| Version 2.5.2.0 |
|
|
Abstract
Grant Number: 1R01HG004873-01 Project Title: SCODA DNA extraction to normalize species representation
PI Information: Name Title MARZIALI, ANDRE andre@physics.ubc.ca ASSOCIATE PROFESSOR Abstract: DESCRIPTION (provided by applicant): To perform a metagenomic analysis of the Human Microbiome, normalization of species abundances prior to library construction is required to allow for both cost effective sequencing by avoiding redundancy of over represented organisms, and also to allow the detection and sequencing of very low abundance species. As a result, there exists a need for a robust DNA purification method that can efficiently extract DNA while rejecting contaminants, that can length select during the extraction process, and that can enrich DNA pools for low abundance sequences to ensure that as many organisms as possible can be detected. We aim to apply our SCODA technology for concentrating and purifying nucleic acids to perform integrated extraction and fragment length selection in a single automated step, in order to reduce the time and labor required to produce clone libraries from contaminated samples. In addition, we aim to develop sequence- specific concentration of nucleic acids as a means to enrich DNA populations for very low abundance species, and for targeted recovery of low abundance genomes. PUBLIC HEALTH RELEVANCE: To perform a metagenomic analysis of the Human Microbiome, normalization of species abundances prior to library construction is required to allow for both cost effective sequencing by avoiding redundancy of over represented organisms, and may also allow the detection and sequencing of very low abundance species. As a result, there exists a need for a robust DNA purification method that can efficiently extract DNA while rejecting contaminants that can length select during the extraction process, and that can enrich DNA pools for low abundance organisms. We aim to apply our SCODA technology for concentrating and purifying nucleic acids to satisfy these requirements in a single automated step, resulting in a cost-effective process for producing high quality sequence libraries for analysis of the Human Microbiome.
Public Health Relevance: Project Narrative To perform a metagenomic analysis of the Human Microbiome, normalization of species abundances prior to library construction is required to allow for both cost effective sequencing by avoiding redundancy of over represented organisms, and may also allow the detection and sequencing of very low abundance species. As a result, there exists a need for a robust DNA purification method that can efficiently extract DNA while rejecting contaminants, that can length select during the extraction process, and that can enrich DNA pools for low abundance organisms. We aim to apply our SCODA technology for concentrating and purifying nucleic acids to satisfy these requirements in a single automated step, resulting in a cost-effective process for producing high quality sequence libraries for analysis of the Human Microbiome.
Thesaurus Terms:
There are no thesaurus terms on file for this project.
Institution: BOREAL GENOMICS INC. NORTH VANCOUVER, BC V7R1Z2 Fiscal Year: 2008 Department: Project Start: 26-SEP-2008 Project End: 31-JUL-2010 ICD: NATIONAL HUMAN GENOME RESEARCH INSTITUTE IRG: ZRG1