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https://www.readbyqxmd.com/read/29789446/validation-of-ion-torrent-tm-inherited-disease-panel-with-the-pgm-tm-sequencing-platform-for-rapid-and-comprehensive-mutation-detection
#1
Abeer E Mustafa, Tariq Faquih, Batoul Baz, Rana Kattan, Abdulelah Al-Issa, Asma I Tahir, Faiqa Imtiaz, Khushnooda Ramzan, Moeenaldeen Al-Sayed, Mohammed Alowain, Zuhair Al-Hassnan, Hamad Al-Zaidan, Mohamed Abouelhoda, Bashayer R Al-Mubarak, Nada A Al Tassan
Quick and accurate molecular testing is necessary for the better management of many inherited diseases. Recent technological advances in various next generation sequencing (NGS) platforms, such as target panel-based sequencing, has enabled comprehensive, quick, and precise interrogation of many genetic variations. As a result, these technologies have become a valuable tool for gene discovery and for clinical diagnostics. The AmpliSeq Inherited Disease Panel (IDP) consists of 328 genes underlying more than 700 inherited diseases...
May 22, 2018: Genes
https://www.readbyqxmd.com/read/29787365/kpc-2-producing-st101-klebsiella-pneumoniae-from-bloodstream-infection-in-india
#2
Chaitra Shankar, Baby Abirami Shankar, Abi Manesh, Balaji Veeraraghavan
This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome sequencing using the Ion Torrent PGM platform with 400 bp chemistry was performed. blaKPC-2 was found on an IncFIIK plasmid associated with ISKpn6 and ISKpn7 without Tn4401. This is the first report of KPC-2 K. pneumoniae from bacteremia in India. The isolate also coded for other resistance genes such as aadA1, aadA2, armA, aac(3)-Ild, aac(6')-Ild for aminoglycoside; blaSHV-11, blaTEM-1B, blaOXA-9, for β-lactams and aac(6')-Ild, oqxA, oqxB, qnrB1 for fluoroquinolones...
May 22, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29785135/mutation-analysis-of-brca1-2-mutations-with-special-reference-to-polymorphic-snps-in-indian-breast-cancer-patients
#3
Nidhi D Shah, Parth S Shah, Yash Y Panchal, Kalpesh H Katudia, Nikunj B Khatri, Hari Shankar P Ray, Upti R Bhatiya, Sandip C Shah, Bhavini S Shah, Mandava V Rao
Background: Germline mutations BRCA1 and BRCA2 contribute almost equally in the causation of breast cancer (BC). The type of mutations in the Indian population that cause this condition is largely unknown. Purpose: In this cohort, 79 randomized BC patients were screened for various types of BRCA1 and BRCA2 mutations including frameshift, nonsense, missense, in-frame and splice site types. Materials and methods: The purified extracted DNA of each referral patient was subjected to Sanger gene sequencing using Codon Code Analyzer and Mutation Surveyor and next-generation sequencing (NGS) methods with Ion torrent software, after appropriate care...
2018: Application of Clinical Genetics
https://www.readbyqxmd.com/read/29782030/the-genomes-of-three-bradyrhizobium-sp-isolated-from-root-nodules-of-lupinus-albescens-grown-in-extremely-poor-soils-display-important-genes-for-resistance-to-environmental-stress
#4
Camille E Granada, Luciano K Vargas, Fernando Hayashi Sant'Anna, Eduardo Balsanelli, Valter Antonio de Baura, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Tiago Falcon, Luciane M P Passaglia
Lupinus albescens is a resistant cover plant that establishes symbiotic relationships with bacteria belonging to the Bradyrhizobium genus. This symbiosis helps the development of these plants in adverse environmental conditions, such as the ones found in arenized areas of Southern Brazil. This work studied three Bradyrhizobium sp. (AS23, NAS80 and NAS96) isolated from L. albescens plants that grow in extremely poor soils (arenized areas and adjacent grasslands). The genomes of these three strains were sequenced in the Ion Torrent platform using the IonXpress library preparation kit, and presented a total number of bases of 1,230,460,823 for AS23, 1,320,104,022 for NAS80, and 1,236,105,093 for NAS96...
