The broad, long term objectives of this proposal are to develop a high-throughput platform for single molecule analysis capable of acquiring large datasets for human genomic analysis commensurate with next generation sequencing. The research proposed aims to integrate robust devices for genome analysis with equally robust biochemical and detection schemes. This high-throughput system, """"""""Nanocoding,"""""""" will feature disposable devices offering """"""""effective"""""""" nanoscale geometries within disposable devices sufficiently small for the presentation of large elongated genomic DNA molecules, for the advancement of whole genome studies as a means for analysis of populations and cancer genomes. The research plan proposes to create disposable silastic devices with nanoconfinement capabilities that closely parallel those found in sub-100 nm devices requiring traditional lithographic approaches. A new single molecule labeling scheme has been shown to introduce fluorochome label at specific sites on genomic DNAs - and offers distinct advantages for robust detection and integration within a system for genome analysis.
The aims focus on presentation, decoration and visualization of single genomic DNA molecules, and potentiate a nanoslit device based on physical modification of large single DNA molecules. The Research Plan describes new developments enabling the Nanocoding system to complete a high-resolution scan in 1-7 days (projected) allowing comprehensive discovery of structural variation within a human genome. This analysis capacity will be extended through software developments for melding and complementing the short comings of next generation sequencing platforms, thus allowing more comprehensive discernment of structural polymorphisms and aberrations. Integration of experimental studies with computational and simulation approaches as well as associated bioinformatic approaches lend promise to make Nanocoding robust and applicable to genome-wide analysis across human populations and cancer samples.

Public Health Relevance

A new single molecule platform, Nanocoding, will be developed for cost-effective analysis of human populations for pinpointing genetic differences. Successful development and wide use of Nanocoding will identify a broad range of genetic differences that will span from entire chromosomes to regions smaller than a gene. These advances will foster large-scale human population studies that will power new drug discoveries, diagnostics, and perhaps, meaningful personal genomic profiles.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG000225-14
Application #
7817087
Study Section
Special Emphasis Panel (ZRG1-GGG-J (10))
Program Officer
Schloss, Jeffery
Project Start
1991-01-01
Project End
2012-04-30
Budget Start
2010-05-01
Budget End
2011-04-30
Support Year
14
Fiscal Year
2010
Total Cost
$580,959
Indirect Cost
Name
University of Wisconsin Madison
Department
Miscellaneous
Type
Other Domestic Higher Education
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
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Kounovsky-Shafer, Kristy L; Hernandez-Ortiz, Juan P; Potamousis, Konstantinos et al. (2017) Electrostatic confinement and manipulation of DNA molecules for genome analysis. Proc Natl Acad Sci U S A 114:13400-13405
Lequieu, Joshua; Schwartz, David C; de Pablo, Juan J (2017) In silico evidence for sequence-dependent nucleosome sliding. Proc Natl Acad Sci U S A 114:E9197-E9205
Lequieu, Joshua; Córdoba, Andrés; Schwartz, David C et al. (2016) Tension-Dependent Free Energies of Nucleosome Unwrapping. ACS Cent Sci 2:660-666
Li, Yang; Zhou, Shiguo; Schwartz, David C et al. (2016) Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Syst 3:21-34
Mendelowitz, Lee M; Schwartz, David C; Pop, Mihai (2016) Maligner: a fast ordered restriction map aligner. Bioinformatics 32:1016-22
Park, Dong-Wook; Kim, Hyungsoo; Bong, Jihye et al. (2016) Flexible bottom-gate graphene transistors on Parylene C substrate and the effect of current annealing. Appl Phys Lett 109:152105
Lee, Seonghyun; Oh, Yeeun; Lee, Jungyoon et al. (2016) DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 44:e6
Zhou, Shiguo; Goldstein, Steve; Place, Michael et al. (2015) A clone-free, single molecule map of the domestic cow (Bos taurus) genome. BMC Genomics 16:644
Hernández-Ortiz, Juan P; de Pablo, Juan J (2015) Self-consistent description of electrokinetic phenomena in particle-based simulations. J Chem Phys 143:014108

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