Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 292.80K | Year: 2013
DESCRIPTION (provided by applicant): Recent advances in massively parallel cDNA sequencing (RNA-seq) have paved the way for comprehensive analysis of the transcriptome, a set of all RNA molecules including mRNA, rRNA, tRNA and other non-coding RNAs in oneor more populations of cells. RNA-Seq can identify the precise location of transcription boundaries, show how exons are connected and reveal sequence variations in transcribed regions. Taken together, RNA-Seq is the first sequencing based method that allows the entire transciptome to be surveyed in a very high- throughput and quantitative manner, offering both single-base resolution for annotation and digital gene expression levels at the genome scale. However, this technology is under active development and there are several enzymatic steps during library preparation that can contribute to sequence dependent bias, hindering comparisons between genomic regions and adversely affecting transriptome profiling. Ligases used to add on adapter sequences in RNA- Seq have structure based preferences, reverse transcriptases that make the first cDNA strand are prone to copy errors and rearrangements, and polymerases used for amplification often stumble when approaching GC / AT rich regions. The goal of this project isto create a library preparation kit for making minimally biased, highly indexed RNA-Seq libraries for deep sequencing that are constructed in a way to allow transcriptome profiles to be easily and fairly interrogated. Our proposal to develop technology tostudy the transcriptome in an unbiased, high-throughput manner should make future clinical applications a reality and propel research in comparative tissue disease profiles, further un-locking transcriptional regulation. PUBLIC HEALTH RELEVANCEPUBLIC HEALTH RELEVANCE: Advances in massively parallel cDNA sequencing (RNA-Seq) have paved the way for comprehensive analysis of the transcriptome, a set of all RNA molecules including mRNA, rRNA, tRNA and other non-coding RNAs in one or more populationsof cells. Our proposal to develop technology to study the transcriptome in an unbiased and quantitative manner should propel research in comparative tissue disease profiles and further un-lock the diagnostic potential of transcript profiling.
Agency: Department of Defense | Branch: Office for Chemical and Biological Defense | Program: SBIR | Phase: Phase I | Award Amount: 150.00K | Year: 2014
Burkholderia pseudomallei and Burkholderia mallei are highly pathogenic Gram-negative bacteria and the causative agents of melioidosis and glanders, respectively. These infections, which occur in humans and other animals, are endemic is wide regions of the developing world. Translational research regarding these pathogens is focused on developing new strategies to detect, treat and ideally protect humans and animals from these infections. In this Phase I SBIR project, we will establish methodologies for the generation of monoclonal antibodies that have high-affinities to Burkholderia antigens. The purpose of these studies is to create new antibody-based prophylactics that can neutralize Burkholderia infections. As a first step, we will isolate carbohydrate antigens from non-pathogenic strains of Burkholderia in forms that will generate appropriate immune responses. We will also assess the relative performance and compatibilities of existing antibodies to bind Burkholderia pathogens, in order to create optimized formulations, which will be assessed for therapeutic benefit in future challenge studies.
