Patents by Inventor Robert Lipshutz
Robert 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).
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Publication number: 20080044920Abstract: 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: ApplicationFiled: February 16, 2007Publication date: February 21, 2008Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, Ronald Sapolsky, Ghassan Ghandour
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Publication number: 20070054286Abstract: 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: April 11, 2006Publication date: March 8, 2007Applicant: AFFYMETRIX, INC.Inventors: Maureen Cronin, Charles Miyada, Earl Hubbell, Mark Chee, Stephen Fodor, Xiaohua Huang, Robert Lipshutz, Peter Lobban, MacDonald Morris, Edward Sheldon
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Publication number: 20060263807Abstract: The invention provides methods of using probe arrays For polymorphism identification and profiling. Such methods entail constructing a first array of probes that span and are complementary to one or more known DNA sequences. This array is hybridized with nucleic acid samples from different individuals to identify a collection of polymorphisms. A second array is then constructed to determine a polymorphic profile of an individual at the collection of polymorphic sites. The polymorphic profile is useful for, e.g., genetic mapping, epidemiology, diagnosis and forensics.Type: ApplicationFiled: March 24, 2006Publication date: November 23, 2006Applicant: AFFYMETRIX, INC.Inventors: Robert Lipshutz, Stephen Fodor
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Publication number: 20060246490Abstract: The present invention provides a miniaturized integrated nucleic acid diagnostic device and system.Type: ApplicationFiled: April 4, 2006Publication date: November 2, 2006Applicant: Affymetrix, Inc.Inventors: Rolfe Anderson, Robert Lipshutz, Richard Rava, Stephen Fodor
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Publication number: 20060229824Abstract: 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: March 3, 2006Publication date: October 12, 2006Applicant: Affymetrix, INC.Inventors: Maureen Cronin, Charles Miyada, Earl Hubbell, Mark Chee, Stephen Fodor, Xiaohua Huang, Robert Lipshutz, Peter Lobban, MacDonald Morris, Edward Sheldon
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Publication number: 20060223097Abstract: 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 napping, screening and manipulation.Type: ApplicationFiled: June 12, 2006Publication date: October 5, 2006Applicant: Affymetrix, INC.Inventors: Ronald Sapolsky, Robert Lipshutz, Thomas Gingeras
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Publication number: 20060204991Abstract: 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 b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids, and c) attaching the pool of nucleic acids to a solid supportType: ApplicationFiled: February 22, 2006Publication date: September 14, 2006Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, MacDonald Morris, Mark Chee, Thomas Gingeras
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Publication number: 20060161355Abstract: A computer system for analyzing nucleic acid sequences is provided The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown basesType: ApplicationFiled: October 14, 2005Publication date: July 20, 2006Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, Michael Walker
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Publication number: 20060110752Abstract: 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.Type: ApplicationFiled: October 11, 2005Publication date: May 25, 2006Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, Ronald Sapolsky, Ghassan Ghandour
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Publication number: 20060063158Abstract: 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: ApplicationFiled: September 16, 2004Publication date: March 23, 2006Applicant: Affymetrix, INC.Inventors: Shoulian Dong, Robert Lipshutz, David Lockhart
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Publication number: 20050250199Abstract: The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The device of the invention is generally capable of performing one or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and most notably, nucleic acid based diagnostic applications and de novo sequencing applications.Type: ApplicationFiled: December 13, 2004Publication date: November 10, 2005Inventors: Rolfe Anderson, Robert Lipshutz, Richard Rava, Stephen Fodor
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Publication number: 20050208517Abstract: Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.Type: ApplicationFiled: November 10, 2004Publication date: September 22, 2005Inventors: Stephen Fodor, Robert Lipshutz, Xiaohua Huang
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Publication number: 20050202504Abstract: The present invention provides a miniaturized integrated nucleic acid diagnostic device and system.Type: ApplicationFiled: May 6, 2005Publication date: September 15, 2005Applicant: Affymetrix, INC.Inventors: Rolfe Anderson, Robert Lipshutz, Richard Rava, Stephen Fodor
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Publication number: 20050196792Abstract: Methods for amplifying a nucleic acid sample while preserving the methylation status of cytosines are disclosed. In some aspects the amplified methylated sample is modified by methylation sensitive modification and analyzed by hybridization to an array to identify cytosines that were methylated in the starting material and cytosines that were not methylated in the starting material. Methods for detecting methylation status are also disclosed. In one embodiment a DNA methyltransferase activity is included in the amplification reaction and this activity methylates the newly synthesized DNA using the methylated genomic template strand as a guide.Type: ApplicationFiled: February 14, 2005Publication date: September 8, 2005Applicant: Affymetrix, INC.Inventors: Stephen Fodor, Robert Lipshutz, Shivani Nautiyal
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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
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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
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Publication number: 20050100946Abstract: The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The device of the invention is generally capable of performing one or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and most notably, nucleic acid based diagnostic applications and de novo sequencing applications.Type: ApplicationFiled: November 24, 2004Publication date: May 12, 2005Applicant: AFFYMETRIX, INC.Inventors: Robert Lipshutz, Richard Rava, Rolfe Anderson
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Publication number: 20050026212Abstract: 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: ApplicationFiled: September 16, 2004Publication date: February 3, 2005Applicants: Affymetrix, INC., Affymax Technologies N.V.Inventors: Ronald Sapolsky, Robert Lipshutz, Thomas Gingeras
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Publication number: 20030219801Abstract: The present invention provides methods to identify target molecules in a biological sample through the use of aptamers designed to bind specific target molecules and by hybridizing nucleic subsequence of the aptamer to a nucleic acid array. The present invention allows the detection and the measure of the amount of the target molecules in a sample and thus can be used for diagnostic medical applications.Type: ApplicationFiled: March 6, 2003Publication date: November 27, 2003Applicant: Affymetrix, INC.Inventor: Robert Lipshutz
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Publication number: 20030165830Abstract: 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: March 1, 2001Publication date: September 4, 2003Inventors: Maureen Cronin, Charles Miyada, Earl Hubbell, Mark Chee, Stephen Fodor, Xiaohua Huang, Robert Lipshutz, Peter Lobban, MacDonald Morris, Edward Shelton