Patents by Inventor Michael H. Shapero
Michael H. Shapero 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: 20240093275Abstract: 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: ApplicationFiled: September 8, 2023Publication date: March 21, 2024Inventors: Michael H. SHAPERO, Lawrence GREENFIELD, Ronald J. SAPOLSKY, Keith JONES, Laurent BELLON, Robert J. LIPSHUTZ, August ESTABROOK, John EFCAVITCH
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Publication number: 20220205041Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.Type: ApplicationFiled: September 8, 2020Publication date: June 30, 2022Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
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Patent number: 11306351Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general, the methods employ allele-specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele-specific oligonucleotides are resistant to proofreading activity from a polymerase and may be extended in an allele-specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele-specific oligonucleotides may be attached to a solid support such as a chip or a bead.Type: GrantFiled: October 9, 2018Date of Patent: April 19, 2022Assignee: AFFYMETRIX, INC.Inventor: Michael H. Shapero
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Patent number: 10329600Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.Type: GrantFiled: June 16, 2016Date of Patent: June 25, 2019Assignee: AFFYMETRIX, INC.Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
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Publication number: 20190144927Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.Type: ApplicationFiled: November 6, 2018Publication date: May 16, 2019Inventors: Keith W. Jones, Michael H. Shapero
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Publication number: 20190071719Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele specific oligonucleotides may be attached to a solid support such as a chip or a bead.Type: ApplicationFiled: October 9, 2018Publication date: March 7, 2019Inventor: Michael H. Shapero
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Patent number: 10155976Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.Type: GrantFiled: June 16, 2016Date of Patent: December 18, 2018Assignee: AFFYMETRIX, INC.Inventors: Keith W. Jones, Michael H. Shapero
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Publication number: 20180305748Abstract: Methods and systems for array-based methods for genotyping multiallelic markers are disclosed. Also disclosed herein are methods for whole genome amplification and locus specific multiplex PCR for selectively biasing amplification for reducing effects of undesired pseudogenes in resulting data.Type: ApplicationFiled: October 18, 2016Publication date: October 25, 2018Inventors: Jeremy Nathan GOLLUB, Michael H. SHAPERO, Dorothy OLIVER, Deborah BLACK, Farooq SIDDIQUI
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Patent number: 10108777Abstract: Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.Type: GrantFiled: April 30, 2012Date of Patent: October 23, 2018Assignee: Affymetrix, Inc.Inventors: Jing Huang, Keith W. Jones, Michael H. Shapero
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Publication number: 20180251845Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.Type: ApplicationFiled: February 21, 2018Publication date: September 6, 2018Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
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Patent number: 9932636Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.Type: GrantFiled: June 26, 2015Date of Patent: April 3, 2018Assignee: AFFYMETRIX, INC.Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
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Publication number: 20170051339Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.Type: ApplicationFiled: June 16, 2016Publication date: February 23, 2017Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
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Publication number: 20160369326Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.Type: ApplicationFiled: June 16, 2016Publication date: December 22, 2016Inventors: Keith W. Jones, Michael H. Shapero
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Publication number: 20160298184Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele specific oligonucleotides may be attached to a solid support such as a chip or a bead.Type: ApplicationFiled: June 16, 2016Publication date: October 13, 2016Inventor: Michael H. Shapero
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Patent number: 9388459Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele specific oligonucleotides may be attached to a solid support such as a chip or a bead.Type: GrantFiled: December 21, 2006Date of Patent: July 12, 2016Assignee: Affymetrix, Inc.Inventor: Michael H. Shapero
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Patent number: 9388457Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.Type: GrantFiled: September 15, 2008Date of Patent: July 12, 2016Assignee: Affymetrix, Inc.Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
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Patent number: 9388461Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.Type: GrantFiled: June 13, 2014Date of Patent: July 12, 2016Assignee: Affymetrix, Inc.Inventors: Keith W. Jones, Michael H. Shapero
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Publication number: 20150292019Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.Type: ApplicationFiled: June 26, 2015Publication date: October 15, 2015Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
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Publication number: 20150284786Abstract: 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: ApplicationFiled: April 3, 2015Publication date: October 8, 2015Inventors: Michael H. Shapero, Lawrence Greenfield, Ronald J. Sapolsky, Keith Jones, Laurent Bellon, Robert J. Lipshutz, August Estabrook, John Efcavitch
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Patent number: 9074244Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.Type: GrantFiled: March 11, 2009Date of Patent: July 7, 2015Assignee: Affymetrix, Inc.Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones