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https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#1
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29331982/a-false-carrier-state-for-the-c-579g-a-mutation-in-the-ncf1-gene-in-ashkenazi-jews
#2
Martin De Boer, Ronit Gavrieli, Karin van Leeuwen, Haike Reznik Wolf, Maya Dushnitzki, Yifaat Bar-Yosef, Anat Bar-Ziv, Doron Behar, Shlomo Lipitz, Tal Elkan Miller, Anton T J Tool, Taco W Kuijpers, Timo K van den Berg, Baruch Wolach, Dirk Roos, Elon Pras
BACKGROUND: Mutations in the NCF1 gene that encodes p47phox, a subunit of the NADPH oxidase complex, cause chronic granulomatous disease (CGD). In Kavkazi Jews, a c.579G>A (p.Trp193Ter) mutation in NCF1 is frequently found, leading to CGD. The same mutation is found in about 1% of Ashkenazi Jews, although Ashkenazi CGD patients with this mutation have never been described. METHODS: We used Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), gene scan analysis and Ion Torrent Next Generation Sequencing for genetic analysis, and measured NADPH oxidase activity and p47phox expression...
January 13, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29330875/performance-of-the-early-access-ampliseq%C3%A2-mitochondrial-panel-with-degraded-dna-samples-using-the-ion-torrent%C3%A2-platform
#3
Ka Tak Wai, Mark Barash, Peter Gunn
The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120 and 240 minutes; total n = 25)...
January 13, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29327717/combined-mutation-and-copy-number-variation-detection-by-targeted-next-generation-sequencing-in-uveal-melanoma
#4
Kyra N Smit, Natasha M van Poppelen, Jolanda Vaarwater, Robert Verdijk, Ronald van Marion, Helen Kalirai, Sarah E Coupland, Sophie Thornton, Neil Farquhar, Hendrikus-Jan Dubbink, Dion Paridaens, Annelies de Klein, Emine Kiliç
Uveal melanoma is a highly aggressive cancer of the eye, in which nearly 50% of the patients die from metastasis. It is the most common type of primary eye cancer in adults. Chromosome and mutation status have been shown to correlate with the disease-free survival. Loss of chromosome 3 and inactivating mutations in BAP1, which is located on chromosome 3, are strongly associated with 'high-risk' tumors that metastasize early. Other genes often involved in uveal melanoma are SF3B1 and EIF1AX, which are found to be mutated in intermediate- and low-risk tumors, respectively...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29316748/-preliminary-study-of-exon-sequence-in-pneumoconiosis-and-pneumoconiosis-complicated-with-lung-cancer-using-high-throughput-sequencing-technology
#5
M F Jiang, L Li, Z Wang, C L Zhang, H Zhang
Objective: The detection and analysis of exon mutations of pneumoconiosis and pneumoco-niosis complicated with lung cancer provide reference evidence for screening, clinical diagnosis and treatment and prognosis in pneumoconiosis and pneumoconiosis complicated with lung cancer. Methods: The pathologi-cal tissue samples from 3 pneumoconiosis patients and 3 pneumoconiosis complicated with lung cancer pa-tients were collected. Genomic DNA was extracted and library was prepared. Exomes of the pathological tissue samples in pneumoconiosis patients and pneumoconiosis complicated with lung cancer patients were se-quenced using Ion Torrent PGM platform...
November 20, 2017: Chinese Journal of Industrial Hygiene and Occupational Diseases
https://www.readbyqxmd.com/read/29301485/strategies-for-identification-of-somatic-variants-using-the-ion-torrent-deep-targeted-sequencing-platform
#6
Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet
BACKGROUND: 'Next-generation' (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT...
January 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29291225/application-of-viromics-a-new-approach-to-the-understanding-of-viral-infections-in-humans
#7
REVIEW
Mageshbabu Ramamurthy, Sathish Sankar, Rajesh Kannangai, Balaji Nandagopal, Gopalan Sridharan
This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes...
December 2017: Virusdisease
https://www.readbyqxmd.com/read/29287889/a-novel-mutation-of-the-eya4-gene-associated-with-post-lingual-hearing-loss-in-a-proband-is-co-segregating-with-a-novel-pax3-mutation-in-two-congenitally-deaf-family-members
#8
Federica Cesca, Elisa Bettella, Roberta Polli, Elona Cama, Pietro Scimemi, Rosamaria Santarelli, Alessandra Murgia
OBJECTIVES: This work was aimed at establishing the molecular etiology of hearing loss in a 9-year old girl with post-lingual non-syndromic mild sensorineural hearing loss with a complex family history of clinically heterogeneous deafness. METHODS: The proband's DNA was subjected to NGS analysis of a 59-targeted gene panel, with the use of the Ion Torrent PGM platform. Conventional Sanger sequencing was used for segregation analysis in all the affected relatives...
