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https://www.readbyqxmd.com/read/28640116/distribution-of-somatic-mutations-of-cancer-related-genes-according-to-microsatellite-instability-status-in-korean-gastric-cancer
#1
Joonhong Park, Han Mo Yoo, Woori Jang, Soyoung Shin, Myungshin Kim, Yonggoo Kim, Seung-Woo Lee, Jeong Goo Kim
In studies of the molecular basis of gastric cancer (GC), microsatellite instability (MSI) is one of the key factors. Somatic mutations found in GC are expected to contribute to MSI-high (H) tumorigenesis. We estimated somatic mutation distribution according to MSI status in 52 matched pair GC samples using the Ion Torrent Ion S5 XL with the AmpliSeq Cancer Hotspot panel.Seventy-five (9.8%) somatic variants consisting of 34 hotspot mutations and 41 other likely pathogenic variants were identified in 34 GC samples...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28636991/non-invasive-detection-of-somatic-mutations-using-next-generation-sequencing-in-primary-central-nervous-system-lymphoma
#2
Maxime Fontanilles, Florent Marguet, Élodie Bohers, Pierre-Julien Viailly, Sydney Dubois, Philippe Bertrand, Vincent Camus, Sylvain Mareschal, Philippe Ruminy, Catherine Maingonnat, Stéphane Lepretre, Elena-Liana Veresezan, Stéphane Derrey, Hervé Tilly, Jean-Michel Picquenot, Annie Laquerrière, Fabrice Jardin
PURPOSE: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). PATIENTS AND METHODS: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®)...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28610586/genotyping-of-high-risk-anal-human-papillomavirus-hpv-ion-torrent-next-generation-sequencing-vs-linear-array
#3
Rebecca G Nowak, Nicholas P Ambulos, Lisa M Schumaker, Trevor J Mathias, Ruth A White, Jennifer Troyer, David Wells, Manhattan E Charurat, Søren M Bentzen, Kevin J Cullen
BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it's diagnostic performance has not been tested in cases with multiple concurrent HPV infections...
June 13, 2017: Virology Journal
https://www.readbyqxmd.com/read/28610385/complete-mitochondrial-genome-and-taxonomic-revision-of-cardiodactylus-muiri-otte-2007-gryllidae-eneopterinae-lebinthini
#4
Jiajia Dong, Natallia Vicente, Ioana C Chintauan-Marquier, Cahyo Ramadi, Agnès Dettai, Tony Robillard
In the present study, we report the high-coverage complete mitochondrial genome (mitogenome) of the cricket Cardiodactylus muiri Otte, 2007. The mitogenome was sequenced using a long-PCR approach on an Ion Torrent Personal Genome Machine (PGM) for next generation sequencing technology. The total length of the amplified mitogenome is 16,328 bp, representing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one noncoding region (D-loop region). The new sets of long-PCR primers reported here are invaluable resources for future comparative evolutionary genomic studies in Orthopteran insects...
May 15, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609449/development-of-next-generation-sequencing-panel-for-umod-and-association-with-kidney-disease
#5
Caitlin Bailie, Jill Kilner, Alexander P Maxwell, Amy Jayne McKnight
Chronic kidney disease (CKD) has a prevalence of approximately 10% in adult populations. CKD can progress to end-stage renal disease (ESRD) and this is usually fatal unless some form of renal replacement therapy (chronic dialysis or renal transplantation) is provided. There is an inherited predisposition to CKD with several genetic risk markers now identified. The UMOD gene has been associated with CKD of varying aetiologies. An AmpliSeq next generation sequencing panel was developed to facilitate comprehensive sequencing of the UMOD gene, covering exonic and regulatory regions...
2017: PloS One
https://www.readbyqxmd.com/read/28606054/variable-order-sequence-modeling-improves-bacterial-strain-discrimination-for-ion-torrent-dna-reads
#6
Thomas M Poulsen, Martin Frith
BACKGROUND: Genome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this approach, where accurate alignment and classification of sequencing data is crucial. Standard mapping methods crudely treat bases as independent from their neighbors. Accuracy might be improved by using higher order paired hidden Markov models (HMMs), which model neighbor effects, but introduce design and implementation issues that have typically made them impractical for read mapping applications...
June 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28576516/a-novel-missense-mutation-in-the-slc26a4-gene-causes-nonsyndromic-hearing-loss-and-enlarged-vestibular-aqueduct
#7
Xiaoguang He, Qi Peng, Siping Li, Pengyuan Zhu, Chunqiu Wu, Chunbao Rao, Jiang Chang, Mingyu Xie, Baimao Zhong, Xiaomei Lu
OBJECTIVES: We aimed to investigate the genetic causes of hearing loss in a Chinese proband with nonsyndromic hearing loss and enlarged vestibular aqueduct syndrome. METHODS: We conducted clinical and genetic evaluations in a deaf proband and his normal-hearing parents. Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to detect the pathogenic mutations. As a control, a group of 1500 previously studied healthy newborns from the same ethnic background were subjected to deafness gene screening using the same method as in our previous study...
