Patents by Inventor Rui Mei
Rui Mei 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: 20130137583Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. 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 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: August 6, 2012Publication date: May 30, 2013Applicant: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Publication number: 20130045872Abstract: The present invention provides methods for targeted sequencing of polynucleotide. In one aspect, the present invention provides a method of sequencing a target polynucleotide with fewer probes. In another aspect, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids.Type: ApplicationFiled: September 10, 2010Publication date: February 21, 2013Inventors: Wei Zhou, Rui Mei, Hajime Matsuzaki
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Publication number: 20120252682Abstract: The present invention provides methods and systems for sequencing long nucleic acid fragments.Type: ApplicationFiled: June 3, 2011Publication date: October 4, 2012Applicant: Maples Corporate Services LimitedInventors: Wei Zhou, Rui Mei, Filip Crnogorac, Guochun Liao, Julian Lucas
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Publication number: 20120083417Abstract: The present invention provides methods for native extension parallel sequencing of polynucleotide.Type: ApplicationFiled: September 23, 2011Publication date: April 5, 2012Applicant: CENTRILLION TECHNOLOGY HOLDING CORPORATIONInventors: Wei Zhou, Rui Mei, Julian Lucas, Guochun Liao
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Publication number: 20120071328Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. 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 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: August 24, 2011Publication date: March 22, 2012Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Publication number: 20110246085Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.Type: ApplicationFiled: June 15, 2011Publication date: October 6, 2011Applicant: AFFYMETRIX, INC.Inventors: Shantanu Kaushikkar, Teresa Webster, Rui Mei, Linda McAllister
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Patent number: 8029999Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. 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 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: GrantFiled: October 18, 2007Date of Patent: October 4, 2011Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Patent number: 7991560Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.Type: GrantFiled: February 10, 2006Date of Patent: August 2, 2011Assignee: Affymetrix, Inc.Inventors: Shantanu V. Kaushikkar, Teresa Webster, Rui Mei, Linda McAllister
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Publication number: 20110160092Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: ApplicationFiled: January 14, 2011Publication date: June 30, 2011Applicant: Affymetrix, INC.Inventors: Teresa A. Webster, Hajime Matsuzaki, Xiaojun Di, Earl A. Hubbell, Rui Mei, Simon Cawley, Gregory Marcus, Keith W. Jones
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Patent number: 7881875Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: GrantFiled: July 13, 2006Date of Patent: February 1, 2011Assignee: Affymetrix, Inc.Inventors: Teresa A. Webster, Hajime Matsuzaki, Xiaojun Di, Earl A. Hubbell, Rui Mei, Simon Cawley, Gregory Marcus, Keith W. Jones
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Patent number: 7629164Abstract: The invention provides nucleic acid sequences that are complementary, in one embodiment, to a collection of human single nucleotide polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel by, for example, allele specific hybridization. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: GrantFiled: July 13, 2004Date of Patent: December 8, 2009Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Rui Mei
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Patent number: 7361468Abstract: Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: GrantFiled: July 5, 2005Date of Patent: April 22, 2008Assignee: Affymetrix, Inc.Inventors: Guoying Liu, Simon Cawley, Hajime Matsuzaki, Earl A. Hubbell, Geoffrey Yang, Teresa A. Webster, Rui Mei, Xiaojun Di, Richard Chiles
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Publication number: 20080070796Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. 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 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: October 18, 2007Publication date: March 20, 2008Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Patent number: 7300788Abstract: The invention provides nucleic acid sequences that are complementary, in one embodiment, to a wide variety of human polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relatesd to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: GrantFiled: October 7, 2003Date of Patent: November 27, 2007Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Rui Mei, Mei-Mei Shen, Giulia C. Kennedy
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Patent number: 7297778Abstract: The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. 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 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: GrantFiled: October 4, 2002Date of Patent: November 20, 2007Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Patent number: 7280922Abstract: Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.Type: GrantFiled: July 14, 2005Date of Patent: October 9, 2007Assignee: Affymetrix, Inc.Inventors: Rui Mei, Teresa Webster
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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: 20070016382Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.Type: ApplicationFiled: July 13, 2006Publication date: January 18, 2007Applicant: Affymetrix, INC.Inventors: Teresa Webster, Hajime Matsuzaki, Xiaojun Di, Earl Hubbell, Rui Mei, Simon Cawley, Gregory Marcus, Keith Jones
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Publication number: 20060216724Abstract: Methods of preparing normalized mixtures from a plurality of nucleic acid samples are disclosed. Nucleic acids are amplified so that similar amounts of a target nucleic acid are generated in a plurality of different reactions. Separate amplification reactions are performed to amplify the same or different targets in a plurality of different reactions. The amounts of amplified product are approximately normalized during the amplification without the need to empirically measure the amount of amplified target.Type: ApplicationFiled: July 29, 2005Publication date: September 28, 2006Applicant: Affymetrix, INC.Inventors: Frederick Christians, Sean Walsh, Rui Mei
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Publication number: 20060167636Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.Type: ApplicationFiled: February 10, 2006Publication date: July 27, 2006Applicant: Affymetrix, INC.Inventors: Shantanu Kaushikkar, Teresa Webster, Rui Mei, Linda McAllister