Methods to assess quality of microarrays

Details Methods to assess quality of microarrays Methods to assess quality of microarrays

2003-06-27

2009-08-04

Kim, Young J (Department: 1637)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

Reexamination Certificate

active

07569343

ABSTRACT:
The present invention relates to methods and compositions for assessing the quality of microarrays. In particular, the invention relates to the use of quality control probes that are synthesized on the microarray monomer by monomer in a step-by-step synthesis. By assessing the degree of signal from the quality control probes and determining their deviation from expected signal intensities, the quality of microarray synthesis can be ascertained. The invention further relates to a method of detecting defects occurring during storage or processing of the microarray. The invention further relates to a method of using a computer to identify microarrays that have had a defect or defects during synthesis, storage, or processing.

REFERENCES:
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5489678 (1996-02-01), Fodor et al.
patent: 5510270 (1996-04-01), Fodor et al.
patent: 5556752 (1996-09-01), Lockhart et al.
patent: 5578832 (1996-11-01), Trulson et al.
patent: 5959098 (1999-09-01), Goldberg
patent: 6028189 (2000-02-01), Blanchard
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6130046 (2000-10-01), Hubbell et al.
patent: 6197506 (2001-03-01), Fodor et al.
patent: 6232072 (2001-05-01), Fisher
patent: 6245518 (2001-06-01), Baier
patent: 6248878 (2001-06-01), Matulic-Adamic et al.
patent: 6258593 (2001-07-01), Schembri et al.
patent: 6346413 (2002-02-01), Fodor et al.
patent: 6362323 (2002-03-01), Usman et al.
patent: 6713257 (2004-03-01), Shoemaker et al.
patent: 0 955 085 (1999-11-01), None
patent: 1 179 368 (2002-02-01), None
patent: 2 355 716 (2001-05-01), None
patent: WO 89/02439 (1989-03-01), None
patent: WO 98/41531 (1998-09-01), None
patent: WO 99/39817 (1999-08-01), None
patent: WO 99/42813 (1999-08-01), None
patent: WO 01/36682 (2001-05-01), None
patent: WO 01/62377 (2001-08-01), None
Blanchard “Synthetic DNA Arrays in Genetic Engineering” 1998, vol. 20 111-123.
Blanchard et al. “Sequence to array: probing the genome's secrets” 1996, Nat Biotechnol 14(13):1649.
Blanchard et al “High-density oligonucleotide arrays” 1996, Biosensors & Bioelectronics 11(7-Jun):687-690.
Cload et al. “Polyether Tethered Oligonucleotide Probes” 1991, J Am Chem Soc 113:6324-6326.
DeRisi et al. “Exploring the metabolic and genetic control of gene expression on a genomic scale” 1997, Science 278(5338):680-6.
Durand et al. “Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability” 1990, Nucleic Acids Res 18(21):6353-6359.
Ferentz et al. “Disulfide Cross-Linked Oligonucleotides” 1991, J Am Chem Soc 113:4000-4002.
Fodor et al. “Light-directed, spatially addressable parallel chemical synthesis” 1991, Science 251(4995):767-773.
Goffeau et al. “Life with 6000 genes” 1996, Science 274(5287):546-567.
Gygi et al. “Quantitative analysis of complex protein mixtures using isotope-coded affinity tags” 1999, Nat Biotechnol 17(10):994-999.
Haab et al. “Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions” 2001, Genome Biol 2(2):RESEARCH0004.1-RESEARCH0004.13.
Holmes et al. “The use of light-directed combinatorial peptide synthesis in epitope mapping” 1995, Biopolymers 37(3):199-211.
Hughes et al. “Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer” 2001, Nat Biotechnol 19(4):342-347.
Jacobs et al. “Combinatorial chemistry—applications of light-directed chemical synthesis” 1994, Trends Biotechnol 12(1):19-26.
Jaschke et al. “Automated Incorporateion of Polyethylene Glycol into Synthetic” 1993, Tetrahedron Letters 34(2):301-304.
Lockhart et al. “Expression monitoring by hybridization to high-density oligonucleotide arrays” 1996, Nat Biotechnol 14(13):1675-1680.
Ma et al. “Design and synthesis of RNA miniduplexes via a synthetic linker approach” 1993, Biochemistry 32(7):1751-1758.
Maskos et al. “Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ” 1992, Nucleic Acids Res 20(7):1679-1684.
Ma et al. “Design and synthesis of RNA miniduplexes via a synthetic linker approach. 2. Generation of covalently closed, double-stranded cyclic HIV-1 TAR RNA analogs with high Tat-binding affinity” 1993, Nucleic Acids Res 21(11):2585-2589.
McCurdy et al., “Deoxyoligonucleotides with Inverted Polarity: Synthesis and Use in Triple-Helix Formation,” 1991, Nucleosides & Nucleotides 10: 287-290.
Ono et al. “DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities” 1991, Biochemistry 30(41):9914-2.
Pease et al. “Light-generated oligonucleotide arrays for rapid DNA sequence analysis” 1994, Proc Natl Acad Sci U S A 91(11):5022-5026.
Richardson et al. “Tethered Oligonucleotide Probes. A Strategy for the Recognition of Structured RNA” 1991, J Am Chem Soc 113(5109):5111.
Schena et al. “Quantitative monitoring of gene expression patterns with a complementary DNA microarray” 1995, Science 270(5235):467-470.
Seela et al. “Oligodeoxyribonucleotides containing 1,3-propanediol as nucleoside substitute” 1987, Nucleic Acids Res 15(7):3113-3129.
Shalon et al. “A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization” 1996, Genome Res 6(7):639-645.
Takeshita et al. “Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases” 1987, J Biol Chem 262(21):10171-10179.
Hubbell et al., 1999, “Fidelity Probes for DNA Arrays,” Proceedings of the International Conference on Intelligent Systems for Molecular Biology, August 6; 113-117.
Supplementary European search report dated May 16, 2007 for European Patent Application No. 03 762 218.0—1222.

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