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https://www.readbyqxmd.com/read/29128266/molecular-profiling-of-patients-with-advanced-colorectal-cancer-princess-margaret-cancer-centre-experience
#1
Joanne W Chiu, Monika K Krzyzanowska, Stefano Serra, Jennifer J Knox, Neesha C Dhani, Helen Mackay, David Hedley, Malcolm Moore, Geoffrey Liu, Ronald L Burkes, Christine Brezden-Masley, Michael H Roehrl, Kenneth J Craddock, Ming-Sound Tsao, Tong Zhang, Celeste Yu, Suzanne Kamel-Reid, Lillian L Siu, Philippe L Bedard, Eric X Chen
BACKGROUND: Molecular aberrations in KRAS, NRAS, BRAF, and PIK3CA have been well-described in advanced colorectal cancer. The incidences of other mutations are less known. We report results of molecular profiling of advanced colorectal cancer in an academic cancer center. PATIENTS AND METHODS: Patients with advanced colorectal were enrolled in an institution-wide molecular profiling program. Profiling was performed on formalin-fixed paraffin embedded archival tissues using a customized MassArray panel (23 genes, 279 mutations) or the Illumina MiSeq TruSeq Cancer Panel (48 genes, 212 amplicons, ≥ 500× coverage) in a Clinical Laboratory Improvement Amendments-certified laboratory...
October 23, 2017: Clinical Colorectal Cancer
https://www.readbyqxmd.com/read/28942092/the-parabasalid-symbiont-community-of-heterotermes-aureus-molecular-and-morphological-characterization-of-four-new-species-and-reestablishment-of-the-genus-cononympha
#2
Daniel E Jasso-Selles, Francesca De Martini, Katalina D Freeman, Mikaela D Garcia, Trevor L Merrell, Rudolf H Scheffrahn, Gillian H Gile
The subterranean termite Heterotermes aureus is endemic to arid regions of southwestern USA and northern Mexico. Like other termites in the family Rhinotermitidae, it harbors a community of protists (Phylum Parabasalia) in its hindgut that aid in cellulose digestion. We investigated the hindgut community of H. aureus using light microscopy, single cell isolation, and high throughput amplicon sequencing. Here we describe four new parabasalid species from the classes Trichonymphea and Spirotrichonymphea. Three of the new species include Pseudotrichonympha aurea (Trichonymphea), Holomastigotoides aureus, and Holomastigotoides oxyrhynchus (Spirotrichonymphea)...
September 6, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28934286/denitrification-potential-of-the-eastern-oyster-microbiome-using-a-16s-rrna-gene-based-metabolic-inference-approach
#3
Ann Arfken, Bongkeun Song, Jeff S Bowman, Michael Piehler
The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons...
2017: PloS One
https://www.readbyqxmd.com/read/28754147/design-and-implementation-of-a-custom-next-generation-sequencing-panel-for-selected-vitamin-d-associated-genes
#4
Katherine Angela Benson, Sourabh Chand, Alexander Peter Maxwell, Laura Jane Smyth, Jill Kilner, Richard Borrows, Amy Jayne McKnight
BACKGROUND: Biologically active vitamin D has an important regulatory role within the genome. It binds the vitamin D receptor (VDR) in order to control the expression of a wide range of genes as well as interacting with the epigenome to modify chromatin and methylation status. Vitamin D deficiency is associated with several human diseases including end-stage renal disease. METHODS: This article describes the design and testing of a custom, targeted next generation sequencing (NGS) panel for selected vitamin D associated genes...
