Patents by Inventor Teresa A. Webster
Teresa A. Webster 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: 11302417Abstract: Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.Type: GrantFiled: November 20, 2018Date of Patent: April 12, 2022Assignee: Affymetrix, Inc.Inventors: Hong Gao, Ali Pirani, Teresa Webster, Mei-Mei Shen
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Publication number: 20190198134Abstract: Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.Type: ApplicationFiled: November 20, 2018Publication date: June 27, 2019Applicant: Affymetrix, Inc.Inventors: Hong Gao, Ali Pirani, Teresa Webster, Mei-Mei Shen
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Patent number: 8467974Abstract: 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: June 15, 2011Date of Patent: June 18, 2013Assignee: Affymetrix, Inc.Inventors: Shantanu V. Kaushikkar, Teresa A. Webster, Rui Mei, Linda McAllister
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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: 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: 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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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: 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: 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
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Patent number: 7031846Abstract: 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: August 15, 2002Date of Patent: April 18, 2006Assignee: Affymetrix, Inc.Inventors: Shantanu Kaushikkar, Teresa Webster, Rui Mei, Linda McAllister
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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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Patent number: 6988040Abstract: 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: August 15, 2002Date of Patent: January 17, 2006Assignee: Affymetrix, Inc.Inventors: Rui Mei, Teresa Webster
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Publication number: 20050250151Abstract: 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: ApplicationFiled: July 14, 2005Publication date: November 10, 2005Applicant: Affymetrix, INC.Inventors: Rui Mei, Teresa Webster
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Publication number: 20050158790Abstract: Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, perfect match intensity, mismatch intensity and the slope of quantitative response of a probe are predicted. A unified quality score is calculated. Probes are selected based on the unified quality score.Type: ApplicationFiled: March 10, 2005Publication date: July 21, 2005Applicant: Affymetrix, INC.Inventors: Rui Mei, Teresa Webster
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Publication number: 20050123971Abstract: A method for calling the genotype of a sample is described comprising the acts of receiving emission data for one or more target sequences each hybridized to a plurality of probe sets, where each of the probe sets comprises a plurality of probe features; calculating a set of values for each of the probe sets associated with each target sequence; selecting one of the set of values for each of the probe sets associated with each target sequence, wherein the value is selected if it is greater than a reference value; determining a significance value from the selected values of all the probe sets associated with each target sequence; and producing a genotype call for each target sequence based upon the significance value.Type: ApplicationFiled: November 12, 2004Publication date: June 9, 2005Applicant: Affymetrix, INC.Inventors: Xiaojun Di, Teresa Webster, Daniel Bartell, Richard Chiles
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Patent number: 6850846Abstract: 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: January 11, 2001Date of Patent: February 1, 2005Assignee: Affymetrix, Inc.Inventors: Eugene Wang, Teresa Webster
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Publication number: 20040259124Abstract: The present invention includes methods for predicting the quantitative response of probes on a microarray. In a preferred embodiment, sequence dependent parameters are predicted and then used to predict probe response.Type: ApplicationFiled: February 19, 2004Publication date: December 23, 2004Applicant: Affymetrix, INC.Inventors: Stefan Bekiranov, Rui Mei, Mei-Mei Shen, Teresa A. Webster
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Publication number: 20040091930Abstract: Systems and methods for detecting monomer changes in a sample when an unknown quantity of expected monomers may also be present. Homogeneous and heterogeneous samples are exposed to polymer probes for hybridization. The hybridization affinities of the polymer probes to the samples are then compared to determine differences between the polymers in the samples. Accordingly, deletion, substitution and insertion mutations may be detected in a heterogeneous sample of nucleic acids.Type: ApplicationFiled: November 7, 2003Publication date: May 13, 2004Applicant: Affymetrix, Inc.Inventor: Teresa A. Webster