Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2011-05-10
2011-05-10
Raymond, Edward (Department: 2857)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
Reexamination Certificate
active
07941279
ABSTRACT:
Methods, computers, and computer program products for detecting the presence of a probe within a sample overlayed on a substrate are provided. The probe comprises a plurality of spatially arranged labels. A data storage module stores a plurality of light images, where each light image has light from the sample at a corresponding wavelength range in a plurality of different wavelength ranges. A label identification module identifies a plurality of labels in the plurality of light images that are proximate to each other on the substrate. A spatial order of the plurality of labels determines a string sequence of the plurality of labels. A probe identification module determines whether the string sequence of the plurality of labels comprises a valid reporter sequence.
REFERENCES:
patent: 5137819 (1992-08-01), Kilburn et al.
patent: 5202247 (1993-04-01), Kilburn et al.
patent: 5293050 (1994-03-01), Chapple-Sokol et al.
patent: 5354707 (1994-10-01), Chapple-Sokol et al.
patent: 5496934 (1996-03-01), Shoseyov et al.
patent: 5840862 (1998-11-01), Bensimon et al.
patent: 6001983 (1999-12-01), Benner
patent: 6054327 (2000-04-01), Bensimon et al.
patent: 6225055 (2001-05-01), Bensimon et al.
patent: 6265153 (2001-07-01), Bensimon et al.
patent: 6303296 (2001-10-01), Bensimon et al.
patent: 6344319 (2002-02-01), Bensimon et al.
patent: 6548255 (2003-04-01), Bensimon et al.
patent: 2003/0157504 (2003-08-01), Chee et al.
patent: 2005/0014217 (2005-01-01), Mattheakis et al.
patent: 2008/0279442 (2008-11-01), Den Boef et al.
patent: 2010/0015607 (2010-01-01), Geiss et al.
patent: 2010/0261026 (2010-10-01), Ferree et al.
Asbury et al, “Trapping of DNA by dielectrophoresis”,Electrophoresis, 23(16):2658-2666 (2002).
Asbury et al., “Trapping of DNA in Nonuniform Oscillating Electric Fields”,Biophys. J., 74:1024-1030 (1998).
Ashkin et al., “Observation of a single-beam gradient force optical trap for dielectric particles”,Opt. Lett., 11(5):288-290 (1986).
Ashkin et al., “Optical trapping and manipulation of single cells using infrared laser beams”,Nature, 330:769-771 (1987).
Ashkin et al., “Optical Trapping and Manipulation of Viruses and Bacteria”,Science, 235:1517-1520 (1987).
Bensimon et al., “Alignment and Sensitive Detection of DNA by a Moving Interface”,Science, 265:2096-2098 (1994).
Blanchard et al., “Sequence to array: Probing the genome's secrets”,Nature Biotech., 14:1649 (1996).
Block et al., “Bead movement by single kinesin molecules studied with optical tweezers”,Nature, 348:348-352 (1990).
Draghici, S., “Image processing”, inData Analysis Tools for DNA Microarrays, Chapman & Hall/CRC, New York, (2003) (36 pages).
Egholm et al., “Peptide Nucleic Acids (PNA). Oligonucleotide Analogues with an Achiral Peptide Backbone”,J. Am. Chem. Soc., 114:1895-1897 (1992).
Singer, B., “Alkyl Bases, Nucleosides, and Nucleotides. UV Spectral Characteristics and Acidic Dissociation Constants of 280 Alkyl Bases, Nucleosides, and Nucleotides”,Practical Handbook of Biochemistry and Molecular Biology, Fasman, Ed., CRC Press, Inc., Boca Raton, FL, pp. 385-395 (1985).
Ferree et al., “Electrokinetic Stretching of Tethered DNA”,Biophys. J., 85(4):2539-2546 (2003).
Ferree et al., “The Hydrodynamics of DNA Electrophoretic Stretch and Relaxation in a Polymer Solution”,Biophys. J., 87(1):468-475 (2004).
Fortina et al., “Digital mRNA Profiling”,Nature Biotech., 26(3):293-294 (2008).
Geiss et al., “Direct multiplexed measurement of gene expression with color-coded probe pairs”,Nature Biotech., 26(3):317-325 (2008).
Goodchild, J., “Conjugates of Oligonucleotides and Modified Oligonucleotides: A Review of Their Synthesis and Properties”,Bioconjugate Chem., 1(3):165-187 (1990).
Grier, D. G., “A revolution in optical manipulation”,Nature, 424:21-27 (2003).
