Austin, TX, United States
Austin, TX, United States

Asuragen is a molecular diagnostics company using genomics to drive better patient management in oncology and genetic diseases through world leading clinical testing solutions. The company uses a breadth of technologies and scientific talent to discover, develop and commercialize diagnostic products and clinical testing services with efficiency and flexibility both internally and its companion diagnostic partners. Asuragen’s products, services and technologies drive countless patient management decisions across oncology, genetic disease and other molecular testing modalities. Wikipedia.

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The present invention concerns methods and compositions for introducing miRNA activity or function into cells using synthetic nucleic acid molecules. Moreover, the present invention concerns methods and compositions for identifying miRNAs with specific cellular functions that are relevant to therapeutic, diagnostic, and prognostic applications wherein synthetic miRNAs and/or miRNA inhibitors are used in library screening assays.


Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 619.94K | Year: 2016

Project Summary The long term goal of this project is to develop validate and commercialize an assay for improved analysis of C orf a gene on chromosome that is linked to frontotemporal dementia FTD and amyotrophic lateral sclerosis ALS Expansion of a guanine and cytosine rich hexanucleotide repeat GGGGCC in the non coding region of C orf is associated with of familial ALS The expansion also appears in of familial frontotemporal dementia FTD cases as well as of sporadic ALS and of sporadic FTD The C orf region is difficult to size accurately because most expansions in affected individuals are andgt repeats in length Currently testing typically relies on homebrew PCR based assays for accurate sizing of andlt repeats or separately Southern blot analysis for crude sizing of andgt repeats We have developed a solution to enable high throughput reliable sensitive and accurate sizing of the repeat region for both short andlt repeats up to repeats and long expansions to at least repeats in a reflex assay The proposed assay offers a solution to these technical challenges based on the repeat primed assay platform AmplideX FMR PCR that Asuragen has developed and successfully commercialized for fragile X syndrome a CGG triplet repeat disorder We will continue to leverage andgt years of experience in optimizing high performance diagnostic assays for GC rich repeat sequences to develop an accurate and robust diagnostic test for C orf Funding for this Phase II will support the efforts necessary to complete the development of the test The specific aims of this proposal are Aim Integrate a novel engineered PCR polymerase system to achieve extreme processivity and reliable amplification of andgt hexanucleotide repeats Aim Develop and integrate a set of controls and standards in an optimized workflow that supports C orf testing Aim Develop a data analysis pipeline and reporting tools within a user friendly application that allows rapid and accurate identification C orf repeat number Aim Evaluate an assay system that integrates the workflow and controls Aims and with the analysis software Aim Validate the integrated system with cell lines and retrospective clinical samples The development of an improved information rich assay for C orf will be useful as a screening and diagnostic test for ALS and FTD as well as a clinical research tool to identify intermediate and or expanded repeat sizes that are potentially relevant to other forms of age onset neurodegeneration In addition this assay can further the understanding of known and novel genotype phenotype associations and enable opportunities for targeted therapeutics and clinical trials Project Narrative We are developing a test to improve diagnosis and screening for genetic alterations that are linked to neurodegenerative diseases Alterations in the gene C ORF are associated with frontotemporal dementia FTD and amyotrophic lateral sclerosis ALS The test will be useful as a clinical research tool to support opportunities for emerging therapeutic options


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 246.86K | Year: 2015

DESCRIPTION provided by applicant A novel andquot Superplexandquot RT qPCR strategy will be optimized for the single tube amplification and quantification of targeted panels of fusion transcripts that can be broadly applicable for the rapid development of clinical cancer diagnostic assays The novel design will enable accurate and reproducible quantitative detection of mid sized RNA panels more than a dozen targets in clinical samples providing a compact cost efficient assay that can be matched to the right clinical need The approach will address diagnostic laboratoriesandapos requirement for reliable harmonized and affordable methods that are easy to implement and can tap a ubiquitous install base of real time PCR instruments The proposed effort will optimize the technology specifically for fusion transcripts and incorporate Asuragenandapos s proprietary Armored RNA technology in the final format as stable and versatile RNA controls approved for clinical diagnostics Together these innovations will provide a solid foundation for the rapid development of a suite of companion diagnostic assays that can be used as tools for cancer diagnosis and to guide precision medicine options for patients Superplex RT qPCR overcomes the limitations of quantitative PCR instruments by increasing the number of targets detected in a single tube through dual readouts of fluorescent intensity and melting temperature to achieve multiplexing in a dimensional solution array The method combines the use of Molecular Beacon probes MBs and an improved version of asymmetric PCR called Linear after the Exponential LATE PCR In Phase I this method will be optimized and verified with cell lines with documented translocations and using synthetic transcripts spiked in total RNA The aims are Specific Aim Develop PCR primers and MB probes for leukemia translocations and one control targets total Specific Aim Optimize primers and probes for performance in the multiplex reaction Specific Aim Analytically verify the fully multiplexed assay Successful completion of phase I will result in a platform on which Asuragen can develop other Superplex assays for hematologic malignancies and leukemia sub types including other panels of clinically actionable cancer fusions such as those in solid tumors In phase II we will expand the number of targets detected incorporate multi categorical analyte RNA and DNA detection and optimize for manufacturing as a kit Additionally RNA standards will be developed to make the kit quantitative and to provide harmonized results across laboratories PUBLIC HEALTH RELEVANCE andquot Superplexandquot quantitative PCR technology will be developed for the detection of cancer from blood or biopsies by testing for multiple chromosomal abnormalities in a single tube This work will establish the foundation for a technology that can be used to develop a series of cancer assays to test for clinically actionable cancer fusions such as those in solid tumors and blood related cancers


