Study of complex genetic traits using a whole genome association strategy is becoming feasible as a result of haplotype and linkage disequilibrium maps being constructed by public and private groups together with highly mutliplexed single nucleotide polymorphism (SNP) genotyping platforms introduced by several companies. Once association is established for a handful of chromosomal regions by whole genome scans, narrowing down the individual regions to the point where mutation scanning of candidate genes is feasible requires the analysis of haplotypes of additional individuals. Because the highly multiplexed genotyping methods are not cost effective or efficient at this stage of the study, and haplotype prediction algorithms introduce errors that reduce the power of detecting association, it is desirable to develop new and robust technologies that determine haplotypes of large number of individuals efficiently and cost effectively. In this application, we propose to develop a molecular haplotyping method that is based on allele-specific tagging of SNPs on long PCR products with single molecule analysis. The final product is a method that can analyze 1,000 haplotypes per week and requires a set of instruments that an average laboratory can afford. To achieve this goal, we plan to (1) develop a robust allele-specific tagging method for long PCR products; (2) develop a method for efficient deposition of DNA molecules onto a glass surface; (3) develop accurate and robust approaches to analyze the DNA image for haplotype determination; (4) automate the DNA analysis process to increase the throughput of the molecular haplotyping method; (5) determine the haplotypes of the HapMap samples in a 500 kb ENCODE region on chromosome 7p. If successful, the method being developed in this project will provide a logical bridge between whole genome scan for association and candidate gene sequence analysis and facilitate the search for genetic factors associated with common genetic traits.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG001720-09
Application #
7194286
Study Section
Genome Study Section (GNM)
Program Officer
Ozenberger, Bradley
Project Start
1997-09-30
Project End
2009-02-28
Budget Start
2007-03-01
Budget End
2009-02-28
Support Year
9
Fiscal Year
2007
Total Cost
$424,382
Indirect Cost
Name
University of California San Francisco
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Clermont, Dominique; Santoni, Sylvain; Saker, Safa et al. (2014) Assessment of DNA encapsulation, a new room-temperature DNA storage method. Biopreserv Biobank 12:176-83
Wan, Eunice; Akana, Matthew; Pons, Jennifer et al. (2010) Green technologies for room temperature nucleic acid storage. Curr Issues Mol Biol 12:135-42
Xiao, Ming; Wan, Eunice; Chu, Catherine et al. (2009) Direct determination of haplotypes from single DNA molecules. Nat Methods 6:199-201
Stanley Jr, Samuel L; Frey, Sharon E; Taillon-Miller, Patricia et al. (2007) The immunogenetics of smallpox vaccination. J Infect Dis 196:212-9
Hillier, LaDeana W; Miller, Raymond D; Baird, Scott E et al. (2007) Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol 5:e167
Xiao, Ming; Phong, Angie; Ha, Connie et al. (2007) Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res 35:e16
Koboldt, Daniel C; Miller, Raymond D; Kwok, Pui-Yan (2006) Distribution of human SNPs and its effect on high-throughput genotyping. Hum Mutat 27:249-54
Chan, Ting-Fung; Ha, Connie; Phong, Angie et al. (2006) A simple DNA stretching method for fluorescence imaging of single DNA molecules. Nucleic Acids Res 34:e113
Miller, Raymond D; Phillips, Michael S; Jo, Inho et al. (2005) High-density single-nucleotide polymorphism maps of the human genome. Genomics 86:117-26
Helms, Cynthia; Saccone, Nancy L; Cao, Li et al. (2005) Localization of PSORS1 to a haplotype block harboring HLA-C and distinct from corneodesmosin and HCR. Hum Genet 118:466-76

Showing the most recent 10 out of 24 publications