January 2018: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/29258555/detection-and-full-genome-characterization-of-two-beta-cov-viruses-related-to-middle-east-respiratory-syndrome-from-bats-in-italy
#9
Ana Moreno, Davide Lelli, Luca de Sabato, Guendalina Zaccaria, Arianna Boni, Enrica Sozzi, Alice Prosperi, Antonio Lavazza, Eleonora Cella, Maria Rita Castrucci, Massimo Cicozzi, Gabriele Vaccari
BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV), which belongs to beta group of coronavirus, can infect multiple host species and causes severe diseases in humans. Multiple surveillance and phylogenetic studies suggest a bat origin. In this study, we describe the detection and full genome characterization of two CoVs closely related to MERS-CoV from two Italian bats, Pipistrellus kuhlii and Hypsugo savii. METHODS: Pool of viscera were tested by a pan-coronavirus RT-PCR...
December 19, 2017: Virology Journal
https://www.readbyqxmd.com/read/29245953/distinctive-dna-mismatch-repair-and-apc-rare-variants-in-african-americans-with-colorectal-neoplasia
#10
Hassan Ashktorab, Hamed Azimi, Sudhir Varma, Payaam Tavakoli, Michael L Nickerson, Hassan Brim
Purpose: African Americans have a higher incidence and mortality from colorectal cancer. This disparity might be due, in part, to the type of mutations in driver genes. In this study, we examined alterations specific to APC, MSH3, and MSH6 genes using targeted exome sequencing to determine distinctive variants in the course of neoplastic transformation. Experimental Design: A total of 140 African American colon samples (30 normal, 21 adenomas, 33 advanced adenomas and 56 cancers) were used as our discovery set on an Ion Torrent platform...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29236923/whole-genome-sequencing-of-leptospira-interrogans-from-southern-brazil-genetic-features-of-a-highly-virulent-strain
#11
Sérgio Jorge, Frederico Schmitt Kremer, Natasha Rodrigues de Oliveira, Gabrielle de Oliveira Sanches Valerio Navarro, Amanda Munari Guimarães, Christian Domingues Sanchez, Rafael Danelon Dos Santos Woloski, Karine Forster Ridieri, Vinícius Farias Campos, Luciano da Silva Pinto, Odir Antônio Dellagostin
BACKGROUND Leptospirosis is the most widespread zoonotic disease. It is caused by infection with pathogenic Leptospira species, of which over 300 serovars have been described. The accurate identification of the causative Leptospira spp. is required to ascertain the pathogenic status of the local isolates. OBJECTIVES This study aimed to obtain the complete genome sequence of a virulent Leptospira interrogans strain isolated from southern Brazil and to describe its genetic features. METHODS The whole genome was sequenced by next-generation sequencing (Ion Torrent)...
February 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29219266/-whole-genome-sequencing-of-human-mtdna-based-on-ion-torrent-pgm%C3%A2-platform
#12
Y Cao, K N Zou, J P Huang, K Ma, Y Ping
OBJECTIVES: To analyze and detect the whole genome sequence of human mitochondrial DNA (mtDNA) by Ion Torrent PGM™ platform and to study the differences of mtDNA sequence in different tissues. METHODS: Samples were collected from 6 unrelated individuals by forensic postmortem examination, including chest blood, hair, costicartilage, nail, skeletal muscle and oral epithelium. Amplification of whole genome sequence of mtDNA was performed by 4 pairs of primer...
August 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29219224/the-effects-of-pastoral-intensification-on-the-feeding-interactions-of-generalist-predators-in-streams
#13
C E Pearson, W O C Symondson, E L Clare, S J Ormerod, E Iparraguirre Bolaños, I P Vaughan
Land use change can alter trophic interactions with wide-ranging functional consequences, yet the consequences for aquatic food webs have been little-studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft-bodied prey. We used next generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with increasingly intensive livestock farming...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29186554/preclinical-validation-of-a-targeted-next-generation-sequencing-based-comprehensive-chromosome-screening-methodology-in-human-blastocysts
#14
R S Zimmerman, X Tao, D Marin, M Werner, K Hong, A Lonczak, J Landis, D Taylor, Y Zhan, R T Scott, N R Treff
STUDY QUESTION: Can a novel targeted next generation sequencing (tNGS) platform accurately detect whole chromosome aneuploidy in a trophectoderm biopsy and provide additional information to improve testing? SUMMARY ANSWER: Karyotypes obtained by tNGS were concordant with other validated platforms and SNP genotyping information obtained can be used for improved detection and quality control. WHAT IS KNOWN ALREADY: qPCR-based whole chromosome aneuploidy screening is highly accurate in comparison to other common methods and has been shown to improve IVF success in two randomized clinical trials...