April 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28544559/pipecraft-flexible-open-source-toolkit-for-bioinformatics-analysis-of-custom-high-throughput-amplicon-sequencing-data
#8
Sten Anslan, Mohammad Bahram, Indrek Hiiesalu, Leho Tedersoo
High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analyzed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user friendly graphical interface that links several public tools for analyzing amplicon sequencing data...
May 25, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28525363/targeted-sequencing-of-tonsillar-and-base-of-tongue-cancer-and-human-papillomavirus-positive-unknown-primary-of-the-head-and-neck-reveals-prognostic-effects-of-mutated-fgfr3
#9
Cinzia Bersani, Lars Sivars, Linnea Haeggblom, Sebastian DiLorenzo, Michael Mints, Andreas Ährlund-Richter, Nikolaos Tertipis, Eva Munck-Wikland, Anders Näsman, Torbjörn Ramqvist, Tina Dalianis
BACKGROUND: Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28511174/noninvasive-prenatal-detection-of-trisomy-21-by-targeted-semiconductor-sequencing-a-technical-feasibility-study
#10
Yanwei Xi, Aryan Arbabi, Amy J M McNaughton, Alison Hamilton, Danna Hull, Helene Perras, Tillie Chiu, Shawna Morrison, Claire Goldsmith, Emilie Creede, Gregory J Anger, Christina Honeywell, Mireille Cloutier, Natasha Macchio, Courtney Kiss, Xudong Liu, Susan Crocker, Gregory A Davies, Michael Brudno, Christine M Armour
OBJECTIVE: To develop an alternate noninvasive prenatal testing method for the assessment of trisomy 21 (T21) using a targeted semiconductor sequencing approach. METHODS: A customized AmpliSeq panel was designed with 1,067 primer pairs targeting specific regions on chromosomes 21, 18, 13, and others. A total of 235 samples, including 30 affected with T21, were sequenced with an Ion Torrent Proton sequencer, and a method was developed for assessing the probability of fetal aneuploidy via derivation of a risk score...
May 17, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28488887/rapid-and-affordable-genome-wide-bisulfite-dna-sequencing-by-xmai-reduced-representation-bisulfite-sequencing
#11
Alexander S Tanas, Marina E Borisova, Ekaterina B Kuznetsova, Viktoria V Rudenko, Kristina O Karandasheva, Marina V Nemtsova, Vera L Izhevskaya, Olga A Simonova, Sergey S Larin, Dmitry V Zaletaev, Vladimir V Strelnikov
AIM: To develop a reduced representation bisulfite sequencing (RRBS) approach for rapid and affordable genome-wide DNA methylation analysis. METHODS: We have selected restriction endonuclease XmaI to produce RRBS library fragments. After digestion and partial fill-in DNA fragments were ligated to barcoded adapters, bisulfite converted, size-selected, and sequenced on the Ion Torrent Personal Genome Machine. XmaI-RRBS results were compared with the previously published RRBS data...
May 10, 2017: Epigenomics
https://www.readbyqxmd.com/read/28487606/effect-of-lactobacillus-rhamnosus-hn001-and-bifidobacterium-longum-bb536-on-the-healthy-gut-microbiota-composition-at-phyla-and-species-level-a-preliminary-study
#12
Marco Toscano, Roberta De Grandi, Laura Stronati, Elena De Vecchi, Lorenzo Drago
AIM: To evaluate the ability of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 to colonize the intestinal environment of healthy subjects and modify the gut microbiota composition. METHODS: Twenty healthy Italian volunteers, eight males and twelve females, participated in the study. Ten subjects took a sachet containing 4 × 10(9) colony-forming units (CFU) of Bifidobacterium longum BB536 and 10(9) CFU of Lactobacillus rhamnosus HN001, 30 min before breakfast (pre-prandial administration), while ten subjects took a sachet of probiotic product 30 min after breakfast (post-prandial administration)...
April 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28482824/novel-missense-mutation-in-the-bzip-transcription-factor-maf-associated-with-congenital-cataract-developmental-delay-seizures-and-hearing-loss-aym%C3%A3-gripp-syndrome
#13
Shari Javadiyan, Jamie E Craig, Shiwani Sharma, Karen M Lower, Theresa Casey, Eric Haan, Emmanuelle Souzeau, Kathryn P Burdon
BACKGROUND: Cataract is a major cause of severe visual impairment in childhood. The purpose of this study was to determine the genetic cause of syndromic congenital cataract in an Australian mother and son. METHOD: Fifty-one genes associated with congenital cataract were sequenced in the proband using a custom Ampliseq library on the Ion Torrent Personal Genome Machine (PGM). Reads were aligned against the human genome (hg19) and variants were annotated. Variants were prioritised for validation by Sanger sequencing if they were novel, rare or previously reported to be associated with paediatric cataract and were predicted to be protein changing...
