Patents by Inventor Michael Shapero
Michael 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: 20230340575Abstract: This disclosure provides methods and systems useful in array-based analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics.Type: ApplicationFiled: December 20, 2022Publication date: October 26, 2023Inventors: Ronald SAPOLSKY, Michael SHAPERO, Jeanette SCHMIDT, Eric FUNG, Orna MIZRAHI MAN, Jiang LI, Monica CHADHA, Anju SHUKLA
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Patent number: 11603557Abstract: This disclosure provides methods and systems useful in array-based analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The disclosure is based on the hybridisation of amplified fragments from the sample, e.g. a maternal sample, which may employ molecular inversion probes MIP to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.Type: GrantFiled: June 1, 2018Date of Patent: March 14, 2023Assignee: Affymetrix, Inc.Inventors: Ronald Sapolsky, Michael Shapero, Jeanette Schmidt, Eric Fung, Orna Mizrahi Man, Jiang Li, Monica Chadha, Anju Shukla
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Publication number: 20230002814Abstract: This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications, and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridization of amplified fragments obtained from the sample, e.g., using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.Type: ApplicationFiled: September 12, 2022Publication date: January 5, 2023Inventors: Michael SHAPERO, Ronald SAPOLSKY, Eric FUNG, Jeanette SCHMIDT, Monica CHADHA, Anju SHUKLA
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Publication number: 20220372654Abstract: 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: August 5, 2022Publication date: November 24, 2022Inventors: Glenn FU, Michael SHAPERO, Pei-Hua WANG
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Patent number: 11441174Abstract: This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridisation of amplified fragments obtained from the sample, e.g. using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.Type: GrantFiled: June 1, 2018Date of Patent: September 13, 2022Inventors: Michael Shapero, Ronald Sapolsky, Eric Fung, Jeanette Schmidt, Monica Chadha, Anju Shukla
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Patent number: 11408094Abstract: 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: May 3, 2019Date of Patent: August 9, 2022Assignee: AFFYMETRIX, INC.Inventors: Glenn Fu, Michael Shapero, Pei-Hua Wang
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Publication number: 20210147920Abstract: This disclosure provides methods and kits useful in analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The method is based on the hybridisation of amplified fragments obtained from the sample, e.g. using molecular inversion probes (MIP) to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.Type: ApplicationFiled: June 1, 2018Publication date: May 20, 2021Inventors: Michael SHAPERO, Ronald SAPOLSKY, Eric FUNG, Jeanette SCHMIDT, Monica CHADHA, Anju SHUKLA
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Publication number: 20210147919Abstract: This disclosure provides methods and systems useful in array-based analysis of mixed nucleic acid populations, including for multiplex genotyping of a mixed nucleic acid sample and for detecting differences in copy number of a target polynucleotide and/or a target chromosome (e.g., microdeletions, duplications and aneuploidies). The disclosure also provides methods and systems useful in the diagnosis of genetic abnormalities in a mixed nucleic acid population taken non-invasively from an organism, such as a sample of blood, plasma, serum, urine stool or saliva. The disclosed methods and systems find use in multiple applications, including prenatal testing and cancer diagnostics. The disclosure is based on the hybridisation of amplified fragments from the sample, e.g. a maternal sample, which may employ molecular inversion probes MIP to an oligonucleotide array and the detection of the alleles based on different signals from the different alleles of the SNP.Type: ApplicationFiled: June 1, 2018Publication date: May 20, 2021Inventors: Ronald SAPOLSKY, Michael SHAPERO, Jeanette SCHMIDT, Eric FUNG, Orna MIZRAHI MAN, Jiang LI, Monica CHADHA, Anju SHUKLA
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Publication number: 20190390262Abstract: 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: May 3, 2019Publication date: December 26, 2019Inventors: Glenn Fu, Michael Shapero, Pei-Hua Wang
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Patent number: 8728767Abstract: Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.Type: GrantFiled: December 21, 2007Date of Patent: May 20, 2014Assignee: Affymetrix, Inc.Inventor: Michael Shapero