May 17, 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29777484/identification-of-differentially-expressed-micrornas-in-sahiwal-bos-indicus-breed-of-cattle-during-thermal-stress
#5
Gyanendra Singh Sengar, Rajib Deb, Umesh Singh, Vivek Junghare, Saugata Hazra, T V Raja, Rani Alex, Ashish Kumar, R R Alyethodi, Rajiv Kant, Subhash Jakshara, C G Joshi
microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in post transcriptional gene regulation that influence various fundamental cellular processes, including the cellular responses during environmental stresses. However, perusal of literatures revealed few reports on the differential expression of miRNA during thermal stress in Indian native (Bos indicus) cattle breeds. The present investigation aimed to identify differentially expressed miRNAs during thermal stress in Sahiwal (Bos indicus) dairy cattle breed of India, adapted with tropical climate over a long period of time...
May 18, 2018: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29771400/inflammatory-cytokines-il-6-il-10-il-13-tnf-%C3%AE-and-peritoneal-fluid-flora-were-associated-with-infertility-in-patients-with-endometriosis
#6
X-M Wang, Z-Y Ma, N Song
OBJECTIVE: To investigate the correlations of inflammatory factors, interleukin-6 (IL-6), IL-10, IL-13 and tumor necrosis factor-α (TNF-α), and composition of bacterial flora in the peritoneal fluid with infertility in endometriosis patients. PATIENTS AND METHODS: A total of 55 patients diagnosed with endometriosis and infertility in the Gynecology Clinic of our hospital from June 2014 to July 2017 were selected as observation group, and another 30 non-endometriosis and non-infertility patients were enrolled as control group...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29770612/identification-of-novel-mutations-causing-pediatric-cataract-in-bhutan-cambodia-and-sri-lanka
#7
Shari Javadiyan, Sionne E M Lucas, Dechen Wangmo, Meng Ngy, Kapila Edussuriya, Jamie E Craig, Adam Rudkin, Robert Casson, Dinesh Selva, Shiwani Sharma, Karen M Lower, James Meucke, Kathryn P Burdon
BACKGROUND: Pediatric cataract is an important cause of blindness and visual impairment in children. A large proportion of pediatric cataracts are inherited, and many genes have been described for this heterogeneous Mendelian disease. Surveys of schools for the blind in Bhutan, Cambodia, and Sri Lanka have identified many children with this condition and we aimed to identify the genetic causes of inherited cataract in these populations. METHODS: We screened, in parallel, 51 causative genes for inherited cataracts in 33 probands by Ampliseq enrichment and sequencing on an Ion Torrent PGM...
May 16, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29755805/analysis-of-bacterial-diversity-in-different-heavy-oil-wells-of-a-reservoir-in-south-oman-with-alkaline-ph
#8
Biji Shibulal, Saif N Al-Bahry, Yahya M Al-Wahaibi, Abdulkadir E Elshafie, Ali S Al-Bemani, Sanket J Joshi
The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis...
2018: Scientifica
https://www.readbyqxmd.com/read/29755687/clinical-application-of-targeted-next-generation-sequencing-for-colorectal-cancer-patients-a-multicentric-belgian-experience
#9
Nicky D'Haene, Quitterie Fontanges, Nancy De Nève, Oriane Blanchard, Barbara Melendez, Monique Delos, Marie-Françoise Dehou, Calliope Maris, Nathalie Nagy, Emmanuel Rousseau, Josse Vandenhove, André Gilles, Carine De Prez, Laurine Verset, Marie-Paule Van Craynest, Pieter Demetter, Jean-Luc Van Laethem, Isabelle Salmon, Marie Le Mercier
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29752895/adaptation-of-an-amplicon-based-human-cancer-next-generation-sequencing-panel-assay-for-murine-tumors
#10
David R Meier, Kristopher A Lofgren, Grzegorz T Gurda, Paraic A Kenny
Unlike humans, inbred genetically engineered mice have minimal inter-individual variation and, consequently, offer substantially increased statistical power for robust definition of recurrent cooperating cancer mutations. While technically feasible, whole exome sequencing is expensive and extremely data-intensive. Somatic mutation analysis using panels of 25-75 genes now provides detailed insight into the biology of human tumors. Here we report an adaptation for mouse tumors of a human PCR amplicon-based panel (Ion Torrent Cancer Hotspot Panel v2) allowing analysis of 18 cancer genes, including Kras, Nras, Hras, Pten, Pik3ca and Smad4, and encompassing regions homologous to more than 2000 known human cancer mutations...
