from which 100 samples were used for standardization and to evaluate the quality of the results produced by this new technique...
September 8, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28874473/revitalization-of-a-forward-genetic-screen-identifies-three-new-regulators-of-fungal-secondary-metabolism-in-the-genus-aspergillus
#5
Brandon T Pfannenstiel, Xixi Zhao, Jennifer Wortman, Philipp Wiemann, Kurt Throckmorton, Joseph E Spraker, Alexandra A Soukup, Xingyu Luo, Daniel L Lindner, Fang Yun Lim, Benjamin P Knox, Brian Haas, Gregory J Fischer, Tsokyi Choera, Robert A E Butchko, Jin-Woo Bok, Katharyn J Affeldt, Nancy P Keller, Jonathan M Palmer
The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA)...
September 5, 2017: MBio
https://www.readbyqxmd.com/read/28854878/comparison-of-rumen-bacterial-communities-in-dairy-herds-of-different-production
#6
Nagaraju Indugu, Bonnie Vecchiarelli, Linda D Baker, James D Ferguson, Jairam K P Vanamala, Dipti W Pitta
BACKGROUND: The purpose of this study was to compare the rumen bacterial composition in high and low yielding dairy cows within and between two dairy herds. Eighty five Holstein dairy cows in mid-lactation (79-179 days in milk) were selected from two farms: Farm 12 (M305 = 12,300 kg; n = 47; 24 primiparous cows, 23 multiparous cows) and Farm 9 (M305 = 9700 kg; n = 38; 19 primiparous cows, 19 multiparous cows). Each study cow was sampled once using the stomach tube method and processed for 16S rRNA gene amplicon sequencing using the Ion Torrent (PGM) platform...
August 30, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28843089/evaluation-of-the-precision-id-identity-panel-for-the-ion-torrent-%C3%A2-pgm-%C3%A2-sequencer
#7
Kelly A Meiklejohn, James M Robertson
In cases where only a partial or incomplete STR profile is obtained from a sample, information contained in single nucleotide polymorphisms (SNPs) can prove informative for human identification. Thermo Fisher Scientific, which developed the high throughput Ion Torrent(™) PGM(™) sequencer, released the Precision ID Identity Panel, a multiplex SNP panel for human identity. We evaluated the reproducibility and sensitivity of this multiplex, which contains primers for the amplification of 90 autosomal SNPs and 34 Y-clade SNPs...
August 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28839118/high-throughput-genetic-screening-of-51-paediatric-cataract-genes-identifies-causative-mutations-in-inherited-paediatric-cataract-in-south-eastern-australia
#8
Shari Javadiyan, Jamie E Craig, Emmanuelle Souzeau, Shiwani Sharma, Karen M Lower, David A Mackey, Sandra E Staffieri, James E Elder, Deepa Taranath, Tania Straga, Joanna Black, John Pater, Theresa Casey, Alex W Hewitt, Kathryn P Burdon
Paediatric cataract is a leading cause of childhood blindness. This study aimed to determine the genetic cause of paediatric cataract in Australian families by screening known disease associated genes using massively parallel sequencing technology. We sequenced 51 previously reported paediatric cataract genes in 33 affected individuals with a family history (cases with previously known or published mutations were excluded) using the Ion Torrent Personal Genome Machine. Variants were prioritised for validation if they were predicted to alter the protein sequence and were absent or rare with minor allele frequency <1% in public databases...
August 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28821955/targeted-next-generation-sequencing-for-analyzing-the-genetic-alterations-in-atypical-adenomatous-hyperplasia-and-adenocarcinoma-in-situ
#9
Xuan Xu, Na Li, Ruiying Zhao, Lei Zhu, Jinchen Shao, Jie Zhang
PURPOSE: Atypical adenomatous hyperplasia (AAH) and adenocarcinoma in situ (AIS) have been defined as preinvasive pulmonary adenocarcinoma lesions according to the 2015 World Health Organization lung adenocarcinoma classification. We aimed to search for the most common gene mutations in patients with AAH and AIS and investigate the distinctions between the two groups at the molecular level. METHODS: We performed targeted next-generation sequencing on 18 cases with AAH and 28 cases with AIS to screen for mutations with the Ion Torrent Oncomine Solid Tumor DNA panel...