July 28, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28735487/targeted-next-generation-sequencing-of-acute-leukemia
#5
Eric Konnick, Christina M Lockwood, David Wu
Mutation profiling of acute leukemias is a valuable tool for identifying genetic mutations with prognostic, predictive, therapeutic, and diagnostic utility. Technological advances, such as massively parallel sequencing, have allowed laboratories to assess for variation across dozens or hundreds of genes simultaneously with relatively low cost per target.Here, we describe a procedure for designing and using a TruSeq Custom Amplicon assay targeting genes involved in acute leukemias. This method is a fully customizable, amplicon-based assay for targeted resequencing, allowing interrogation of selected genomic regions of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28683838/a-novel-ultra-high-throughput-16s-rrna-gene-amplicon-sequencing-library-preparation-method-for-the-illumina-hiseq-platform
#6
Eric J de Muinck, Pål Trosvik, Gregor D Gilfillan, Johannes R Hov, Arvind Y M Sundaram
BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28658281/next-generation-sequencing-of-the-human-trpv1-gene-and-the-regulating-co-players-ltb4r-and-ltb4r2-based-on-a-custom-ampliseq%C3%A2-panel
#7
Dario Kringel, Marco Sisignano, Sebastian Zinn, Jörn Lötsch
BACKGROUND: Transient receptor potential cation channel subfamily V member 1 (TRPV1) are sensitive to heat, capsaicin, pungent chemicals and other noxious stimuli. They play important roles in the pain pathway where in concert with proinflammatory factors such as leukotrienes they mediate sensitization and hyperalgesia. TRPV1 is the target of several novel analgesics drugs under development and therefore, TRPV1 genetic variants might represent promising candidates for pharmacogenetic modulators of drug effects...
2017: PloS One
https://www.readbyqxmd.com/read/28622802/rapid-multiplex-dna-amplification-on-an-inexpensive-microdevice-for-human-identification-via-short-tandem-repeat-analysis
#8
Jacquelyn A DuVall, Delphine Le Roux, Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Daniel L Mills, An-Chi Tsuei, Martin G Ensenberger, Cindy Sprecher, Douglas R Storts, Brian E Root, James P Landers
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28544559/pipecraft-flexible-open-source-toolkit-for-bioinformatics-analysis-of-custom-high-throughput-amplicon-sequencing-data
#9
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 analysed 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 analysing amplicon sequencing data...
May 25, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28497333/next-generation-sequencing-based-genomic-profiling-of-brain-metastases-of-primary-ovarian-cancer-identifies-high-number-of-brca-mutations
#10
S Balendran, S Liebmann-Reindl, A S Berghoff, T Reischer, N Popitsch, C B Geier, L Kenner, P Birner, B Streubel, M Preusser
Ovarian cancer represents the most common gynaecological malignancy and has the highest mortality of all female reproductive cancers. It has a rare predilection to develop brain metastases (BM). In this study, we evaluated the mutational profile of ovarian cancer metastases through Next-Generation Sequencing (NGS) with the aim of identifying potential clinically actionable genetic alterations with options for small molecule targeted therapy. Library preparation was conducted using Illumina TruSight Rapid Capture Kit in combination with a cancer specific enrichment kit covering 94 genes...
July 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28429088/an-snp-panel-for-the-analysis-of-paternally-inherited-alleles-in-maternal-plasma-using-ion-torrent-pgm
#11
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/28423360/tiam1-variants-improve-clinical-outcome-in-neuroblastoma
#12
Elena Sanmartín, Yania Yáñez, Victoria Fornés-Ferrer, José L Zugaza, Adela Cañete, Victoria Castel, Jaime Font de Mora
Identification of tumor driver mutations is crucial for improving clinical outcome using a personalized approach to the treatment of cancer. Neuroblastoma is a tumor of the peripheral sympathetic nervous system for which only a few driver alterations have been described including MYCN amplification and ALK mutations. We assessed 106 primary neuroblastoma tumors by next generation sequencing using a customized amplicon-based gene panel. Our results reveal that genetic variants in TIAM1 gene associate with better clinical outcome, suggesting a role for these TIAM1 variants in preventing progression of this disease...
July 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28356599/towards-personalized-medicine-in-melanoma-implementation-of-a-clinical-next-generation-sequencing-panel
#13
Blanca de Unamuno Bustos, Rosa Murria Estal, Gema Pérez Simó, Inmaculada de Juan Jimenez, Begoña Escutia Muñoz, Mercedes Rodríguez Serna, Victor Alegre de Miquel, Margarita Llavador Ros, Rosa Ballester Sánchez, Eduardo Nagore Enguídanos, Sarai Palanca Suela, Rafael Botella Estrada
Molecular diagnostics are increasingly performed routinely in the diagnosis and management of patients with melanoma due to the development of novel therapies that target specific genetic mutations. The development of next-generation sequencing (NGS) technologies has enabled to sequence multiple cancer-driving genes in a single assay, with improved sensitivity in mutation detection. The main objective of this study was the design and implementation of a melanoma-specific sequencing panel, and the identification of the spectrum of somatic mutations in a series of primary melanoma samples...
