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.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG004873-02
Application #
7691838
Study Section
Special Emphasis Panel (ZRG1-IDM-P (50))
Program Officer
Schloss, Jeffery
Project Start
2008-09-26
Project End
2012-07-31
Budget Start
2009-08-01
Budget End
2012-07-31
Support Year
2
Fiscal Year
2009
Total Cost
$366,271
Indirect Cost
Name
Boreal Genomics Inc.
Department
Type
DUNS #
243495715
City
Vancouver
State
BC
Country
Canada
Zip Code
V6 1-Z3
Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta et al. (2012) Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment. PLoS One 7:e31597