Patents by Inventor MacDonald S. Morris
MacDonald S. Morris has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 8637434Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.Type: GrantFiled: September 28, 2012Date of Patent: January 28, 2014Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Martin Diggelman, Earl A. Hubbell, Glenn H. McGall, Ngo Nam, MacDonald S. Morris, Melvin Yamamoto, Jennifer Tan, Richard Rava
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Publication number: 20130150248Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.Type: ApplicationFiled: December 2, 2010Publication date: June 13, 2013Applicant: AFFYMETRIX, INC.Inventors: Maureen T. Cronin, Charles G. Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Publication number: 20120329677Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.Type: ApplicationFiled: August 18, 2006Publication date: December 27, 2012Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Patent number: 7846659Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.Type: GrantFiled: April 11, 2006Date of Patent: December 7, 2010Assignee: Affymetrix, Inc.Inventors: Maureen T. Cronin, Charles G Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Publication number: 20080261832Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.Type: ApplicationFiled: August 18, 2006Publication date: October 23, 2008Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Patent number: 7399584Abstract: The invention provides methods of comparing a target nucleic acid with a reference nucleic acid using nucleic acid arrays.Type: GrantFiled: February 22, 2000Date of Patent: July 15, 2008Assignee: Affymetrix, Inc.Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Patent number: 7115364Abstract: The invention provides chips of immobilized probes, and methods employing the chips, for comparing a reference polynucleotide sequence of known sequence with a target sequence showing substantial similarity with the reference sequence, but differing in the presence of e.g., mutations.Type: GrantFiled: August 2, 1995Date of Patent: October 3, 2006Assignee: Affymetrix, Inc.Inventors: Mark Chee, Maureen T. Cronin, Stephen P. A. Fodor, Thomas R. Gingeras, Xiaohua C. Huang, Earl A. Hubbell, Robert J. Lipshutz, Peter E. Lobban, Charles Garrett Miyada, Macdonald S. Morris, Nila Shah, Edward L. Sheldon
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Patent number: 6828104Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence.Type: GrantFiled: August 14, 2002Date of Patent: December 7, 2004Assignee: Affymetrix, Inc.Inventors: Robert J. Lipshutz, MacDonald S. Morris, Mark S. Chee, Thomas R. Gingeras
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Publication number: 20040146901Abstract: Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.Type: ApplicationFiled: November 5, 2003Publication date: July 29, 2004Applicant: AFFYMETRIX, INC.Inventors: MacDonald S. Morris, Daniel D. Shoemaker, Ronald W. Davis, Michael P. Mittmann
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Publication number: 20030220748Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: ApplicationFiled: May 15, 2003Publication date: November 27, 2003Applicant: AFFYMETRIX, INC., a California corporationInventors: Teresa A. Webster, MacDonald S. Morris, Michael P. Mittmann, David J. Lockhart, Ming-Hsiu Ho, Derek Bernhart, Luis C. Jevons
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Publication number: 20030165823Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.Type: ApplicationFiled: February 22, 2000Publication date: September 4, 2003Inventors: Maureen T. Cronin, Charles Garrett Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
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Patent number: 6600996Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: GrantFiled: March 28, 1997Date of Patent: July 29, 2003Assignee: Affymetrix, Inc.Inventors: Teresa A. Webster, MacDonald S. Morris, Michael P. Mittmann, David J. Lockhart, Ming-Hsiu Ho, Derek Bernhart, Luis C. Jevons
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Publication number: 20030134291Abstract: The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, e.g., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.Type: ApplicationFiled: March 28, 2002Publication date: July 17, 2003Applicant: Affymetrix, Inc.Inventors: Robert J. Lipshutz, Mark S. Chee, Maureen T. Cronin, Stephen P.A. Fodor, Earl A. Hubbell, MacDonald S. Morris, Charles Garrett Miyada
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Publication number: 20030104436Abstract: Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.Type: ApplicationFiled: August 23, 2002Publication date: June 5, 2003Applicant: AFFYMETRIX, INC.Inventors: MacDonald S. Morris, Daniel D. Shoemaker, Ronald W. Davis, Michael P. Mittmann
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Publication number: 20030013114Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence.Type: ApplicationFiled: August 14, 2002Publication date: January 16, 2003Applicant: Affymetrix, INC.Inventors: Robert J. Lipshutz, MacDonald S. Morris, Mark S. Chee, Thomas R. Gingeras
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Publication number: 20020183933Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: ApplicationFiled: March 28, 1997Publication date: December 5, 2002Inventors: TERESA A. WEBSTER, MACDONALD S. MORRIS, MICHAEL P. MITTMANN, DAVID J. LOCKHART, DEREK BERNHART, LUIS C. JEVONS
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Patent number: 6468744Abstract: The invention provides methods for detecting variations in polymorphic sites and/or variations in gene copy number. The methods are particularly useful for analysis of biotransformation genes, such as cytochromes P450.Type: GrantFiled: November 17, 1999Date of Patent: October 22, 2002Assignee: Affymetrix, Inc.Inventors: Maureen T. Cronin, Edward L. Sheldon, Charles G. Miyada, Earl A. Hubbell, Mark Chee, Stephen P. A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris
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Publication number: 20020147548Abstract: Using data electrophoretic trace data from conventional nucleic acid sequencing equipment, a method for base calling that is tolerant to variable peak spacing is described. The method generates high-quality basecalls and reliable quality scores. In addition, a new type of quality score that estimates the probability of a deletion error between the current and the following basecall is described. A new protocol for benchmarking that better discerns basecaller performance is also provided.Type: ApplicationFiled: August 10, 2001Publication date: October 10, 2002Inventors: Dirk Walther, Gabor T. Bartha, MacDonald S. Morris
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Patent number: 6458530Abstract: Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.Type: GrantFiled: April 4, 1996Date of Patent: October 1, 2002Assignee: Affymetrix Inc.Inventors: Macdonald S. Morris, Daniel D. Shoemaker, Ronald W. Davis, Michael P. Mittmann
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Patent number: 6440677Abstract: Nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of the surface, the density of the oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of the different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence. b) amplifying the multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.Type: GrantFiled: July 20, 2001Date of Patent: August 27, 2002Assignee: Affymetrix, Inc.Inventors: Robert J. Lipshutz, MacDonald S. Morris, Mark S. Chee, Thomas R. Gingeras