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Publication number: 20110217710Abstract: 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: December 21, 2006Publication date: September 8, 2011Applicant: Affymetrix, INC.Inventor: Michael Shapero
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Publication number: 20100311128Abstract: Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.Type: ApplicationFiled: December 21, 2007Publication date: December 9, 2010Applicant: Affymetrix, INC.Inventor: Michael Shapero
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Patent number: 7314714Abstract: Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.Type: GrantFiled: December 19, 2003Date of Patent: January 1, 2008Assignee: Affymetrix, Inc.Inventor: Michael Shapero
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Publication number: 20070269817Abstract: 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: December 21, 2006Publication date: November 22, 2007Applicant: Affymetrix, INC.Inventor: Michael Shapero
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Publication number: 20070065816Abstract: Novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample are provided. A reduced complexity sample is generated and then analyzed. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample. Analysis may be by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.Type: ApplicationFiled: May 19, 2003Publication date: March 22, 2007Applicant: Affymetrix, INC.Inventors: Shoulian Dong, Keith Jones, Giulia Kennedy, WeiWei Liu, Hajime Matsuzaki, Michael Shapero
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Publication number: 20070048756Abstract: Methods for determining the genotype of more than 400,000 Single Nucleotide Polymorphisms (SNPs) in samples of genomic DNA are provided. A collection of SNPs that may be interrogated by the methods is disclosed in SEQ ID NO: 1-1,074,930. Each sequence is the sequence of a human SNP allele and the 16 bases flanking the SNP on either side. A sequence for each allele is included. In some aspects arrays of probes to interrogate the genotype of a collection of SNPs are disclosed. In preferred aspects the probes are 17 or more contiguous nucleotides from a sequence in SEQ ID NO: 1-1,074,930 or its complement.Type: ApplicationFiled: April 18, 2006Publication date: March 1, 2007Applicant: Affymetrix, INC.Inventors: Rui Mei, Sean Walsh, Hajime Matsuzaki, Michael Shapero, Keith Jones
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Publication number: 20070020639Abstract: Methods are provided for amplifying a template DNA strand using locus-specific primers and enzymes. The method involves denaturing template DNA and then annealing a primer to the single-stranded DNA strand. The primer is then extended using a DNA polymerase. The primer is cleaved downstream of the 3? end of the inosine base by an endonuclease and subsequently, a first copy of the complementary sequence is displaced. The primer is then extended using a DNA polymerase to form a second extension product. The nicking, displacing, and extending steps are repeated to obtain multiple copies of single stranded DNA complementary to said template DNA sequence.Type: ApplicationFiled: July 20, 2005Publication date: January 25, 2007Applicant: Affymetrix, INC.Inventor: Michael Shapero
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Publication number: 20060292597Abstract: The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. Selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Reduced complexity samples generated by the disclosed methods may be interrogated for the genotypes of SNPs in the sample.Type: ApplicationFiled: May 1, 2006Publication date: December 28, 2006Applicant: Affymetrix, INC.Inventors: Michael Shapero, Keith Jones
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Patent number: 7108976Abstract: The present invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. In one embodiment complexity reduction can be accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers. The locus specific capture probes may be attached to a solid support. Multiple DNA sequences may be amplified simultaneously to produce a reduced complexity sample. The invention further provides for analysis of the above sample to interrogate sequences of interest such as polymorphisms. The amplified sample may be hybridized to an array, which may be specifically designed to interrogate the desired fragments for the presence or absence of a polymorphism.Type: GrantFiled: October 14, 2002Date of Patent: September 19, 2006Assignee: Affymetrix, Inc.Inventors: Keith W. Jones, Michael Shapero, Weiwei Liu
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Publication number: 20060134674Abstract: 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: ApplicationFiled: December 5, 2005Publication date: June 22, 2006Applicant: Affymetrix, INC.Inventors: Jing Huang, Keith Jones, Michael Shapero