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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
Valentina Ferradini, Marco Cassone, Sara Nuovo, Ilaria Bagni, 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...
April 17, 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
#7
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)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419429/mutational-landscape-of-b-cell-post-transplant-lymphoproliferative-disorders
#8
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
#9
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
https://www.readbyqxmd.com/read/28416601/csreport-a-new-computational-tool-designed-for-automatic-analysis-of-class-switch-recombination-junctions-sequenced-by-high-throughput-sequencing
#10
François Boyer, Hend Boutouil, Iman Dalloul, Zeinab Dalloul, Jeanne Cook-Moreau, Jean-Claude Aldigier, Claire Carrion, Bastien Herve, Erwan Scaon, Michel Cogné, Sophie Péron
B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions...
April 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28396619/the-complete-mitogenome-of-orcula-dolium-draparnaud-1801-ultra-deep-sequencing-from-a-single-long-range-pcr-using-the-ion-torrent-pgm
#11
D S J Groenenberg, J Harl, E Duijm, E Gittenberger
BACKGROUND: With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages...
2017: Hereditas
https://www.readbyqxmd.com/read/28392550/comparison-of-ion-personal-genome-machine-platforms-for-the-detection-of-variants-in-brca1-and-brca2
#12
Sang Mee Hwang, Ki Chan Lee, Min Seob Lee, Kyoung Un Park
Purpose: Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. Materials and Methods: The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2...
April 7, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28391895/identification-of-a-novel-lmf1-nonsense-mutation-responsible-for-severe-hypertriglyceridemia-by-targeted-next-generation-sequencing
#13
Angelo B Cefalù, Rossella Spina, Davide Noto, Valeria Ingrassia, Vincenza Valenti, Antonina Giammanco, Francesca Fayer, Gabriella Misiano, Gianfranco Cocorullo, Chiara Scrimali, Ornella Palesano, Grazia I Altieri, Antonina Ganci, Carlo M Barbagallo, Maurizio R Averna
BACKGROUND: Severe hypertriglyceridemia (HTG) may result from mutations in genes affecting the intravascular lipolysis of triglyceride (TG)-rich lipoproteins. OBJECTIVE: The aim of this study was to develop a targeted next-generation sequencing panel for the molecular diagnosis of disorders characterized by severe HTG. METHODS: We developed a targeted customized panel for next-generation sequencing Ion Torrent Personal Genome Machine to capture the coding exons and intron/exon boundaries of 18 genes affecting the main pathways of TG synthesis and metabolism...
January 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/28387325/hpv-negative-penile-squamous-cell-carcinoma-disruptive-mutations-in-the-tp53-gene-are-common
#14
Karl Kashofer, Elke Winter, Iris Halbwedl, Andrea Thueringer, Marisa Kreiner, Stefan Sauer, Sigrid Regauer
The majority of penile squamous cell carcinomas is caused by transforming human papilloma virus (HPV) infection. The etiology of HPV-negative cancers is unclear, but TP53 mutations have been implicated. Archival tissues of 108 invasive squamous cell carcinoma from a single pathology institution in a low-incidence area were analyzed for HPV-DNA and p16(ink4a) overexpression and for TP53 mutations by ion torrent next-generation sequencing. Library preparation failed in 32/108 squamous cell carcinomas. Institutional review board approval was obtained...
April 7, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28369462/drvm-a-new-tool-for-efficient-genome-assembly-of-known-eukaryotic-viruses-from-metagenomes
#15
Hsin-Hung Lin, Yu-Chieh Liao
Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data...
February 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28368926/basal-cell-carcinoma-with-matrical-differentiation-clinicopathologic-immunohistochemical-and-molecular-biological-study-of-22-cases
#16
Liubov Kyrpychova, Richard A Carr, Petr Martinek, Tomas Vanecek, Raul Perret, Magdalena Chottová-Dvořáková, Michal Zamecnik, Ladislav Hadravsky, Michal Michal, Dmitry V Kazakov
Basal cell carcinoma (BCC) with matrical differentiation is a fairly rare neoplasm, with about 30 cases documented mainly as isolated case reports. We studied a series of this neoplasm, including cases with an atypical matrical component, a hitherto unreported feature. Lesions coded as BCC with matrical differentiation were reviewed; 22 cases were included. Immunohistochemical studies were performed using antibodies against BerEp4, β-catenin, and epithelial membrane antigen (EMA). Molecular genetic studies using Ion AmpliSeq Cancer Hotspot Panel v2 by massively parallel sequencing on Ion Torrent PGM were performed in 2 cases with an atypical matrical component (1 was previously subjected to microdissection to sample the matrical and BCC areas separately)...
March 31, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28359267/aberrant-expression-of-alk-and-ezh2-in-merkel-cell-carcinoma
#17
Tuukka Veija, Virve Koljonen, Tom Bohling, Mia Kero, Sakari Knuutila, Virinder Kaur Sarhadi
BACKGROUND: Distinct characteristic features categorize Merkel cell carcinoma (MCC) into two subgroups according to the Merkel cell polyomavirus infection. Many mutational studies on MCC have been carried out in recent years without identifying a prominent driver mutation. However, there is paucity reporting the expression of cancer genes at the RNA level in MCC tumors. In this study, we studied the RNA expression profiles of 26 MCC tumors, with a goal to identify prospective molecular targets that could improve the treatment strategies of MCC...
March 31, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28349918/land-use-types-and-soil-chemical-properties-influence-soil-microbial-communities-in-the-semiarid-loess-plateau-region-in-china
#18
Qin Tian, Takeshi Taniguchi, Wei-Yu Shi, Guoqing Li, Norikazu Yamanaka, Sheng Du
Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land...
March 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28342798/allele-frequencies-and-other-forensic-parameters-of-the-hid-ion-ampliseq%C3%A2-identity-panel-markers-in-basques-using-the-ion-torrent-pgm%C3%A2-platform
#19
O García, A Soto, I Yurrebaso
The HID-Ion AmpliSeq™ Identity Panel amplifies 90 autosomal SNPs and 34 Y- SNPs with massively parallel sequencing (MPS) using the Ion Torrent PGM™ platform. In the present study, 105 Basques were analyzed to assess this panel. All loci were in Hardy-Weinberg equilibrium and no association between them was detected. Forensic parameters were calculated as 5.74×10(-36) for combined match probability and 99.99998% for combined power of exclusion. In conclusion, the HID Identity panel and the use of this new MPS technology are very promising tools for paternity testing and human identification in routine casework in the forensic field...
March 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#20
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
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