5 R21 R21HG03714
Haplotype Sequencing via Single Molecule Hybridization
| Principal Investigator: |
BHUBANESWAR MISHRA
NEW YORK UNIVERSITY
COURANT INST OF MATHEMATICAL SCI
251 MERCER ST
|
Project Period: 08/01/2005 - 08/31/2008
Abstract (from grant application):
DESCRIPTION (provided by applicant): We seek funding to develop, within 10 years, a technology to sequence a human size genome of about 6 Gigabases including both haplotypes. We aim to accomplish these goals by successfully integrating three different component technologies: (1) Optical Mapping to create Ordered Restriction Maps with respect to an enzyme, (2) Hybridization of a pool of oiigonucleotide probes (LNA probes) with Single Genomic DNAs on surface, and (3) Algorithms to solve localized versions of PSBH (Positional Sequencing by Hybridization) problems over the whole genome. The project is planned in two stages: (1) Pilot Study to Assess Scientific Soundness [R21] and (2) Large-Scale System Engineering [R33]. The R21 phase aims to demonstrate first the soundness of whole-genome mapping of LNA probe hybridization sites, and then algorithmic feasibility of combining these maps into haplotype sequences. The potential for success of these two aims may be inferred from our preliminary work on (1) haplotype mapping of T. pseudonana and a segment of human chromosome 4; (2) fluorescent imaging of DNA and its validation by AFM technology; and (3) existing body of work on optical mapping by our investigators. The R33 phase aims to engineer the final system by constructing in succession: (1) high throughput optical system, (2) preliminary validation by sequencing 100bp segment of P. falciparum genome (small-size), (3) more complex validation by sequencing 100bp segment of H. sapiens genome (large-size), (4) final system engineering and validation by sequencing the entire H. sapiens genome.
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