March 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253235/simple-multiplexed-pcr-based-barcoding-of-dna-for-ultrasensitive-mutation-detection-by-next-generation-sequencing
#14
Anders Ståhlberg, Paul M Krzyzanowski, Matthew Egyud, Stefan Filges, Lincoln Stein, Tony E Godfrey
Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28218638/metagaap-a-novel-pipeline-to-estimate-community-composition-and-abundance-from-non-model-sequence-data
#15
Christopher Noune, Caroline Hauxwell
Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28185542/analysis-of-amplicon-based-ngs-data-from-neurological-disease-gene-panels-a-new-method-for-allele-drop-out-management
#16
Susanna Zucca, Margherita Villaraggia, Stella Gagliardi, Gaetano Salvatore Grieco, Marialuisa Valente, Cristina Cereda, Paolo Magni
BACKGROUND: Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28137276/towards-standardization-of-next-generation-sequencing-of-ffpe-samples-for-clinical-oncology-intrinsic-obstacles-and-possible-solutions
#17
Maxim Ivanov, Konstantin Laktionov, Valery Breder, Polina Chernenko, Ekaterina Novikova, Ekaterina Telysheva, Sergey Musienko, Ancha Baranova, Vladislav Mileyko
BACKGROUND: Next generation sequencing has a potential to revolutionize the management of cancer patients within the framework of precision oncology. Nevertheless, lack of standardization decelerated entering of the technology into the clinical testing space. Here we dissected a number of common problems of NGS diagnostics in oncology and introduced ways they can be resolved. METHODS: DNA was extracted from 26 formalin fixed paraffin embedded (FFPE) specimens and processed with the TrueSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) targeting 48 cancer-related genes and sequenced in single run...
January 31, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27986441/silent-genetic-alterations-identified-by-targeted-next-generation-sequencing-in-pheochromocytoma-paraganglioma-a-clinicopathological-correlations
#18
Suja Pillai, Vinod Gopalan, Chung Y Lo, Victor Liew, Robert A Smith, Alfred King Y Lam
AIMS: The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma. METHODS: Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer...
February 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27940662/deep-targeted-exon-sequencing-reveals-renal-polymorphisms-associate-with-postexercise-hypotension-among-african-americans
#19
Linda S Pescatello, Elizabeth D Schifano, Garrett I Ash, Gregory A Panza, Lauren Lamberti, Ming-Hui Chen, Ved Deshpande, Amanda Zaleski, Paulo Farinatti, Beth A Taylor, Paul D Thompson
We found variants from the Angiotensinogen-Converting Enzyme (ACE), Angiotensin Type 1 Receptor (AGTR1), Aldosterone Synthase (CYP11B2), and Adducin (ADD1) genes exhibited intensity-dependent associations with the ambulatory blood pressure (BP) response following acute exercise, or postexercise hypotension (PEH). In a validation cohort, we sequenced exons from these genes for their associations with PEH Obese (30.9 ± 3.6 kg m(-2)) adults (n = 23; 61% African Americans [AF], 39% Caucasian) 42.0 ± 9...
October 2016: Physiological Reports
https://www.readbyqxmd.com/read/27940449/next-generation-sequencing-of-circulating-cell-free-dna-for-evaluating-mutations-and-gene-amplification-in-metastatic-breast-cancer
#20
Karen Page, David S Guttery, Daniel Fernandez-Garcia, Allison Hills, Robert K Hastings, Jinli Luo, Kate Goddard, Vedia Shahin, Laura Woodley-Barker, Brenda M Rosales, R Charles Coombes, Justin Stebbing, Jacqueline A Shaw
BACKGROUND: Breast cancer tissues are heterogeneous and show diverse somatic mutations and somatic copy number alterations (CNAs). We used a novel targeted next generation sequencing (NGS) panel to examine cell-free DNA (cfDNA) to detect somatic mutations and gene amplification in women with metastatic breast cancer (MBC). METHODS: cfDNA from pretreated patients (n = 42) and 9 healthy controls were compared with matched lymphocyte DNA by NGS, using a custom 158 amplicon panel covering hot-spot mutations and CNAs in 16 genes, with further validation of results by droplet digital PCR...
February 2017: Clinical Chemistry
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