Patents Assigned to Affymetrix, Inc.
  • 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
  • Publication number: 20180341802
    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: May 30, 2018
    Publication date: November 29, 2018
    Applicant: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 10119162
    Abstract: Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5? or 3? flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5? and 3? flaps are generated. The flaps are cleaved using 5? or 3? flap endonucleases or 3? to 5? exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.
    Type: Grant
    Filed: November 16, 2016
    Date of Patent: November 6, 2018
    Assignee: AFFYMETRIX, INC.
    Inventors: Jianbiao Zheng, Li Weng, Malek Faham
  • Patent number: 10108777
    Abstract: 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: Grant
    Filed: April 30, 2012
    Date of Patent: October 23, 2018
    Assignee: Affymetrix, Inc.
    Inventors: Jing Huang, Keith W. Jones, Michael H. Shapero
  • Patent number: 10019620
    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: August 25, 2017
    Date of Patent: July 10, 2018
    Assignee: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 9982293
    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. Targets are circularized by hybridization to probes followed by ligation of the ends of the target to form a closed circle. The targets are then used as template for extension of an array bound probe resulting in extended probes having multiple copies of the target. The extended probes can then be analyzed. The methods may be used for genotyping, sequencing and analysis of copy number.
    Type: Grant
    Filed: May 5, 2014
    Date of Patent: May 29, 2018
    Assignee: Affymetrix, Inc.
    Inventors: Glenn K. Fu, Glenn H. Mcgall, Robert G. Kuimelis, Jing Hu, Pei-Hua Wang
  • Publication number: 20180096190
    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: August 25, 2017
    Publication date: April 5, 2018
    Applicant: Affymetrix, Inc.
    Inventors: David Stern, Chuan Gao, Melvin Yamamoto, Devin Nguyen
  • Patent number: 9932636
    Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.
    Type: Grant
    Filed: June 26, 2015
    Date of Patent: April 3, 2018
    Assignee: AFFYMETRIX, INC.
    Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
  • Patent number: 9933365
    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 21, 2017
    Date of Patent: April 3, 2018
    Assignee: Affymetrix, Inc.
    Inventors: Bei-Shen Sywe, Mark Borodkin, Chuan Gao, Liana Ilkova, Devin Nguyen
  • Patent number: 9896538
    Abstract: The invention provides for polyfluoreno[4,5-cde]oxepine conjugates and their use in methods of analyte detection.
    Type: Grant
    Filed: March 27, 2017
    Date of Patent: February 20, 2018
    Assignees: AAT Bioquest, Inc., Affymetrix, Inc.
    Inventors: Zhenjun Diwu, Haitao Guo, Ruogu Peng, Qin Zhao, Travis Jennings, Castle Funatake
  • Publication number: 20180039727
    Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.
    Type: Application
    Filed: August 17, 2017
    Publication date: February 8, 2018
    Applicant: Affymetrix, Inc.
    Inventors: Earl A. Hubbell, Simon Cawley
  • Publication number: 20180011970
    Abstract: Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions).
    Type: Application
    Filed: September 22, 2017
    Publication date: January 11, 2018
    Applicant: Affymetrix, Inc.
    Inventors: Carl A. Dowds, Jody C. Courtney, Edgar E. Erwin, Garret D. Wilson, Pragna B. Parmar, Breck S. Ohlson, Richard D. Shippy, Francisco J. Cifuentes
  • Patent number: 9845490
    Abstract: 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: Grant
    Filed: December 3, 2013
    Date of Patent: December 19, 2017
    Assignee: Affymetrix, Inc.
    Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
  • Patent number: 9845494
    Abstract: The invention relates to methods for enzymatic, genotyping of polymorphisms on solid supports. In some aspects the methods include ligation of allele or base specific interrogation probes to an array probe. The array probe is labeled by ligation of the interrogation probe. Ligation is dependent on the identity of the base immediately adjacent to the end of the array probe. In other aspects array bound probes are labeled by template dependent extension.
    Type: Grant
    Filed: October 18, 2007
    Date of Patent: December 19, 2017
    Assignee: Affymetrix, Inc.
    Inventors: Glenn K. Fu, Keith W. Jones