RVC - Polymer Plate for improved biomedical analyses by tissue imaging MALDI-TOF

Award Information
Agency:
Department of Health and Human Services
Branch
n/a
Amount:
$150,000.00
Award Year:
2013
Program:
SBIR
Phase:
Phase I
Contract:
1R43HG007501-01
Award Id:
n/a
Agency Tracking Number:
R43HG007501
Solicitation Year:
2013
Solicitation Topic Code:
NHGRI
Solicitation Number:
PA12-088
Small Business Information
2905 Parmenter St., MIDDLETON, WI, -
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
19710669
Principal Investigator:
AUDREY KLINGELE
(608) 831-9011
aklingele@lucigen.com
Business Contact:
AUDREY KLINGELE
(608) 831-9011
aklingele@lucigen.com
Research Institution:
Stub




Abstract
DESCRIPTION (provided by applicant): The genetic basis of disease remains a significant research problem, impacting the fields of cancer biology, neurology, cardiology, development, and even microbiology, as recently realized by the Human Microbiome Project. Determination of the genomic sequence underlying observed phenotypes is now widespread. Genomic sequencing is becoming faster and cheaper, allowing access to more genomic information and greater understanding of the relationships between genotype and phenotype. Increasingly, these technologies are being applied to smaller and smaller sample sizes, down to single cells. A single cell contains all the necessary genetic information, and theoretically can be amplified repeatedly. However, generating enough amplified DNA from such small samples for genomic sequencing is constrained by several features of current technologies. Current amplification protocols use phi29 polymerase and DNA primed with random hexamers. Although this system has allowed for the studyof disease using single cells, it has numerous disadvantages. Primary among these are primer amplification artifacts and high bias which is especially exacerbated when the amount of target DNA is low. Biased amplification from single genomes results in loss of sequence information such as allelic dropout and complicates copy number variant analysis. This bias is stochastic because it results from the initial annealing of random hexamers to begin amplification from random regions. Such stochastic bias makescomparison between single cells nearly impossible. The goal of this Phase I proposal is to enable primer-free DNA synthesis, to vastly improve the efficiency and coverage of amplified DNA from samples as small as single cells. Removing primers will eliminate unproductive side-reactions and decrease bias in the final product. This system is expected to operate isothermally at higher temperatures, without the need for an initial denaturation step. The commercial result of our proposed study will be a reagentkit for high fidelity, low bias (high coverage) amplification of DNA from single cells without primer background issues. This work will advance the study of single cell genomics by providing higher sequence coverage, enabling research into cancer, stem cells, biofilms, and the human microbiome. PUBLIC HEALTH RELEVANCE PUBLIC HEALTH RELEVANCE: Whole genome amplification (WGA) is essential for genomic studies of single cell samples. Unfortunately, current methods have high bias and produce wasteful non-amplification artifacts. We propose a novel thermostable primer-free WGA system that generates high coverage low bias amplified genomic DNA.

* information listed above is at the time of submission.

Agency Micro-sites


SBA logo

Department of Agriculture logo

Department of Commerce logo

Department of Defense logo

Department of Education logo

Department of Energy logo

Department of Health and Human Services logo

Department of Homeland Security logo

Department of Transportation logo

Enviromental Protection Agency logo

National Aeronautics and Space Administration logo

National Science Foundation logo
US Flag An Official Website of the United States Government