Patents by Inventor Robert J. Lipshutz

Robert J. Lipshutz 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: 20150284786
    Abstract: The invention provides methods and compositions to enhance the efficiency and sensitivity of molecular inversion probe (MIP) reactions. Probes include elements that allow MIP ends to abut for ligation while avoiding the possibility of polymerase strand displacement errors. Elements facilitate multiplexed detections, including MIP reaction product detections employing next generation sequencing (NGS) techniques.
    Type: Application
    Filed: April 3, 2015
    Publication date: October 8, 2015
    Inventors: Michael H. Shapero, Lawrence Greenfield, Ronald J. Sapolsky, Keith Jones, Laurent Bellon, Robert J. Lipshutz, August Estabrook, John Efcavitch
  • Publication number: 20130150248
    Abstract: 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: Application
    Filed: December 2, 2010
    Publication date: June 13, 2013
    Applicant: 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
  • Patent number: 8445201
    Abstract: A method, device and system for hybridizing a target oligonucleotide to at least one array comprising a plurality of mixing beads are provided. A target solution is mixed by agitating the mixing beads while the target oligonucleotides are hybridizing to the complementary probes on the array. In another embodiment, a permeable barrier contains the mixing beads, thereby preventing them from contacting the array surface.
    Type: Grant
    Filed: July 30, 2010
    Date of Patent: May 21, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Bellon Laurent, Martin J. Goldberg, Robert J. Lipshutz, Kaliyur Narasimhan
  • Publication number: 20120329677
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
    Type: Application
    Filed: August 18, 2006
    Publication date: December 27, 2012
    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
  • Publication number: 20120258868
    Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
    Type: Application
    Filed: June 14, 2011
    Publication date: October 11, 2012
    Applicants: Affymax Technologies N.V., AFFYMETRIX, INC.
    Inventors: Ronald J. Sapolsky, Robert J. Lipshutz, Thomas R. Gingeras
  • Publication number: 20120258879
    Abstract: 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, i.e., the heterozygote or either of the two homozygotes.
    Type: Application
    Filed: November 15, 2011
    Publication date: October 11, 2012
    Applicant: AFFYMETRIX, INC.
    Inventors: Robert J. Lipshutz, Ronald Sapolsky, Ghassan Ghandour
  • Publication number: 20120178081
    Abstract: Methods of detecting nucleic acids, proteins and cells including methods of detecting two or more nucleic acids, proteins and cells in multiplex bDNA assays, are provided. Assays may be conducted at least in vitro, in vivo, in cellulo, and in situ. Nucleic acids are detected, through cooperative hybridization that results in specific association of a label probe system with target nucleic acids. Embodiments are directed to concurrent detection of one or more nucleic acids and/or one or more proteins. The detected proteins may be intracellular or external markers on the surface of the cell. Detection of protein components is accomplished by use of specific antibodies and a label probe system and/or coated microparticles which bind to the outside surface of specific cells and contain specific probes that can be detected using the same label probe system. Compositions, kits, and systems related to the methods are also described.
    Type: Application
    Filed: January 3, 2012
    Publication date: July 12, 2012
    Applicant: Affymetrix. Inc.
    Inventors: Quan N. Nguyen, Robert J. Lipshutz, Yunqing Ma
  • Publication number: 20120172246
    Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Compositions, kits, and systems related to the methods are also described.
    Type: Application
    Filed: January 3, 2012
    Publication date: July 5, 2012
    Applicant: AFFYMETRIX, INC.
    Inventors: Quan N. Nguyen, Robert J. Lipshutz, Gary K. McMaster, Yunqing Ma, Yen-Chieh Wu, Audrey Lin, Chunfai Lai, Cung-Tuong Nguyen
  • Patent number: 8095323
    Abstract: 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, i.e., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.
    Type: Grant
    Filed: January 25, 2010
    Date of Patent: January 10, 2012
    Assignee: Affymetrix, Inc.
    Inventors: Robert J. Lipshutz, Ronald J. Sapolsky, Ghassan Ghandour
  • Patent number: 7985547
    Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
    Type: Grant
    Filed: November 17, 2008
    Date of Patent: July 26, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Ronald J. Sapolsky, Robert J. Lipshutz, Thomas R. Gingeras
  • Publication number: 20110028352
    Abstract: A method, device and system for hybridizing a target oligonucleotide to at least one array comprising a plurality of mixing beads are provided. A target solution is mixed by agitating the mixing beads while the target oligonucleotides are hybridizing to the complementary probes on the array. In another embodiment, a permeable barrier contains the mixing beads, thereby preventing them from contacting the array surface.
    Type: Application
    Filed: July 30, 2010
    Publication date: February 3, 2011
    Applicant: Affymetrix, INC.
    Inventors: Bell Laurent, Martin J. Goldberg, Robert J. Lipshutz, Kaliyur Narasimhan
  • Patent number: 7846659
    Abstract: 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: Grant
    Filed: April 11, 2006
    Date of Patent: December 7, 2010
    Assignee: 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
  • Publication number: 20100286924
    Abstract: 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, i.e., the heterozygote or either of the two homozygotes.
    Type: Application
    Filed: January 25, 2010
    Publication date: November 11, 2010
    Applicant: AFFYMETRIX, INC.
    Inventors: ROBERT J. LIPSHUTZ, RONALD SAPOLSKY, GHASSAN GHANDOUR
  • Publication number: 20100261616
    Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
    Type: Application
    Filed: November 17, 2008
    Publication date: October 14, 2010
    Applicant: Affymetrix, INC.
    Inventors: Ronald J. Sapolsky, Robert J. Lipshutz, Thomas R. Gingeras
  • Patent number: 7674587
    Abstract: 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, i.e., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.
    Type: Grant
    Filed: February 16, 2007
    Date of Patent: March 9, 2010
    Assignee: Affymetrix, Inc.
    Inventors: Robert J. Lipshutz, Ronald J. Sapolsky, Ghassan Ghandour
  • Patent number: 7662559
    Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
    Type: Grant
    Filed: September 16, 2004
    Date of Patent: February 16, 2010
    Assignee: Affymetrix, Inc.
    Inventors: Ronald J. Sapolsky, Robert J. Lipshutz, Thomas R. Gingeras
  • Publication number: 20080261832
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
    Type: Application
    Filed: August 18, 2006
    Publication date: October 23, 2008
    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
  • Patent number: 7399584
    Abstract: The invention provides methods of comparing a target nucleic acid with a reference nucleic acid using nucleic acid arrays.
    Type: Grant
    Filed: February 22, 2000
    Date of Patent: July 15, 2008
    Assignee: 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
  • Patent number: 7267966
    Abstract: The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.
    Type: Grant
    Filed: July 12, 2001
    Date of Patent: September 11, 2007
    Assignee: Affymetrix, Inc.
    Inventors: Shoulian Dong, Robert J. Lipshutz, David Lockhart
  • Patent number: 7115364
    Abstract: 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: Grant
    Filed: August 2, 1995
    Date of Patent: October 3, 2006
    Assignee: 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