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https://www.readbyqxmd.com/read/28808243/comparison-of-error-correction-algorithms-for-ion-torrent-pgm-data-application-to-hepatitis-b-virus
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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...
July 26, 2017: Virology
https://www.readbyqxmd.com/read/28753539/clinical-features-and-genotyping-of-patients-with-primary-carnitine-deficiency-identified-by-newborn-screening
#11
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
https://www.readbyqxmd.com/read/28751392/draft-genome-sequence-of-rathayibacter-sp-strain-vkm-ac-2630-isolated-from-leaf-gall-induced-by-the-knapweed-nematode-mesoanguina-picridis-on-acroptilon-repens
#12
Irina P Starodumova, Sergey V Tarlachkov, Natalia V Prisyazhnaya, Lubov V Dorofeeva, Elena V Ariskina, Vladimir N Chizhov, Sergei A Subbotin, Lyudmila I Evtushenko, Oleg V Vasilenko
A draft genome sequence of Rathayibacter sp. strain VKM Ac-2630 was derived using Ion Torrent sequencing technology. The genome size of this strain is 3.88 Mb, with an average G+C content of 72.0%. Genomic evidence of an aerobic mode of respiration and a heterotrophic lifestyle of this bacterium was obtained.
July 27, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28748475/next-generation-sequencing-to-investigate-urinary-micrornas-from-macaca-fascicularis-cynomolgus-monkey
#13
Yaligara Veeranagouda, Jean-François Léonard, Jean-Charles Gautier, Eric Boitier
Advanced sequencing technologies like next-generation sequencing (NGS) not only detect microRNAs (miRNAs) in biological samples but also facilitate de novo identification of miRNAs. Using an Ion Torrent's Ion Proton System, here we described miRNAs sequencing of urine samples collected from Macaca fascicularis (Cynomolgus monkey) to investigate miRNAs as potential novel biomarkers of nephrotoxicity in this species. Urinary miRNA sequencing methodologies described here include (a) urinary exosomal RNA isolation, (b) sequencing library preparation, (c) sequencing template preparation, and (d) template library sequencing using Ion Proton System...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730229/molecular-analysis-of-brca1-and-brca2-genes-by-next-generation-sequencing-and-ultrastructural-aspects-of-breast-tumor-tissue
#14
Corina Elena Mihalcea, Ana Maria Moroşanu, Daniela Murăraşu, Liliana Puiu, Sabin Aurel Cinca, Silviu Cristian Voinea, Nicolae Mirancea
In this paper, we focus our interest on the dynamics alterations of the tumor-stroma interface at the ultrastructural level and to detect BRCA1 and BRCA2 mutations using next generation sequencing (NGS) of breast tumor tissue. Electron microscopic investigation revealed some peculiar infrastructural alterations of the tumor cells per se as well as of the tumor-stroma interface: invadopodia, shedding microvesicles, altered morphology and reduced number of telocytes, different abnormalities of the microvasculature...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28724405/environmental-drivers-of-viral-community-composition-in-antarctic-soils-identified-by-viromics
#15
Evelien M Adriaenssens, Rolf Kramer, Marc W Van Goethem, Thulani P Makhalanyane, Ian Hogg, Don A Cowan
BACKGROUND: The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS: Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28721658/microbial-communities-in-different-tissues-of-atta-sexdens-rubropilosa-leaf-cutting-ants
#16
Alexsandro S Vieira, Manuela O Ramalho, Cintia Martins, Vanderlei G Martins, Odair C Bueno
Bacterial endosymbionts are common in all insects, and symbiosis has played an integral role in ant evolution. Atta sexdens rubropilosa leaf-cutting ants cultivate their symbiotic fungus using fresh leaves. They need to defend themselves and their brood against diseases, but they also need to defend their obligate fungus gardens, their primary food source, from infection, parasitism, and usurpation by competitors. This study aimed to characterize the microbial communities in whole workers and different tissues of A...
July 18, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28710620/genome-sequencing-of-steroid-producing-bacteria-using-ion-torrent-technology-and-a-reference-genome
#17
Alberto Sola-Landa, Antonio Rodríguez-García, Carlos Barreiro, Rosario Pérez-Redondo
The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28702355/whole-genome-sequencing-and-annotation-of-halophilic-salinicoccus-sp-bab-3246-isolated-from-the-coastal-region-of-gujarat
#18
Vishal Mevada, Shradhdha Patel, Jignesh Pandya, Himani Joshi, Rajesh Patel
Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp identified by with second largest size for Salinicoccus sp...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28690591/characterization-of-the-microbiome-along-the-gastrointestinal-tract-of-growing-turkeys
#19
Toby J Wilkinson, A A Cowan, H E Vallin, L A Onime, Linda B Oyama, S J Cameron, Charlotte Gonot, J M Moorby, K Waddams, V J Theobald, D Leemans, S Bowra, C Nixey, Sharon A Huws
The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28685159/the-aurora-pilot-study-for-molecular-screening-of-patients-with-advanced-breast-cancer-a-study-of-the-breast-international-group
#20
Marion Maetens, David Brown, Alexandre Irrthum, Philippe Aftimos, Giuseppe Viale, Sibylle Loibl, Jean-François Laes, Peter J Campbell, Alastair Thompson, Javier Cortes, Sabine Seiler, Sara Vinnicombe, Mafalda Oliveira, Françoise Rothé, Yacine Bareche, Debora Fumagalli, Dimitrios Zardavas, Christine Desmedt, Martine Piccart, Sherene Loi, Christos Sotiriou
Several studies have demonstrated the feasibility of molecular screening of tumour samples for matching patients with cancer to targeted therapies. However, most of them have been carried out at institutional or national level. Herein, we report on the pilot phase of AURORA (NCT02102165), a European multinational collaborative molecular screening initiative for advanced breast cancer patients. Forty-one patients were prospectively enroled at four participating centres across Europe. Metastatic tumours were biopsied and profiled using an Ion Torrent sequencing platform at a central facility...
2017: NPJ Breast Cancer
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