August 18, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28808243/comparison-of-error-correction-algorithms-for-ion-torrent-pgm-data-application-to-hepatitis-b-virus
#10
Liting Song, Wenxun Huang, Juan Kang, Yuan Huang, Hong Ren, Keyue Ding
Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed next-generation sequencing platform with a relatively high insertion and deletion (indel) error rate. A full systematic assessment of the effectiveness of various error correction algorithms in PGM viral datasets (e.g., hepatitis B virus (HBV)) has not been performed. We examined 19 quality-trimmed PGM datasets for the HBV reverse transcriptase (RT) region and found a total error rate of 0.48% ± 0.12%. Deletion errors were clearly present at the ends of homopolymer runs...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797240/a-comparison-of-illumina-and-ion-torrent-sequencing-platforms-in-the-context-of-differential-gene-expression
#11
Nicholas F Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Eun Ji Kim, Giacomo Baruzzo, Katharina E Hayer, Tapan Ganguly, Jonathan Schug, Gregory R Grant
BACKGROUND: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28771972/a-new-insight-into-cftr-allele-frequency-in-brazil-through-next-generation-sequencing
#12
Luisa M Nunes, Roberto Ribeiro, Vivian D T Niewiadonski, Ester Sabino, Guilherme L Yamamoto, Débora R Bertola, Nelson Gaburo, Luiz Vicente R F da Silva Filho
BACKGROUND: As of 2013, fewer than 20% of patients in the Brazilian CF Registry had two CFTR mutations identified. The aim of this study was to sequence the coding region of the CFTR in Brazilian CF patients and determine the frequency of mutations in this cohort. METHODS: Patients with CF and those with suspected atypical CF or CFTR-related disorders were invited to enroll. Total DNA was extracted from blood samples, quantified, and purified. Library preparation was performed using Ion Xpress™ Plus gDNA and Amplicon Library preparation kits (Life Technologies), as well as sequencing using the Ion Torrent platform (Life Technologies)...
August 3, 2017: Pediatric Pulmonology
https://www.readbyqxmd.com/read/28771548/differentially-expressed-genes-in-mycorrhized-and-nodulated-roots-of-common-bean-are-associated-with-defense-cell-wall-architecture-n-metabolism-and-p-metabolism
#13
Kalpana Nanjareddy, Manoj-Kumar Arthikala, Brenda-Mariana Gómez, Lourdes Blanco, Miguel Lara
Legumes participate in two important endosymbiotic associations, with phosphorus-acquiring arbuscular mycorrhiza (AM, soil fungi) and with nitrogen-fixing bacterial rhizobia. These divergent symbionts share a common symbiotic signal transduction pathway that facilitates the establishment of mycorrhization and nodulation in legumes. However, the unique and shared downstream genes essential for AM and nodule development have not been identified in crop legumes. Here, we used ion torrent next-generation sequencing to perform comparative transcriptomics of common bean (Phaseolus vulgaris) roots colonized by AM or rhizobia...
2017: PloS One
https://www.readbyqxmd.com/read/28769920/unraveling-the-microbial-interactions-and-metabolic-potentials-in-pre-and-post-treated-sludge-from-a-wastewater-treatment-plant-using-metagenomic-studies
#14
Chandni Sidhu, Surendra Vikram, Anil Kumar Pinnaka
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28769798/molecular-characterization-of-somatic-alterations-in-dukes-b-and-c-colorectal-cancers-by-targeted-sequencing
#15
Shafina-Nadiawati Abdul, Nurul-Syakima Ab Mutalib, Khor S Sean, Saiful E Syafruddin, Muhiddin Ishak, Ismail Sagap, Luqman Mazlan, Isa M Rose, Nadiah Abu, Norfilza M Mokhtar, Rahman Jamal
Despite global progress in research, improved screening and refined treatment strategies, colorectal cancer (CRC) remains as the third most common malignancy. As each type of cancer is different and exhibits unique alteration patterns, identifying and characterizing gene alterations in CRC that may serve as biomarkers might help to improve diagnosis, prognosis and predict potential response to therapy. With the emergence of next generation sequencing technologies (NGS), it is now possible to extensively and rapidly identify the gene profile of individual tumors...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28767674/versatile-ion-s5xl-sequencer-for-targeted-next-generation-sequencing-of-solid-tumors-in-a-clinical-laboratory
#16
COMPARATIVE STUDY
Meenakshi Mehrotra, Dzifa Yawa Duose, Rajesh R Singh, Bedia A Barkoh, Jawad Manekia, Michael A Harmon, Keyur P Patel, Mark J Routbort, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
BACKGROUND: Next generation sequencing based tumor tissue genotyping involves complex workflow and a relatively longer turnaround time. Semiconductor based next generation platforms varied from low throughput Ion PGM to high throughput Ion Proton and Ion S5XL sequencer. In this study, we compared Ion PGM and Ion Proton, with a new Ion S5XL NGS system for workflow scalability, analytical sensitivity and specificity, turnaround time and sequencing performance in a clinical laboratory. METHODS: Eighteen solid tumor samples positive for various mutations as detected previously by Ion PGM and Ion Proton were selected for study...