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 225.00K | Year: 2015

DESCRIPTION provided by applicant The goal of this project is to develop a validated quantitative assay for the fragile X mental retardation protein FMRP to aid in the clinical management of those with fragile X syndrome FXS autism and other disorders and to advance FXS research FXS is the leading form of inheritable intellectual disability ranging from mild to severe and is the most common known mutation in autism It is caused by CGG repeat expansion in the X linked FMR gene In non affected individuals to repeats occur in the FMR andapos UTR whereas in those with FXS andgt repeats are observed causing substantially reduced levels of FMRP and intellectual disability Expansion to repeats results in normal or much smaller reductions in FMRP These individuals are unaffected or present a varying less serious degree of cognitive behavioral and emotional dysfunctions Individuals with fewer than repeats almost never manifest FMR related clinical features FMRP diagnostic testing is already recognized in the ACMG fragile X guidelines However reliable correlation between FMRP levels and patient diagnosis and prognosis has been undermined by both biological and technical issues There is a critical need for a well validated and standardized quantitative FMRP assay to support researchers and clinicians in their efforts to understand FXS biology and to aid in patient management Biological challenges to the reliable interpretation of FMR molecular tests include somatic mosaicism or the presence of varying genotypes and or methylation states in different tissues Importantly case studies have revealed tissue specific differences for fragile X mutations wherein buccal cells that share an ectodermal developmental lineage with brain tissue may be more clinically informative than blood We will test the feasibility of using BCs to assay FMRP because they may better represent fragile X biology in the brain Technical challenges include pre analytical limitations substandard antibodies and the lack of quantitative FMRP standards Recently an FMRP assay was published that addresses these issues including compatibility with dried blood spots DBS and a workflow on the Luminex platform that is amendable to routine testing Our overall objective is to make improvements to this assay by reducing sources of variation validating the test with annotated clinical samples and then launching the assay for the analysis of blood and buccal cells stabilized on andquot andquot paper This technology will enable the accurate quantification of FMRP and FMR genotyping from a single sample thereby simplifying the collection of a comprehensive FXS dataset enabling diagnostic and prognostic applications and improving our overall understanding of FXS biology Specific Aim Complete a multi site validation of the published assay using common reagents and samples Specific Aim Develop the protocols and reagents to normalize for the FMRP producing blood cells in a DBS sample Specific Aim Demonstrate the feasibility of using buccal cells stored on papers for assaying FMRP and perform a pilot clinical study PUBLIC HEALTH RELEVANCE We are developing a test to improve the diagnosis and screening for fragile X syndrome and other related disorders Fragile X is one of the most commonly inherited forms of mental retardation and can also cause conditions such as ADHD and autism Alterations in the fragile X gene are associated with changes in the fragile x protein The test detects this protein from a small drop of blood spotted on paper to support diagnosis and to help guide decisions for current and emerging treatments


The present invention provides a method of identifying or classifying a patient as having a condition characterized by aberrant neovascularization and suitable for treatment with a synthetic miR-184 molecule. The method includes the step of determining the expression level of miR-184 (SEQ. ID. NO:2) in a biological sample obtained from a tissue characterized by aberrant neovascularization.


The present invention concerns methods and compositions for introducing miRNA activity or function into cells using synthetic nucleic acid molecules. Moreover, the present invention concerns methods and compositions for identifying miRNAs with specific cellular functions that are relevant to therapeutic, diagnostic, and prognostic applications wherein synthetic miRNAs and/or miRNA inhibitors are used in library screening assays.


The present invention concerns methods and compositions for introducing miRNA activity or function into cells using synthetic nucleic acid molecules. Moreover, the present invention concerns methods and compositions for identifying miRNAs with specific cellular functions that are relevant to therapeutic, diagnostic, and prognostic applications wherein synthetic miRNAs and/or miRNA inhibitors are used in library screening assays.


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 1.49M | Year: 2015

Not Available


The present invention concerns methods and compositions for introducing miRNA activity or function into cells using synthetic nucleic acid molecules. Moreover, the present invention concerns methods and compositions for identifying miRNAs with specific cellular functions that are relevant to therapeutic, diagnostic, and prognostic applications wherein synthetic miRNAs and/or miRNA inhibitors are used in library screening assays.

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