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Sah S.,Asuragen, Inc. | Eveleigh D.,Asuragen, Inc. | Wilson M.,Asuragen, Inc.
BMC Research Notes | Year: 2010

Background. microRNAs (miRNA) are short, endogenous transcripts that negatively regulate the expression of specific mRNA targets. The relative abundance of miRNAs is linked to function in vivo and miRNA expression patterns are potentially useful signatures for the development of diagnostic, prognostic and therapeutic biomarkers. Finding. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. Conclusions. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision. © 2010 Irizarry et al; licensee BioMed Central Ltd.


Chen L.,Asuragen, Inc. | Hadd A.G.,Asuragen, Inc. | Sah S.,Asuragen, Inc. | Houghton J.F.,Asuragen, Inc. | And 5 more authors.
Genetics in Medicine | Year: 2011

Purpose: Fragile X syndrome is associated with the expansion of CGG trinucleotide repeats and subsequent methylation of the FMR1 gene. Molecular diagnosis of fragile X currently requires Southern blot analysis to assess methylation. This study describes the evaluation of a polymerase chain reaction-only workflow for the determination of methylation status across a broad range of FMR1 genotypes in male and female specimens. Methods: We evaluated a novel method that combines allele-specific methylation polymerase chain reaction and capillary electrophoresis with eight cell line and 80 clinical samples, including 39 full mutations. Methylation status was determined using a three-step workflow: (1) differential treatment of genomic DNA using a methylation-sensitive restriction enzyme; (2) polymerase chain reaction with two sets of dye-tagged primers; and (3) amplicon sizing by capillary electrophoresis. All samples were analyzed by both methylation polymerase chain reaction and Southern blot analysis. Results: FMR1 methylation status and CGG repeat sizing were accurately and reproducibly determined in a set of methylation controls and genomic DNA samples representing a spectrum of CGG repeat lengths and methylation states. Moreover, methylation polymerase chain reaction revealed allele-specific methylation patterns in premutation alleles that were unobtainable using Southern blot analysis. Conclusions: Methylation polymerase chain reaction enabled high throughput, high resolution, and semiquantitative methylation assessments of FMR1 alleles, as well as determinations of CGG repeat length. Results for all samples were concordant with corresponding Southern blot analyses. As a result, this study presents a polymerase chain reaction-based method for comprehensive FMR1 analysis. In addition, the identification of novel methylation mosaic patterns revealed after polymerase chain reaction and capillary electrophoresis may be relevant to several FMR1 disorders. © 2011 Lippincott Williams & Wilkins.


