Patents Assigned to Affymetrix, Inc.
  • Publication number: 20200265213
    Abstract: In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
    Type: Application
    Filed: January 21, 2020
    Publication date: August 20, 2020
    Applicant: Affymetrix, inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Publication number: 20200234791
    Abstract: Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.
    Type: Application
    Filed: November 25, 2019
    Publication date: July 23, 2020
    Applicant: Affymetrix, Inc.
    Inventors: Jeanette Pruzan Schmidt, Christopher Davies, Brant Wong
  • Publication number: 20200167916
    Abstract: Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log2 ratio data.
    Type: Application
    Filed: October 30, 2019
    Publication date: May 28, 2020
    Applicant: Affymetrix, Inc.
    Inventors: Benjamin M. Bolstad, Harry Zuzan
  • Patent number: 10648030
    Abstract: The disclosure provides a method of determining the presence or absence of a plurality of target polynucleotides in a sample including combining a sample that may comprise one or more of the plurality of target polynucleotides with a plurality of sets of complementary polynucleotides; incubating the polynucleotides under conditions that allow hybridization of complementary sequences; joining the first and second complementary polynucleotides to form one or more product polynucleotides; and detecting the presence or absence of one or more product polynucleotides to determine the presence or absence of one or more of the plurality of target polynucleotides in the sample.
    Type: Grant
    Filed: January 14, 2013
    Date of Patent: May 12, 2020
    Assignee: Affymetrix, Inc.
    Inventors: John D. Curry, Heather Koshinsky, Amanda Kay Lindholm-Perry, Richard Mark Thallman
  • Patent number: 10648021
    Abstract: Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.
    Type: Grant
    Filed: October 30, 2017
    Date of Patent: May 12, 2020
    Assignee: AFFYMETRIX, INC.
    Inventors: Eugeni A. Namsaraev, Xin Miao, John E. Blume
  • Patent number: 10586095
    Abstract: In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
    Type: Grant
    Filed: April 3, 2019
    Date of Patent: March 10, 2020
    Assignee: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 10535420
    Abstract: Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: January 14, 2020
    Assignee: Affymetrix, Inc.
    Inventors: Jeanette Pruzan Schmidt, Christopher Davies, Brant Wong
  • Patent number: 10515447
    Abstract: Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log2 ratio data.
    Type: Grant
    Filed: November 29, 2012
    Date of Patent: December 24, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Benjamin M. Bolstad, Harry Zuzan
  • Publication number: 20190311780
    Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
    Type: Application
    Filed: March 12, 2019
    Publication date: October 10, 2019
    Applicant: AFFYMETRIX, INC.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • Publication number: 20190311178
    Abstract: In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
    Type: Application
    Filed: April 3, 2019
    Publication date: October 10, 2019
    Applicant: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 10422750
    Abstract: Disclosed are calibration apparatuses for fluorescent microscopy instruments and methods of making and using them. Specifically, disclosed are calibration apparatuses with a fluorescent layer, such as photoresist, deposited on a substrate, with an optional layer of a reflective material, such as chrome. Illumination of the fluorescent and/or reflective layers, and detection and analysis of the resulting emissions allows evaluation of the instrument with respect to both reflective and fluorescent channels. Selection of appropriate fluorescent materials for the one or more fluorescent layers allows the evaluation of an instrument with respect to different fluorophores, as would be used with an instrument capable of two color detection.
    Type: Grant
    Filed: February 6, 2018
    Date of Patent: September 24, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Bei-Shen Sywe, Mark Borodkin, Chuan Gao, Liana Ilkova, Devin Nguyen
  • Publication number: 20190287650
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Application
    Filed: January 10, 2019
    Publication date: September 19, 2019
    Applicant: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Patent number: 10407717
    Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.
    Type: Grant
    Filed: September 30, 2016
    Date of Patent: September 10, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Shivani Nautiyal, Malek Faham
  • Publication number: 20190198134
    Abstract: 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: Application
    Filed: November 20, 2018
    Publication date: June 27, 2019
    Applicant: Affymetrix, Inc.
    Inventors: Hong Gao, Ali Pirani, Teresa Webster, Mei-Mei Shen
  • Patent number: 10329600
    Abstract: 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: Grant
    Filed: June 16, 2016
    Date of Patent: June 25, 2019
    Assignee: AFFYMETRIX, INC.
    Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
  • Patent number: 10303922
    Abstract: In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.
    Type: Grant
    Filed: May 30, 2018
    Date of Patent: May 28, 2019
    Assignee: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 10275568
    Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
    Type: Grant
    Filed: March 27, 2012
    Date of Patent: April 30, 2019
    Assignee: Affymetrix, Inc.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • Patent number: 10229244
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Grant
    Filed: June 20, 2008
    Date of Patent: March 12, 2019
    Assignee: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Patent number: 10213762
    Abstract: Silanation compositions containing a mixture of two or more silanation reagents, where at least one silanation reagent includes a functional group capable of supporting polymer synthesis and at least one silanation reagent includes no functional group capable of supporting polymer synthesis are useful in modulating the active site density and hydrolytic stability of a surface. These compositions are particularly useful in silanating a surface prior to preparation of a polymer array and provide for increased hybridization results.
    Type: Grant
    Filed: January 27, 2017
    Date of Patent: February 26, 2019
    Assignee: AFFYMETRIX, INC.
    Inventors: Glenn H. McGall, Robert G. Kuimelis
  • Patent number: 10155976
    Abstract: 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: Grant
    Filed: June 16, 2016
    Date of Patent: December 18, 2018
    Assignee: AFFYMETRIX, INC.
    Inventors: Keith W. Jones, Michael H. Shapero