Abstract

In this research we first propose to further develop the use of spatially defined arrays of oligonucleotide probes for sequence checking and de novo sequencing. Second, we will implement the technology in a pilot scale sequencing project. To accomplish this we will use the integrated chips, instrumentation, and software platform as defined in project 2 to explore: * Assays that discriminate perfect matches from mismatches. * Prediction of the hybridization intensities of probe-target combinations to aid in target specific array design. * Data analysis and sequence reconstruction algorithms using hybridization data. * The effectiveness of the assays in a pilot scale sequencing project. Successful completion of this work could lead to sequencing instrumentation that will provide order of magnitude improvements in DNA sequencing productivity.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Program Projects (P01)
Project #
5P01HG001323-03
Application #
6109113
Study Section
Project Start
1997-09-30
Project End
1999-08-31
Budget Start
1996-10-01
Budget End
1997-09-30
Support Year
3
Fiscal Year
1997
Total Cost
Indirect Cost

  Institution

Name
Affymetrix, Inc.
Department
Type
DUNS #
804682573
City
Santa Clara
State
CA
Country
United States
Zip Code
95051

  Publications

Lee, Albert; Henras, Anthony K; Chanfreau, Guillaume (2005) Multiple RNA surveillance pathways limit aberrant expression of iron uptake mRNAs and prevent iron toxicity in S. cerevisiae. Mol Cell 19:39-51
Danin-Kreiselman, Michal; Lee, Chrissie Young; Chanfreau, Guillaume (2003) RNAse III-mediated degradation of unspliced pre-mRNAs and lariat introns. Mol Cell 11:1279-89
Patti, Mary Elizabeth; Butte, Atul J; Crunkhorn, Sarah et al. (2003) Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A 100:8466-71
Zheng, Z; Venkatapathy, S; Rao, G et al. (2002) Expression profiling of B cell chronic lymphocytic leukemia suggests deficient CD1-mediated immunity, polarized cytokine response, altered adhesion and increased intracellular protein transport and processing of leukemic cells. Leukemia 16:2429-37
Schulze, A; Lehmann, K; Jefferies, H B et al. (2001) Analysis of the transcriptional program induced by Raf in epithelial cells. Genes Dev 15:981-94
Soulez, M; Parker, M G (2001) Identification of novel oestrogen receptor target genes in human ZR75-1 breast cancer cells by expression profiling. J Mol Endocrinol 27:259-74
Nadler, S T; Stoehr, J P; Schueler, K L et al. (2000) The expression of adipogenic genes is decreased in obesity and diabetes mellitus. Proc Natl Acad Sci U S A 97:11371-6
Gentalen, E; Chee, M (1999) A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays. Nucleic Acids Res 27:1485-91
Sapolsky, R J; Hsie, L; Berno, A et al. (1999) High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays. Genet Anal 14:187-92
Lelivelt, M J; Culbertson, M R (1999) Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol Cell Biol 19:6710-9

Showing the most recent 10 out of 17 publications