Patents by Inventor Hajime Matsuzaki
Hajime Matsuzaki 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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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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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: 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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Patent number: 7053206Abstract: A method is described for predetermining ratios of primer pairs present in a single reaction vessel so as to achieve approximately equimolar yield of products. The ratios are determined as a function of the length of the amplicon and the length of other amplicons being simultaneously tested. The primers may desirably be for p53 gene sequences.Type: GrantFiled: December 23, 2003Date of Patent: May 30, 2006Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Eric Murphy
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Publication number: 20060024715Abstract: 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: ApplicationFiled: July 5, 2005Publication date: February 2, 2006Applicant: Affymetrix, Inc.Inventors: Guoying Liu, Simon Cawley, Hajime Matsuzaki, Earl Hubbell, Geoffrey Yang, Teresa Webster, Rui Mei, Xiaojun Di, Richard Chiles
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Publication number: 20050260628Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. 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.Type: ApplicationFiled: March 7, 2005Publication date: November 24, 2005Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Xing Su, Guilia Kennedy
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Publication number: 20050227244Abstract: 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: ApplicationFiled: July 13, 2004Publication date: October 13, 2005Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Rui Mei
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Publication number: 20050191646Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: October 7, 2004Publication date: September 1, 2005Applicant: Affymetrix, Inc.Inventors: David Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen Cronin, Danny Lee, Huu Tran, Hajime Matsuzaki, Glenn McGall, Anthony Barone
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Publication number: 20050158772Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: December 23, 2004Publication date: July 21, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen Cronin, Danny Lee, Huu Tran, Hajime Matsuzaki, Glenn McGall, Anthony Barone
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Publication number: 20040146890Abstract: 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: ApplicationFiled: October 7, 2003Publication date: July 29, 2004Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Rui Mei, Mei-Mei Shen, Giulia C. Kennedy
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Publication number: 20040126806Abstract: A method is described for predetermining ratios of primer pairs present in a single reaction vessel so as to achieve approximately equimolar yield of products. The ratios are determined as a function of the length of the amplicon and the length of other amplicons being simultaneously tested. The primers may desirably be for p53 gene sequences.Type: ApplicationFiled: December 23, 2003Publication date: July 1, 2004Applicant: AFFYMETRIX, INC.Inventors: Hajime Matsuzaki, Eric A. Murphy
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Publication number: 20040067493Abstract: 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 4, 2002Publication date: April 8, 2004Applicant: Affymetrix, INC.Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
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Patent number: 6673579Abstract: A method is described for predetermining ratios of primer pairs present in a single reaction vessel so as to achieve approximately equimolar yield of products. The ratios are determined as a function of the length of the amplicon and the length of other amplicons being simultaneously tested. The primers may desirably be for p53 gene sequences.Type: GrantFiled: November 21, 2001Date of Patent: January 6, 2004Assignee: Affymetrix, Inc.Inventors: Hajime Matsuzaki, Eric Murphy
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Publication number: 20030186279Abstract: In one embodiment of the invention, methods are provided for genotyping a large number of SNPs. The methods include a sample preparation protocol that requires only few primers and few reaction vessels.Type: ApplicationFiled: December 10, 2002Publication date: October 2, 2003Applicant: Affymetrix, INC.Inventors: Giulia Kennedy, Hajime Matsuzaki, Shoulian Dong, Xing Su, Keith Jones, Weimin Liu
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Publication number: 20030064364Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.Type: ApplicationFiled: April 11, 2002Publication date: April 3, 2003Inventors: David J. Lockhart, Mark Chee, Kevin Gunderson, Chaoqiang Lai, Lisa Wodicka, Maureen T. Cronin, Danny H. Lee, Huu M. Tran, Hajime Matsuzaki, Glenn H. McGall, Anthony D. Barone