This report studies Proteomic Cancer Biomarkers in Global market, especially in North America, Europe, China, Japan, Southeast Asia and India, focuses on top manufacturers in global market, with Production, price, revenue and market share for each manufacturer, covering  Abbott Diagnostics  Agilent Technologies  Eli Lilly & Co.  EUSA Pharma  CytoCore, Inc.  GE Healthcare  Bruker Daltonics, Inc.  Biomarker Technologies, LLC  BioCurex, Inc.  Asuragen, Inc.  DiagnoCure, Inc.  Beckman Coulter, Inc. For more information or any query mail at [email protected] Market Segment by Regions, this report splits Global into several key Regions, with production, consumption, revenue, market share and growth rate of Proteomic Cancer Biomarkers in these regions, from 2011 to 2021 (forecast), like  North America  Europe  China  Japan  Southeast Asia  India Split by product type, with production, revenue, price, market share and growth rate of each type, can be divided into  Type I  Type II  Type III Split by application, this report focuses on consumption, market share and growth rate of Proteomic Cancer Biomarkers in each application, can be divided into  Colorectal  Prostate  Lung  Breast  Ovarian Global Proteomic Cancer Biomarkers Market Research Report 2016  1 Proteomic Cancer Biomarkers Market Overview  1.1 Product Overview and Scope of Proteomic Cancer Biomarkers  1.2 Proteomic Cancer Biomarkers Segment by Type  1.2.1 Global Production Market Share of Proteomic Cancer Biomarkers by Type in 2015  1.2.2 Type I  1.2.3 Type II  1.2.4 Type III  1.3 Proteomic Cancer Biomarkers Segment by Application  1.3.1 Proteomic Cancer Biomarkers Consumption Market Share by Application in 2015  1.3.2 Colorectal  1.3.3 Prostate  1.3.4 Lung  1.3.5 Breast  1.3.6 Ovarian  1.4 Proteomic Cancer Biomarkers Market by Region  1.4.1 North America Status and Prospect (2011-2021)  1.4.2 Europe Status and Prospect (2011-2021)  1.4.3 China Status and Prospect (2011-2021)  1.4.4 Japan Status and Prospect (2011-2021)  1.4.5 Southeast Asia Status and Prospect (2011-2021)  1.4.6 India Status and Prospect (2011-2021)  1.5 Global Market Size (Value) of Proteomic Cancer Biomarkers (2011-2021) 7 Global Proteomic Cancer Biomarkers Manufacturers Profiles/Analysis  7.1 Abbott Diagnostics  7.1.1 Company Basic Information, Manufacturing Base and Its Competitors  7.1.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.1.2.1 Type I  7.1.2.2 Type II  7.1.3 Abbott Diagnostics Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.1.4 Main Business/Business Overview  7.2 Agilent Technologies  7.2.1 Company Basic Information, Manufacturing Base and Its Competitors  7.2.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.2.2.1 Type I  7.2.2.2 Type II  7.2.3 Agilent Technologies Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.2.4 Main Business/Business Overview  7.3 Eli Lilly & Co.  7.3.1 Company Basic Information, Manufacturing Base and Its Competitors  7.3.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.3.2.1 Type I  7.3.2.2 Type II  7.3.3 Eli Lilly & Co. Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.3.4 Main Business/Business Overview  7.4 EUSA Pharma  7.4.1 Company Basic Information, Manufacturing Base and Its Competitors  7.4.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.4.2.1 Type I  7.4.2.2 Type II  7.4.3 EUSA Pharma Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.4.4 Main Business/Business Overview  7.5 CytoCore, Inc.  7.5.1 Company Basic Information, Manufacturing Base and Its Competitors  7.5.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.5.2.1 Type I  7.5.2.2 Type II  7.5.3 CytoCore, Inc. Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.5.4 Main Business/Business Overview  7.6 GE Healthcare  7.6.1 Company Basic Information, Manufacturing Base and Its Competitors  7.6.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.6.2.1 Type I  7.6.2.2 Type II  7.6.3 GE Healthcare Proteomic Cancer Biomarkers Production, Revenue, Price and Gross Margin (2015 and 2016)  7.6.4 Main Business/Business Overview  7.7 Bruker Daltonics, Inc.  7.7.1 Company Basic Information, Manufacturing Base and Its Competitors  7.7.2 Proteomic Cancer Biomarkers Product Type, Application and Specification  7.7.2.1 Type I  7.7.2.2 Type II For more information or any query mail at [email protected] Wise Guy Reports is part of the Wise Guy Consultants Pvt. Ltd. and offers premium progressive statistical surveying, market research reports, analysis & forecast data for industries and governments around the globe. Wise Guy Reports features an exhaustive list of market research reports from hundreds of publishers worldwide. We boast a database spanning virtually every market category and an even more comprehensive collection of market research reports under these categories and sub-categories.


Kolb P.,University of California at San Francisco | Kolb P.,University of Marburg | Phan K.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases | Gao Z.-G.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases | And 4 more authors.
PLoS ONE | Year: 2012

G protein-coupled receptors (GPCRs) are attractive targets for pharmaceutical research. With the recent determination of several GPCR X-ray structures, the applicability of structure-based computational methods for ligand identification, such as docking, has increased. Yet, as only about 1% of GPCRs have a known structure, receptor homology modeling remains necessary. In order to investigate the usability of homology models and the inherent selectivity of a particular model in relation to close homologs, we constructed multiple homology models for the A1 adenosine receptor (A1AR) and docked ~2.2 M lead-like compounds. High-ranking molecules were tested on the A1AR as well as the close homologs A2AAR and A3AR. While the screen yielded numerous potent and novel ligands (hit rate 21% and highest affinity of 400 nM), it delivered few selective compounds. Moreover, most compounds appeared in the top ranks of only one model. These findings have implications for future screens.


