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https://www.readbyqxmd.com/read/28544559/pipecraft-flexible-open-source-toolkit-for-bioinformatics-analysis-of-custom-high-throughput-amplicon-sequencing-data
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28435379/shifts-of-subgingival-bacterial-population-after-nonsurgical-and-pharmacological-therapy-of-localized-aggressive-periodontitis-followed-for-1-year-by-ion-torrent-pgm-platform
#14
Giuseppina Campisciano, Annamaria Toschetti, Manola Comar, Rosanna Di Taranto, Federico Berton, Claudio Stacchi
The possibility of targeting the hypervariable region V3 of the 16S rRNA gene using Ion Torrent Personal Genome Machine (PGM) could provide a complete analysis of subgingival plaque samples, potentially able to identify microbiological species missed by culture-based methods. A 16-year-old female smoker patient, affected by localized aggressive periodontitis, underwent a full-mouth disinfection protocol and was inserted in a 3-month recall program. Microbiological samples were collected at baseline and at 30, 100, 365 days follow-up and analyzed by Ion Torrent PGM...
January 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28432352/low-cost-low-bias-and-low-input-rna-seq-with-high-experimental-verifiability-based-on-semiconductor-sequencing
#15
Zhibiao Mai, Chuanle Xiao, Jingjie Jin, Gong Zhang
Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429088/an-snp-panel-for-the-analysis-of-paternally-inherited-alleles-in-maternal-plasma-using-ion-torrent-pgm
#16
Donggui Yang, Hao Liang, Shaobin Lin, Qing Li, Xiaoyan Ma, Jun Gao, Hongyu Sun, Qingqing Chen, Jianzhu Wu, Xueling Ou
Researchers have sought to develop an effective protocol for paternity analysis using cell-free DNA (cfDNA) in maternal plasma. The use of massively parallel sequencing (MPS) technology for SNP testing is attractive because of its high-throughput capacity and resolution to single-base precision. In this study, we designed a customized SNP panel for cfDNA sequencing that includes 720 short amplicons (< 140 bp) targeting SNPs on the autosome and Y chromosome. The systemic performance was evaluated using the Ion Torrent PGM, indicating balanced coverage among most of the included loci, except for 78 poorly performing SNPs that were observed to have an inconsistent allele balance, lower coverage reads or high background signals...
April 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28427807/targeted-next-generation-sequencing-in-patients-with-myotonia-congenita
#17
Valentina Ferradini, Marco Cassone, Sara Nuovo, Ilaria Bagni, Maria Rosaria D'Apice, Annalisa Botta, Giuseppe Novelli, Federica Sangiuolo
INTRODUCTION: Myotonia Congenita (MC) is a nondystrophic skeletal muscle disease characterized by muscle stiffness, weakness, delayed skeletal relaxation and hypertrophic muscle. The disease can be inherited as dominant or recessive. More than 130 mutations in CLCN1 gene have been identified. MATERIALS AND METHODS: We analyzed the entire coding region and exon-intron boundaries of the CLCN1 gene in 40 MC patients. Samples already Sanger-sequenced were successively evaluated by Next Generation Sequencing (NGS), on Ion Torrent PGM...
July 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#18
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419429/mutational-landscape-of-b-cell-post-transplant-lymphoproliferative-disorders
#19
Thomas Menter, Darius Juskevicius, Mary Alikian, Juerg Steiger, Stephan Dirnhofer, Alexandar Tzankov, Kikkeri N Naresh
It is currently unclear whether post-transplant diffuse large B-cell lymphomas (PT-DLBCL) display a similar genomic landscape as DLBCL in immunocompetent patients (IC-DLBCL). We investigated 50 post-transplant lymphoproliferative disorders (PTLDs) including 37 PT-DLBCL samples for somatic mutations frequently observed in IC-DLBCL. Targeted Next Generation Sequencing (NGS) using the Ion Torrent platform and a customized panel of 68 genes was performed on genomic DNA. Non-tumoural tissue was sequenced to exclude germline variants in cases where available...
April 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28418920/complementary-utility-of-targeted-next-generation-sequencing-and-immunohistochemistry-panels-as-a-screening-platform-to-select-targeted-therapy-for-advanced-gastric-cancer
#20
Hyo Song Kim, Hanna Lee, Su-Jin Shin, Seung-Hoon Beom, Minkyu Jung, Sujin Bae, Eun Young Lee, Kyu Hyun Park, Yoon Young Choi, Taeil Son, Hyoung-Il Kim, Jae-Ho Cheong, Woo Jin Hyung, Jun Chul Park, Sung Kwan Shin, Sang Kil Lee, Yong Chan Lee, Woong Sub Koom, Joon Seok Lim, Hyun Cheol Chung, Sung Hoon Noh, Sun Young Rha, Hyunki Kim, Soonmyung Paik
We tested the clinical utility of combined profiling of Ion Torrent PGM based next-generation sequencing (NGS) and immunohistochemistry (IHC) for assignment to molecularly targeted therapies. A consecutive cohort of 93 patients with advanced/metastatic GC who underwent palliative chemotherapy between March and December 2015 were prospectively enrolled. Formalin fixed paraffin embedded tumor biopsy specimens were subjected to a 10 GC panels [Epstein Barr virus encoding RNA in-situ hybridization, IHC for mismatch repair proteins (MMR; MLH1, PMS2, MSH2, and MSH6), receptor tyrosine kinases (HER2, EGFR, and MET), PTEN, and p53 protein], and a commercial targeted NGS panel of 52 genes (Oncomine Focus Assay)...
March 21, 2017: Oncotarget
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