May 9, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29744712/next-generation-sequencing-library-preparation-method-for-identification-of-rna-viruses-on-the-ion-torrent-sequencing-platform
#11
Guiqian Chen, Yuan Qiu, Qingye Zhuang, Suchun Wang, Tong Wang, Jiming Chen, Kaicheng Wang
Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids...
May 9, 2018: Virus Genes
https://www.readbyqxmd.com/read/29723602/non-small-cell-lung-cancers-with-isocitrate-dehydrogenase-1-or-2-idh1-2-mutations
#12
Laura N Toth, Francine B de Abreu, Laura J Tafe
Isocitrate dehydrogenase 1 and 2 (IDH1/2) are important metabolic enzymes that convert isocitrate to α-ketoglutarate. IDH1/2 mutations are associated with the development of multiple malignancies. In this study, we examine the prevalence and features of non-small cell lung cancers (NSCLC) with IDH1/2 mutations. From May 2013 - March 2017, 800 lung cancer samples were successfully sequenced for somatic mutations on the Ion Torrent PGM with the 50 gene AmpliSeq Cancer Hotspot Panel v2 on the Ion Torrent PGM (318 chip)...
April 30, 2018: Human Pathology
https://www.readbyqxmd.com/read/29707819/effects-of-pure-plant-secondary-metabolites-on-methane-production-rumen-fermentation-and-rumen-bacteria-populations-in-vitro
#13
M Joch, J Mrázek, E Skřivanová, L Čermák, M Marounek
In this study, the effects of seven pure plant secondary metabolites (PSMs) on rumen fermentation, methane (CH4 ) production and rumen bacterial community composition were determined. Two in vitro trials were conducted. In trial 1, nine concentrations of 8-hydroxyquinoline, α-terpineol, camphor, bornyl acetate, α-pinene, thymoquinone and thymol were incubated on separate days using in vitro 24-hr batch incubations. All compounds tested demonstrated the ability to alter rumen fermentation parameters and decrease CH4 production...
April 29, 2018: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/29695638/molecular-profile-of-advanced-thyroid-carcinomas-by-next-generation-sequencing-characterizing-tumors-beyond-diagnosis-for-targeted-therapy
#14
Hui Chen, Rajyalakshmi Luthra, Mark J Routbort, Keyur P Patel, Maria E Cabanillas, Russell R Broaddus, Michelle D Williams
Next generation sequencing (NGS) for molecular diagnostics allows simultaneous testing of activating oncogenes and tumor suppressor mutations in multiple signal pathways. Extended mutational profiling of advanced thyroid cancers may enhance considerations for targeted therapies. We analyzed clinically derived molecular profiling of 216 patients with advanced thyroid carcinoma using NGS (Ion Torrent Personal Genome Machine) from 4/2012-2/2014. We examined substitutions and small indels in 46/50 cancer-related genes using Ampliseq Cancer Hotspot panel in respect to tumor diagnosis and clinical correlations...
April 25, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29694208/demonstration-of-single-barium-ion-sensitivity-for-neutrinoless-double-beta-decay-using-single-molecule-fluorescence-imaging
#15
A D McDonald, B J P Jones, D R Nygren, C Adams, V Álvarez, C D R Azevedo, J M Benlloch-Rodríguez, F I G M Borges, A Botas, S Cárcel, J V Carrión, S Cebrián, C A N Conde, J Díaz, M Diesburg, J Escada, R Esteve, R Felkai, L M P Fernandes, P Ferrario, A L Ferreira, E D C Freitas, A Goldschmidt, J J Gómez-Cadenas, D González-Díaz, R M Gutiérrez, R Guenette, K Hafidi, J Hauptman, C A O Henriques, A I Hernandez, J A Hernando Morata, V Herrero, S Johnston, L Labarga, A Laing, P Lebrun, I Liubarsky, N López-March, M Losada, J Martín-Albo, G Martínez-Lema, A Martínez, F Monrabal, C M B Monteiro, F J Mora, L M Moutinho, J Muñoz Vidal, M Musti, M Nebot-Guinot, P Novella, B Palmeiro, A Para, J Pérez, M Querol, J Repond, J Renner, S Riordan, L Ripoll, J Rodríguez, L Rogers, F P Santos, J M F Dos Santos, A Simón, C Sofka, M Sorel, T Stiegler, J F Toledo, J Torrent, Z Tsamalaidze, J F C A Veloso, R Webb, J T White, N Yahlali
A new method to tag the barium daughter in the double-beta decay of ^{136}Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba^{++}) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (∼2  nm), and detected with a statistical significance of 12.9σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers...