AUSTIN, Texas--(BUSINESS WIRE)--Asuragen, Inc., a global molecular diagnostics company, announced today that it has entered into a collaboration agreement with Thermo Fisher Scientific for the development and commercialization of capillary electrophoresis-based in vitro diagnostics (IVDs). Asuragen will leverage its AmplideX® PCR/CE product technologies to develop diagnostic kits for the 3500 Dx Series Genetic Analyzer CS2 instrument. Asuragen’s kits for PCR/CE provide unparalleled performance for analyzing repetitive sequences. In addition, they integrate Asuragen’s analytics and reporting suite, the AmplideX® Reporter, providing a straightforward sample-to-answer solution. “More than half the genome is made up of repetitive sequences and short structural variations that are not well served by current diagnostic technologies, including next generation sequencing. The combination of Thermo Fisher’s capillary electrophoresis instruments’ performance and our novel AmplideX chemistries provides the level of resolution required for these emerging biomarkers,” said Matt McManus, MD, PhD, President and CEO of Asuragen. “Our AmplideX PCR/CE products are built under design control and manufactured in our cGMP facility, providing the high quality required for IVD products.” “We welcome the opportunity to collaborate with Asuragen to expand the diagnostic products for our 3500 Dx Genetic Analyzer platform,” said Kim Kelderman, Vice President and General Manager for the Genetic Analysis Business at Thermo Fisher Scientific. “Asuragen is recognized for delivering high performance and quality molecular diagnostic products in the fields of genetics and oncology. We look forward to working with them on products serving significant clinical needs.” Asuragen is a global diagnostic products company delivering solutions that build knowledge and understanding of complex clinical questions. Asuragen’s application of its deep scientific heritage and molecular expertise delivers diagnostic products in oncology and genetics that provide the best answers with optimal workflows – so time can be spent delivering actionable insights, rather than searching for them. With innovative approaches to kit development and a broad range of molecular chemistries, Asuragen produces assays that ensure reproducible results. From discovery and development to regulatory support to global commercialization, we also provide a tailored approach that efficiently delivers custom and companion diagnostic products for our partners. We believe people deserve better answers. For more information, visit www.asuragen.com.


Smith D.L.,Asuragen, Inc. | Lamy A.,University of Rouen | Beaudenon-Huibregtse S.,Asuragen, Inc. | Sesboue R.,University of Rouen | And 3 more authors.
Archives of Pathology and Laboratory Medicine | Year: 2014

Context. - Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information. Objective. - To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens. Design. - Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates. Results. - Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%-100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%-99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%-99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451-48 078). Conclusions. - The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.


Nolin S.L.,New York State Institute for Basic Research | Glicksman A.,New York State Institute for Basic Research | Ersalesi N.,New York State Institute for Basic Research | Dobkin C.,New York State Institute for Basic Research | And 6 more authors.
Genetics in Medicine | Year: 2015

Fragile X CGG repeat alleles often contain one or more AGG interruptions that influence allele stability and risk of a full mutation transmission from parent to child. We have examined transmissions of maternal and paternal alleles with 45-90 repeats to quantify the effect of AGG interruptions on fragile X repeat instability.Methods:A novel FMR1 polymerase chain reaction assay was used to determine CGG repeat length and AGG interruptions for 1,040 alleles from 705 families.Results:We grouped transmissions into nine categories of five repeats by parental size and found that in every size category, alleles with no AGGs had the greatest risk for instability. For maternal alleles <75 repeats, 89% (24/27) that expanded to a full mutation had no AGGs. Two contractions in maternal transmission were accompanied by loss of AGGs, suggesting a mechanism for generating alleles that lack AGG interruptions. Maternal age was examined as a factor in full mutation expansions using prenatal samples to minimize ascertainment bias, and a possible effect was observed though it was not statistically significant (P = 0.06).Conclusion:These results strengthen the association of AGG repeats with CGG repeat stability and provide more accurate risk estimates of full mutation expansions for women with 45-90 repeat alleles. © American College of Medical Genetics and Genomics.