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 298.94K | Year: 2016
DESCRIPTION provided by applicant DNA methylation has been shown to be associated with cancer inflammatory and metabolic disorders neuronal plasticity and memory formation Up to now DNA methylation has been largely studied by whole genome bisulfite sequencing of populations of cells Studies like the Epigenomics Project and the Genomes Projects have contributed significantly to our understanding of genetic phenotypic and epigenetic variations amongst individuals in a population However all of these studies are essentially averaged snapshots or normalized fixed time assessments of our genetic and epigenetic makeup Nowhere is it more important to study dynamic variation than in epigenomics Almost all our understanding of the epigenome and its regulation has been derived from studies carried out at the population level thousands of cells being sequenced together There is considerable evidence indicating that cell to cell variability in gene expression is ubiquitous even amongst andapos homogeneousandquot populations of cells The extent of epigenetic heterogeneity in diverse cell types in tissues remains largely unknown Our goal in this grant application is to develop a solution to this problem by developing at least two single cell methyl sequencing library preparation protocols that will allow investigators to interrogate epigenetic modifications amongst individual cells of a population PUBLIC HEALTH RELEVANCE DNA methylation has been shown to be associated with cancer inflammatory and metabolic disorders neuronal plasticity and memory formation Up to now DNA methylation has been largely studied by whole genome sequencing populations of cells Our goal is to develop technology that allows for the examination of methylation patterns and stochastic intercellular variation in the epigenomes of single cells
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 161.70K | Year: 2013
DESCRIPTION (provided by applicant): Diabetes is a serious, life-threatening disease caused by improper absorption and metabolism of glucose. Increased glucose levels can lead to an accumulation of toxic sugar degradation products, such as methylglyoxal (MG), in the bloodstream. MG is a reactive molecule which can modify and inactivate blood proteins which in turn leads to hypertension, neuropathy, and heart disease. Consequently, MG has been shown to be an excellent biomarker for a number of diabetes-related complications. Unfortunately, all current methods to directly measure MG levels in blood are very expensive, time-consuming and laborious. To fully realize the diagnostic potential of MG, rapid analytical methods are needed for the routine determinationof MG in biomedical samples such as blood. Our proposed Phase I research will create a unique test to measure MG levels in blood samples such as plasma and serum. This unique test will permit researchers to conveniently study the accumulation of reactiveMG in blood before damage to proteins and vasculature has occurred. Our novel assay will use a recombinant bacterial oxidoreductase enzyme (MG-R) capable of specifically and rapidly converting MG into a detectable colorimetric signal in a 96 well plate assay format. To boost sensitivity, we will link our enzymatic detection reaction to an NADP+/NADPH visible colorimetric amplification loop to increase assay sensitivity more than 100-fold. The assay will be optimized and validated using rat and mouse plasmaand serum spiked with known amounts of MG. After validation, we will commercially launch a rapid test kit to directly detect MG in preclinical and other biomedical samples. PUBLIC HEALTH RELEVANCE PUBLIC HEALTH RELEVANCE: Diabetes is a major health threat in the US; this life-threatening disease is rapidly spreading throughout our country (23 million Americans currently affected). Recently, scientists have discovered that a sugar metabolite called methylglyoxal plays a central role in the progression of diabetes - unfortunately there are no methods currently available for routine analysis of methylglyoxal. Our research will create a unique method to rapidly measure methylglyoxal levels in normal and diabetic blood samples; our new analytical method will provide researchers with a critical new diagnostic tool to more-effectively combat diabetes and associated cardiovascular disease.
Agency: NSF | Branch: Standard Grant | Program: | Phase: SMALL BUSINESS PHASE II | Award Amount: 900.00K | Year: 2014
The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase II project is the development of a technology to accurately measure small RNA expression. This is an enabling life science research tool. Small RNAs are ubiquitous gene regulators found in the body. Products of the same microRNA gene that vary in length by one or two nucleotides may be involved in a host of diseases, including cancer. The value for developing a method to measure the true profile of microRNAs in a sample would be immense for the research community studying transcriptional regulation, and would open the doors to those interested in drug development and diagnostics. The goal of this proposal is to develop a library preparation kit for non-biased small RNA libraries for Next Generation sequencing. These kits will increase the quality and rate at which global microRNA profiles may be determined for research and clinical applications.
This SBIR Phase II project proposes to develop next generation sequencing technology for small RNA more quantitative and less biased. High throughput sequencing has transformed the landscape of genomic research with its ability to produce gigabases of data in a single run. This has enabled researchers to perform genome wide and high depth sequencing studies that would normally not be possible. Despite this capacity, amplification artifacts introduced during polymerase chain reaction (PCR) assays increase the chance of duplicate reads and uneven distribution of read coverage. Accurate profiling using deep sequencing also has been undermined by biases with over- or under-represented microRNAs. The presence of these biases significantly limits the incredible sensitivity and accuracy made possible by next generation sequencing. The goal of this proposal is to develop novel bias-reducing technology for making small RNA libraries. The proposed kits and protocols will increase the rate at which global microRNA profiles can be determined, and between-sample and within-sample differences (as well as newly discovered small RNAs) can be subsequently validated. This product will result in a major shift in the way small RNA sequencing is performed, and will pave the way for the discovery of new small RNAs.