2017: PloS One
https://www.readbyqxmd.com/read/28764195/whole-exomes-sequencing-delineates-gene-variants-profile-in-a-young-saudi-male-with-familial-hypercholesterolemia-case-report
#17
Edem Nuglozeh
Familial hypercholesterolemia is an autosomal dominant genetic disease characterized by earlier elevated Low-Density Lipoprotein (LDL) cholesterol levels and increased risk for premature Myocardial Infarction (MI). Albeit the diagnosis of some medical Familial Hypercholesterolemia (FH) cases are due to mutations in PCSK9, APOB, or LDLR, detection of mutation rate and profiles relies heavily on different gene pools and ethnicity. We ran exome sequencing on blood genomic DNA (gDNA) from a 26-year-old Saudi patient on Ion Proton Platform (Ion Torrent, Guilford, Connecticut, USA) as part of a pilot study preluding the establishment of the Saudi Human Genome project...
June 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28757314/using-ion-torrent-sequencing-to-study-genetic-mutation-profiles-of-fatal-thyroid-cancers
#18
Jin-Ying Lu, Wern-Cherng Cheng, Kuen-Yuan Chen, Chia-Chi Lin, Ching-Chung Chang, Kuan-Ting Kuo, Pei-Lung Chen
BACKGROUND/PURPOSE: Surgery followed by radioiodine is a mainstay of treatment for thyroid cancers of follicular origins. However, about 5% of the thyroid cancers are non-operable and/or radioiodine-refractory diseases, which are either locally advanced or metastatic and result in a survival of less than 5 years. How to treat this population of thyroid cancer patients becomes a critical issue requiring further understanding of the tumor's genetic information. METHODS: We used formalin-fixed paraffin-embedded specimens of 22 fatal thyroid cancers and their corresponding non-tumor parts, if available, to yield genomic DNA, and applied the Ion Torrent™ Personal Genome Machine (IT-PGM) System (Life Technologies), a next generation sequencing technology, to interrogate 740 mutational hotspots in 46 oncogenes...
July 27, 2017: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/28755588/genomic-characterization-of-zika-virus-isolated-from-indonesia
#19
Frilasita A Yudhaputri, Hidayat Trimarsanto, Aditya Perkasa, Benediktus Yohan, Sotianingsih Haryanto, Ageng Wiyatno, Amin Soebandrio, Khin Saw Myint, Jeremy P Ledermann, Ronald Rosenberg, Ann M Powers, R Tedjo Sasmono
Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000...
October 2017: Virology
https://www.readbyqxmd.com/read/28753539/clinical-features-and-genotyping-of-patients-with-primary-carnitine-deficiency-identified-by-newborn-screening
#20
Yun Sun, Yan-Yun Wang, Tao Jiang
BACKGROUND: The objective of the study was to investigate clinical and gene mutation characteristics of primary carnitine deficiency (PCD) patients identified by newborn screening using tandem mass spectrometry (MS/MS). METHODS: Tandem mass spectrometry (MS/MS) was applied to screen inherited metabolic disease and seven patients with PCD were diagnosed among 62,568 samples. The SLC22A5 gene was detected by using diagnosis panel of genetic and metabolic diseases based on Ion Torrent Semiconductor Sequencing Technology...
August 28, 2017: Journal of Pediatric Endocrinology & Metabolism: JPEM
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