Patents by Inventor Mark Chee
Mark Chee 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).
-
Publication number: 20050202500Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample.Type: ApplicationFiled: April 28, 2005Publication date: September 15, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Eugene Brown, Gordon Wong, Mark Chee, Thomas Gingeras
-
Publication number: 20050191698Abstract: The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface.Type: ApplicationFiled: April 14, 2005Publication date: September 1, 2005Applicant: ILLUMINA, INC.Inventors: Mark Chee, John Stuelpnagel
-
Publication number: 20050191675Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.Type: ApplicationFiled: February 7, 2005Publication date: September 1, 2005Applicant: Affymetrix, Inc.Inventors: Erik Gentalen, Mark Chee
-
Publication number: 20050191646Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: October 7, 2004Publication date: September 1, 2005Applicant: Affymetrix, Inc.Inventors: David Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen Cronin, Danny Lee, Huu Tran, Hajime Matsuzaki, Glenn McGall, Anthony Barone
-
Publication number: 20050186581Abstract: A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.Type: ApplicationFiled: March 1, 2004Publication date: August 25, 2005Applicant: AFFYMETRIX, INC.Inventors: Mark Chee, Chunwei Wang, Luis Jevons, Derek Bernhart, Robert Lipshutz
-
Publication number: 20050181440Abstract: The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface.Type: ApplicationFiled: April 14, 2005Publication date: August 18, 2005Applicant: ILLUMINA, INC.Inventors: Mark Chee, John Stuelpnagel
-
Patent number: 6927032Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample.Type: GrantFiled: January 28, 2003Date of Patent: August 9, 2005Assignee: Affymetrix, Inc.Inventors: David J. Lockhart, Eugene L. Brown, Gordon G. Wong, Mark Chee, Thomas R. Gingeras
-
Publication number: 20050170412Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.Type: ApplicationFiled: February 7, 2005Publication date: August 4, 2005Applicant: Affymetrix, Inc.Inventors: Erik Gentalen, Mark Chee
-
Publication number: 20050158772Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: December 23, 2004Publication date: July 21, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen Cronin, Danny Lee, Huu Tran, Hajime Matsuzaki, Glenn McGall, Anthony Barone
-
Publication number: 20050158702Abstract: A biosensor, sensor array, sensing method and sensing apparatus are provided in which individual cells or randomly mixed populations of cells, having unique response characteristics to chemical and biological materials, are deployed in a plurality of discrete sites on a substrate. In a preferred embodiment, the discrete sites comprise microwells formed at the distal end of individual fibers within a fiber optic array. The biosensor array utilizes an optically interrogatable encoding scheme for determining the identity and location of each cell type in the array and provides for simultaneous measurements of large number of individual cell respnses to target analyses. The sensing method utilizes the unique ability of cell populations to respond to biologically significant compounds in a characteristic and detectable manner.Type: ApplicationFiled: September 5, 2001Publication date: July 21, 2005Inventors: John Stuelpnagel, Mark Chee
-
Publication number: 20050158746Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample.Type: ApplicationFiled: November 23, 2004Publication date: July 21, 2005Applicant: Affymetrix Inc.Inventors: David Lockhart, Eugene Brown, Gordon Wong, Mark Chee, Thomas Gingeras
-
Publication number: 20050136414Abstract: The present invention includes methods and compositions relating to locus-specific arrays. More specifically, this invention includes methods for making locus-specific arrays from universal arrays in situ, the custom arrays made using those methods, and methods of using the custom arrays to detect target nucleotides.Type: ApplicationFiled: December 23, 2003Publication date: June 23, 2005Inventors: Kevin Gunderson, David Barker, Mark Chee, Tim McDaniel, Robert Yang
-
Publication number: 20050118633Abstract: 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.Type: ApplicationFiled: November 8, 2004Publication date: June 2, 2005Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, MacDonald Morris, Mark Chee, Thomas Gingeras
-
Publication number: 20050100893Abstract: The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.Type: ApplicationFiled: October 15, 2002Publication date: May 12, 2005Inventors: Kevin Gunderson, John Stuelpnagel, Mark Chee
-
Patent number: 6852490Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provide methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.Type: GrantFiled: August 14, 2001Date of Patent: February 8, 2005Assignee: Affymetrix, Inc.Inventors: Erik Gentalen, Mark Chee
-
Publication number: 20040248176Abstract: The invention provides iterative methods of analyzing a target nucleic acid that represents a variant of a reference nucleic acid. An array of probes is designed to be complementary to an estimated sequence of a target nucleic acid. The array of probes is then hybridized to the target nucleic acid. The target sequence is reestimated from hybridization pattern of the array to the target nucleic acid. A further array of probes is then designed to be complementary to the reestimated sequence, and this array is used to obtain a further reestimate of the sequence of the target nucleic acid. By performing iterative cycles of array design and target sequence estimation, the estimated sequence of the target converges with the true sequence.Type: ApplicationFiled: April 20, 2004Publication date: December 9, 2004Applicant: Affymetrix, INC.Inventor: Mark Chee
-
Publication number: 20040121364Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. The invention provides a method of detecting a target sequence. The method consists of: (a) contacting a first and second probe with a target sequence under conditions where complementary probes form a hybridization complex with the target sequence, the first probe comprising an upstream universal priming site and a target-specific sequence, the second probe comprising a downstream universal priming site and a target-specific sequence, wherein one of the first or second probes comprise an adapter sequence; (b) extending the first or second probe of the hybridization complex to form a modified probe; (c) amplifying the modified probe to form an amplicon, and (d) detecting the amplicon. A method of detecting the relative amounts of two or more target sequences is also provided.Type: ApplicationFiled: July 15, 2003Publication date: June 24, 2004Inventors: Mark Chee, Jian-Bing Fan, Kevin Gunderson
-
Publication number: 20040114456Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: ApplicationFiled: December 3, 2003Publication date: June 17, 2004Applicant: Affymetrix, Inc.Inventors: James L. Winkler, Mark Chee, David Lockhart
-
Publication number: 20040076987Abstract: Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acidsType: ApplicationFiled: June 10, 2003Publication date: April 22, 2004Applicant: Affymetrix, Inc.Inventors: Glenn McGall, Anthony D. Barone, Martin Diggelmann, David J. Lockhart, Ann Maria Caviani Pease, Mark Chee
-
Patent number: 6705754Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: GrantFiled: January 30, 2002Date of Patent: March 16, 2004Assignee: Affymetrix, Inc.Inventors: James L. Winkler, Mark Chee, David Lockhart