May 8, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28475299/consistency-and-reproducibility-of-next-generation-sequencing-and-other-multigene-mutational-assays-a-worldwide-ring-trial-study-on-quantitative-cytological-molecular-reference-specimens
#14
Umberto Malapelle, Clara Mayo-de-Las-Casas, Miguel A Molina-Vila, Rafael Rosell, Spasenija Savic, Michel Bihl, Lukas Bubendorf, Manuel Salto-Tellez, Dario de Biase, Giovanni Tallini, David H Hwang, Lynette M Sholl, Rajyalakshmi Luthra, Birgit Weynand, Sara Vander Borght, Edoardo Missiaglia, Massimo Bongiovanni, Daniel Stieber, Philippe Vielh, Fernando Schmitt, Alessandra Rappa, Massimo Barberis, Francesco Pepe, Pasquale Pisapia, Nicola Serra, Elena Vigliar, Claudio Bellevicine, Matteo Fassan, Massimo Rugge, Carlos E de Andrea, Maria D Lozano, Fulvio Basolo, Gabriella Fontanini, Yuri E Nikiforov, Suzanne Kamel-Reid, Gilda da Cunha Santos, Marina N Nikiforova, Sinchita Roy-Chowdhuri, Giancarlo Troncone
BACKGROUND: Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears...
May 5, 2017: Cancer
https://www.readbyqxmd.com/read/28453579/studies-on-bacterial-community-composition-are-affected-by-the-time-and-storage-method-of-the-rumen-content
#15
Yury Tatiana Granja-Salcedo, Ricardo Andrés Ramirez-Uscategui, Elwi Guillermo Machado, Juliana Duarte Messana, Luciano Takeshi Kishi, Ana Veronica Lino Dias, Telma Teresinha Berchielli
The objective of this study was to investigate three storage methods and four storage times for rumen sampling in terms of quality and yield of extracted metagenomic DNA as well as the composition of the rumen bacterial community. One Nellore steer fitted with a ruminal silicone-type cannula was used as a donor of ruminal contents. The experiment comprised 11 experimental groups: pellet control (PC), lyophilized control (LC), P-20: pellet stored frozen at -20°C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C for a period of 3, 6, and 12 months...
2017: PloS One
https://www.readbyqxmd.com/read/28449808/validation-of-quantitative-pcr-based-assays-for-detection-of-gene-copy-number-aberrations-in-formalin-fixed-paraffin-embedded-solid-tumor-samples
#16
Meenakshi Mehrotra, Rajyalakshmi Luthra, Ronald Abraham, Bal Mukund Mishra, Shumaila Virani, Hui Chen, Mark J Routbort, Keyur P Patel, L Jeffrey Medeiros, Rajesh R Singh
Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28448473/transcriptomic-analysis-of-calcium-remodeling-in-colorectal-cancer
#17
Enrique Pérez-Riesgo, Lucía G Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary P Moyer, Lucía Núñez, Carlos Villalobos
Colorectal cancer (CRC) cells undergo the remodeling of intracellular Ca(2+) homeostasis, which contributes to cancer hallmarks such as enhanced proliferation, invasion and survival. Ca(2+) remodeling includes critical changes in store-operated Ca(2+) entry (SOCE) and Ca(2+) store content. Some changes have been investigated at the molecular level. However, since nearly 100 genes are involved in intracellular Ca(2+) transport, a comprehensive view of Ca(2+) remodeling in CRC is lacking. We have used Next Generation Sequencing (NGS) to investigate differences in expression of 77 selected gene transcripts involved in intracellular Ca(2+) transport in CRC...
April 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28446532/next-generation-sequencing-ngs-analysis-on-single-circulating-tumor-cells-ctcs-with-no-need-of-whole-genome-amplification-wga
#18
Raffaele Palmirotta, Domenica Lovero, Erica Silvestris, Claudia Felici, Davide Quaresmini, Paola Cafforio, Franco Silvestris
BACKGROUND: Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28445014/detection-of-immunoglobulin-heavy-chain-gene-clonality-by-next-generation-sequencing-for-minimal-residual-disease-monitoring-in-b-lymphoblastic-leukemia
#19
Saeam Shin, In Sik Hwang, Jieun Kim, Kyung A Lee, Seung Tae Lee, Jong Rak Choi
Minimal residual disease (MRD) following B-lymphoblastic leukemia (B-ALL) treatment has gained prognostic importance. Clonal immunoglobulin heavy chain (IGH) gene rearrangement is a useful follow-up marker in B-ALL owing to its high positivity rate. We evaluated the performance and clinical applicability of a next-generation sequencing (NGS) assay for IGH rearrangement in B-ALL MRD monitoring. IGH rearrangement was tested by using fluorescence PCR-fragment analysis and the NGS assay in eight B-ALL patients...
July 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28443228/genome-sequencing-analysis-of-atypical-shigella-flexneri-isolated-in-korea
#20
Nan-Ok Kim, Hae-Young Na, Su-Mi Jung, Gyung Tae Chung, Hyo Sun Kawk, Sahyun Hong
OBJECTIVES: An atypical Shigella flexneri strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains. METHODS: The genomic DNA of atypical S. flexneri strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA)...
February 2017: Osong Public Health and Research Perspectives
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