Gryaznov et al., “Oligodeoxyribonucleotide N3′→P5′ Phosphoramidates: Synthesis and Hybridization Properties”,J. Am. Chem. Soc., 116:3143-3144 (1994).
Guan et al., “Vectors that facilitate the expression and purification of foreign peptides inEscherichia coliby fusion to maltose-binding protein”,Gene, 67:21-30 (1988).
Henegariu et al., “Rapid DNA Fiber Technique for Size Measurements of Linear and Circular DNA Probes”,BioTech., 31(2):246-250 (2001).
Hyrup et al., “Peptide nucleic acids (PNA): synthesis, properties and potential applications”,Bioorg. Med. Chem., 4(1):5-23 (1996).
Kabata et al., “Visualization of Single Molecules of RNA Polymerase Sliding along DNA”,Science, 262(5139):1561-1563 (1993).
Kraus et al., “High-resolution comparative hybridization to combed DNA fibers”,Human Genet., 99:374-380 (1997).
Lockhart et al., “Expression monitoring by hybridization to high-density oligonucleotide arrays”,Nature Biotech., 14:1675-1680 (1996).
Mathews et al., “Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure”,J. Mol. Biol., 288:911-940 (1999).
Matsuura et al., “One-End Immobilization of Individual DNA Molecules on a Functional Hydrophobic Glass Surface”,J. Biomol. Struct. Dyn., 20(3):429-436 (2002).
Matsuura et al., “Real-time observation of a single DNA digestion by λ exonuclease under a fluorescence microscope field”,Nucl. Acids Res., 29(16):E79 (2001).
Michalet et al., “Dynamic Molecular Combing: Stretching the Whole Human Genome for High-Resolution Studies”,Science, 277:1518-1523 (1997).
Otobe et al., “Behavior of DNA fibers stretched by precise meniscus motion control”,Nucl. Acids Res., 29(22):E109 (2001).
Park et al., “Automatic Microarray Image Segmentation Based on Watershed Transformation”,Proceedings of the 17th International Conference on Pattern Recognition, 3:786-789 (2004).
Pease et al., “Light-generated oligonucleotide arrays for rapid DNA sequence analysis”,Proc. Natl. Acad. Sci. U.S.A., 91:5022-5026 (1994).
Perkins et al., “Relaxation of a Single DNA Molecule Observed by Optical Microscopy”,Science, 264:822-826 (1994).
Perry-O'Keefe et al., “Peptide nucleic acid pre-gel hybridization: an alternative to southern hybridization”,Proc. Natl. Acad. Sci. U.S.A., 93:14670-14675 (1996).
Schena et al., Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA MicroarrayScience, 270:467-470 (1995).
Simmons et al., “Quantitative Measurements of Force and Displacement Using an Optical Trap”,Biophys. J., 70:1813-1822 (1996).
Smith, D. B., “Purification of Glutathione S-Transferase Fusion Proteins”,Meth. Mol. Cell Biol., 4:220-229 (1993).
Smith, G., Statistical Reasoning, 3rd Ed., Allyn and Bacon, Ed., Boston, pp. 724-730 (1991).
Stigter et al., “Theory for the Hydrodynamic and Electrophoretic Stretch of Tethered B-DNA”,Biophys. J., 75(3):1197-1210 (1998).
Tomme et al., “An internal cellulose-binding domain mediates adsorption of an engineered bifunctional xylanase/cellulase”,Protein Eng., 7(1):117-123 (1994).
Uhlman et al., “Antisense Oligonucleotides: A New Therapeutic Principle”,Chem. Rev., 90(4):544-584 (1990).
Vincent et al., “Watersheds in Digital Spaces: An Efficient Algorithm Based on Immersion Simulations”,IEEE Transactions on Pattern Analysis and Machine Intelligence, 13(6):583-598 (1991).
Yokota et al., “A new method for straightening DNA molecules for optical restriction mapping”,Nucl. Acids Res., 25(5):1064-1070 (1997).
Zimmermann et al., “DNA stretching on functionalized gold surfaces”,Nucl. Acids Res., 22(3):492-497 (1994).
Zuker, M., “Mfold web server for nucleic acid folding and hybridization prediction”,Nucl. Acids Res., 31(13):3406-3415 (2003).
Hwang Jenq-Neng
Mitton Jeffrey D.
Elrifi, Esq. Ivor R.
Mintz Levin Cohn Ferris Glovsky and Popeo P.C.
Nanostring Technologies, Inc.
Raymond Edward
LandOfFree
Systems and methods for analyzing nanoreporters does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Systems and methods for analyzing nanoreporters, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Systems and methods for analyzing nanoreporters will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2623162