Next-generation sequencing has created of wealth of information about the genetic basis of disease and natural variation. The major flaw of next-generation sequencers is the short read length, which creates problems in piecing together a complete genome. The goal of this proposal is to use molecular biology to create DNA libraries that can be sequenced and more easily assembled into long contiguous stretches. The proposal will first focus on creating contig sequences of 5,000 nucleotides that have been assembled from each sub-region of the genome. Next, the goal is to create stretches of 50,000 nucleotide assemblies, also pieced together in parallel across the genome. Computer scripts to optimize the assembly of the genomic regions will also be developed. These longer contiguous sequences will greatly improve the ability of researchers to accurately determine the proper order of genes in a genome, which will speed discovery of the DNA changes that give rise to altered phenotypes in model organisms, non-model organisms and humans.

Public Health Relevance

Understanding the sequence of a genome helps researchers make new discoveries about biology and health more quickly. This application proposes to develop methods to help put a genome sequence together in the proper order, simplifying the process of reading a genome.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21HG006036-02
Application #
8261085
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Schloss, Jeffery
Project Start
2011-05-01
Project End
2013-04-30
Budget Start
2012-05-01
Budget End
2013-04-30
Support Year
2
Fiscal Year
2012
Total Cost
$213,000
Indirect Cost
$63,000
Name
University of Oregon
Department
Biochemistry
Type
Organized Research Units
DUNS #
948117312
City
Eugene
State
OR
Country
United States
Zip Code
97403
Kamps-Hughes, Nick; Quimby, Aine; Zhu, Zhenyu et al. (2013) Massively parallel characterization of restriction endonucleases. Nucleic Acids Res 41:e119
Davey, John W; Hohenlohe, Paul A; Etter, Paul D et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499-510