Giordano T.J.,University of Michigan | Beaudenon-Huibregtse S.,Asuragen, Inc. | Shinde R.,Asuragen, Inc. | Langfield L.,Asuragen, Inc. | And 3 more authors.
Human Pathology | Year: 2014

Molecular testing for oncogenic gene alterations provides clinically actionable information essential for the optimal management of follicular cell thyroid cancer. We aimed to establish the distribution and frequency of common oncogenic gene mutations and chromosomal rearrangements in a comprehensive set of benign and malignant thyroid lesions. A case-control study was conducted in 413 surgical cases comprising 17 distinct histopathologic categories, 244 malignant, 169 benign, and 304 double-blinded specimens. Seventeen alterations of BRAF, HRAS, KRAS, NRAS, PAX8, and RET genes were evaluated using a single validated technology platform. Following verification of analytical sensitivity, accuracy, and precision in model and surgical specimens, 152 molecular positive results were generated in lesions representing multiple stages of progression and epithelial differentiation as well as rare subtypes of primary, secondary, or recurring tumors. Single mutations were found in 58% of primary malignant lesions and 12% of benign (P <.001). In the blinded validation set, mutation distribution and frequency were distinct across variants of follicular and papillary carcinomas. BRAF or RET-PTC was detected exclusively in malignant lesions but not in follicular carcinomas (P <.001). RAS or PAX8-PPARG were present in 23% of adenomas, and NRAS was found in a single nonneoplastic lesion (P =.0014). These data substantiate the diagnostic utility of molecular testing for oncogenic mutations and validate its performance in a variety of surgical specimens. Standardized and validated multianalyte molecular panels can complement the preoperative and postoperative assessment of thyroid nodules and support a growing number of clinical and translational applications with potential diagnostic, prognostic, or theranostic utility. © 2014 Elsevier Inc.


Wylie D.,Asuragen, Inc. | Shelton J.,Asuragen, Inc. | Choudhary A.,Asuragen, Inc. | Adai A.T.,Asuragen, Inc.
BMC Research Notes | Year: 2011

Background: Normalization is critical for accurate gene expression analysis. A significant challenge in the quantitation of gene expression from biofluids samples is the inability to quantify RNA concentration prior to analysis, underscoring the need for robust normalization tools for this sample type. In this investigation, we evaluated various methods of normalization to determine the optimal approach for quantifying microRNA (miRNA) expression from biofluids and tissue samples when using the TaqMan Megaplex high-throughput RT-qPCR platform with low RNA inputs. Findings. We compared seven normalization methods in the analysis of variation of miRNA expression from biofluid and tissue samples. We developed a novel variant of the common mean-centering normalization strategy, herein referred to as mean-centering restricted (MCR) normalization, which is adapted to the TaqMan Megaplex RT-qPCR platform, but is likely applicable to other high-throughput RT-qPCR-based platforms. Our results indicate that MCR normalization performs comparable to or better than both standard mean-centering and other normalization methods. We also propose an extension of this method to be used when migrating biomarker signatures from Megaplex to singleplex RT-qPCR platforms, based on the identification of a small number of normalizer miRNAs that closely track the mean of expressed miRNAs. Conclusions: We developed the MCR method for normalizing miRNA expression from biofluids samples when using the TaqMan Megaplex RT-qPCR platform. Our results suggest that normalization based on the mean of all fully observed (fully detected) miRNAs minimizes technical variance in normalized expression values, and that a small number of normalizer miRNAs can be selected when migrating from Megaplex to singleplex assays. In our study, we find that normalization methods that focus on a restricted set of miRNAs tend to perform better than methods that focus on all miRNAs, including those with non-determined (missing) values. This methodology will likely be most relevant for studies in which a significant number of miRNAs are not detected. © 2011 Wylie et al; licensee BioMed Central Ltd.


Sah S.,Asuragen, Inc. | Chen L.,Asuragen, Inc. | Houghton J.,Asuragen, Inc. | Kemppainen J.,Asuragen, Inc. | And 3 more authors.
Genome Medicine | Year: 2013

The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay ('QFI-PCR') that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. © 2013 Sah et al.; licensee BioMed Central Ltd.

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