November 25, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29179949/antisense-long-non-coding-rnas-are-deregulated-in-skin-tissue-of-patients-with-systemic-sclerosis
#15
Tobias C Messemaker, Loubna Chadli, Guoshuai Cai, Varshna S Goelela, Maaike Boonstra, Annemarie L Dorjée, Stefan N Andersen, Harald M M Mikkers, Peter van 't Hof, Hailiang Mei, Oliver Distler, Harmen H M Draisma, Michael E Johnson, Nicole M Orzechowski, Robert W Simms, Rene E M Toes, Jamil Aarbiou, Tom W Huizinga, Michael L Whitfield, Jeroen DeGroot, Jeska de Vries-Bouwstra, Fina Kurreeman
Systemic sclerosis (SSc) is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. Here we studied differentially expressed coding and non-coding genes in relation to SSc pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from fourteen early SSc patients and six healthy individuals were sequenced with ion-torrent and analysed using DEseq2. Overall, 4901 genes with a fold change >1.5 and a false discovery rate < 5% were detected in patients versus controls...
November 24, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29179676/hla-genotyping-by-next-generation-sequencing-of-complementary-dna
#16
Hidenobu Segawa, Yoji Kukita, Kikuya Kato
BACKGROUND: Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis...
November 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29178883/whole-genome-sequence-and-a-phylogenetic-analysis-of-the-g8p-14-group-a-rotavirus-strain-from-roe-deer
#17
Urska Jamnikar-Ciglenecki, Urska Kuhar, Andrej Steyer, Andrej Kirbis
BACKGROUND: Group A rotaviruses (RVA) are associated with acute gastroenteritis in children and in young domestic and wild animals. A RVA strain was detected from a roe deer for the first time during a survey of game animals in Slovenia in 2014. A further RVA strain (SLO/D110-15) was detected from a roe deer during 2015. The aim of this study was to provide a full genetic profile of the detected RVA strain from roe deer and to obtain additional information about zoonotic transmitted strains and potential reassortments between human rotavirus strains and zoonotic transmitted rotavirus strains...
November 25, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29146836/complete-genome-sequences-of-bk-polyomavirus-strains-from-two-patients-with-urinary-tract-infection-sequenced-using-the-ion-torrent-platform
#18
Graham Rose, Kyriaki Ranellou, Raju Misra, Colin Crump, David Wooldridge, Surendra Parmar, Christopher Maddren, Saheer Gharbia, Hamid Jalal
BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29141311/-study-on-mosaicism-of-scn1a-gene-mutation-in-parents-of-children-with-dravet-syndrome
#19
A J Liu, X X Yang, X J Xu, Q X Wu, X J Tian, X L Yang, X R Wu, L P Wei, Y H Zhang
Objective: To investigate the clinical phenotypes and the mutant allele proportion of parents with SCN1A gene mutation mosaicism of Dravet syndrome (DS) children, thus to provide guidance for family reproduction and prenatal diagnosis. Method: The clinical data and peripheral blood DNA samples of DS patients with a SCN1A gene mutation proved by Sanger sequencing were collected prospectively from February 2005 to November 2016 in Department of Pediatrics, Peking University First Hospital. The same mutation was searched in parents and other available relatives...
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29140103/salmonella-gallinarum-field-isolates-and-its-relationship-to-vaccine-strain-sg9r
#20
P K V Koerich, B B Fonseca, E Balestrin, V Tagliari, P G Hoepers, C Ueira-Vieira, I Oldoni, R H Rauber, L Ruschel, V P Do Nascimento
1. The aim of the present study was to determine if the 9R-strain of the Salmonella gallinarum live vaccine was responsible for having fowl typhoid outbreaks in chicken flocks from both chicken and turkey breeders as well as to verify the antimicrobial resistance of the isolates from the outbreaks. 2. The triplex polymerase chain reaction (PCR), standard antimicrobial test, beta-lactamase genes identification and Ion Torrent PMG whole genome sequence were used in the field isolates and in the vaccine strain of S...
November 15, 2017: British Poultry Science
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