March 30, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29669586/genetic-characterization-of-a-novel-picorna-like-virus-in-culex-spp-mosquitoes-from-mozambique
#16
Harindranath Cholleti, Juliette Hayer, Jose Fafetine, Mikael Berg, Anne-Lie Blomström
BACKGROUND: Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique. METHODS: The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform...
April 18, 2018: Virology Journal
https://www.readbyqxmd.com/read/29662631/overlap-at-the-molecular-and-immunohistochemical-levels-between-angioimmunoblastic-t-cell-lymphoma-and-a-subgroup-of-peripheral-t-cell-lymphomas-without-specific-morphological-features
#17
Rebeca Manso, Julia González-Rincón, Manuel Rodríguez-Justo, Giovanna Roncador, Sagrario Gómez, Margarita Sánchez-Beato, Miguel A Piris, Socorro M Rodríguez-Pinilla
The overlap of morphology and immunophenotype between angioimmunoblastic T-cell lymphoma (AITL) and other nodal peripheral T-cell lymphomas (n-PTCLs) is a matter of current interest whose clinical relevance and pathogenic background have not been fully established. We studied a series of 98 n-PTCL samples (comprising 57 AITL and 41 PTCL-NOS) with five TFH antibodies (CD10, BCL-6, PD-1, CXCL13, ICOS), looked for mutations in five of the genes most frequently mutated in AITL ( TET2 , DNMT3A, IDH2, RHOA and PLCG1 ) using the Next-Generation-Sequencing Ion Torrent platform, and measured the correlations of these characteristics with morphology and clinical features...
March 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29656754/malignant-cells-from-pleural-fluids-in-malignant-mesothelioma-patients-reveal-novel-mutations
#18
Sophie Sneddon, Ian Dick, Y C Gary Lee, A W Bill Musk, Ann-Marie Patch, John V Pearson, Nicola Waddell, Richard J N Allcock, Robert A Holt, Bruce W S Robinson, Jenette Creaney
OBJECTIVES: Malignant mesothelioma (MM) is an asbestos related tumour affecting cells of serosal cavities. More than 70% of MM patients develop pleural effusions which contain tumour cells, representing a readily accessible source of malignant cells for genetic analysis. Although common somatic mutations and losses have been identified in solid MM tumours, the characterization of tumour cells within pleural effusions could provide novel insights but is little studied. MATERIALS AND METHODS: DNA and RNA were extracted from cells from short term cultures of 27 human MM pleural effusion samples...
May 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29611381/determining-genotypic-drug-resistance-by-ion-semiconductor-sequencing-with-the-ion-ampliseq%C3%A2-tb-panel-in-multidrug-resistant-mycobacterium-tuberculosis-isolates
#19
Joonhong Park, So Youn Shin, Kyungjong Kim, Kuhn Park, Soyoung Shin, Chunhwa Ihm
BACKGROUND: We examined the feasibility of a full-length gene analysis for the drug resistance-related genes inhA, katG, rpoB, pncA, rpsL, embB, eis, and gyrA using ion semiconductor next-generation sequencing (NGS) and compared the results with those obtained from conventional phenotypic drug susceptibility testing (DST) in multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates. METHODS: We extracted genomic DNA from 30 pure MDR-TB isolates with antibiotic susceptibility profiles confirmed by phenotypic DST for isoniazid (INH), rifampin (RIF), ethambutol (EMB), pyrazinamide (PZA), amikacin (AMK), kanamycin (KM), streptomycin (SM), and fluoroquinolones (FQs) including ofloxacin, moxifloxacin, and levofloxacin...
July 2018: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/29608791/integrated-massively-parallel-sequencing-of-15-autosomal-strs-and-amelogenin-using-a-simplified-library-preparation-approach
#20
Jian Xue, Riga Wu, Yajiao Pan, Shunxia Wang, Baowang Qu, Ying Qin, Yuequn Shi, Chuchu Zhang, Ran Li, Liyan Zhang, Cheng Zhou, Hongyu Sun
Massively parallel sequencing (MPS) technologies, also termed as next-generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two-round PCR that requires more steps, making it time-consuming (about 2 days), laborious and expensive. In this study, a 16-plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database-type samples (bloodstains, saliva stains, etc...
April 2, 2018: Electrophoresis
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