Patents Assigned to Affymetrix, Inc.
  • Multiplex capture of nucleic acids
    Patent number: 9663822
    Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also described.
    Type: Grant
    Filed: December 12, 2013
    Date of Patent: May 30, 2017
    Assignee: Affymetrix, Inc.
    Inventors: Yuling Luo, Yunqing Ma, Gary McMaster, Quan Ngoc Nguyen, Frank Witney, Wen Yang
  • Methods, systems and apparatuses for testing and calibrating fluorescent scanners
    Patent number: 9599561
    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: October 12, 2012
    Date of Patent: March 21, 2017
    Assignee: Affymetrix, Inc.
    Inventors: Bei-Shen Sywe, Mark Borodkin, Chuan Gao, Liana Ilkova, Devin Nguyen
  • Silane mixtures
    Patent number: 9556360
    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: December 8, 2011
    Date of Patent: January 31, 2017
    Assignee: Affymetrix, Inc.
    Inventors: Glenn H. McGall, Robert G. Kuimelis
  • Multiplex targeted amplification using flap nuclease
    Patent number: 9528148
    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: March 23, 2015
    Date of Patent: December 27, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Jianbiao Zheng, Li Weng, Malek Faham
  • Multiplex targeted amplification using flap nuclease
    Patent number: 9523122
    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: February 16, 2015
    Date of Patent: December 20, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Jianbiao Zheng, Li Weng, Malek Faham
  • System, method, and product for imaging probe arrays with small feature sizes
    Patent number: 9445025
    Abstract: An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.
    Type: Grant
    Filed: August 23, 2013
    Date of Patent: September 13, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Michael D. Kaiser, David R. Smith
  • Locus specific amplification using array probes
    Patent number: 9388457
    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: September 15, 2008
    Date of Patent: July 12, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
  • Complexity management of genomic DNA
    Patent number: 9388460
    Abstract: 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 amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the to presence or absence of a polymorphism.
    Type: Grant
    Filed: June 25, 2013
    Date of Patent: July 12, 2016
    Assignee: Affymetrix, Inc.
    Inventor: Shoulian Dong
  • Methods for genotyping
    Patent number: 9388459
    Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele specific oligonucleotides may be attached to a solid support such as a chip or a bead.
    Type: Grant
    Filed: December 21, 2006
    Date of Patent: July 12, 2016
    Assignee: Affymetrix, Inc.
    Inventor: Michael H. Shapero
  • Methods for genotyping selected polymorphism
    Patent number: 9388461
    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 13, 2014
    Date of Patent: July 12, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Keith W. Jones, Michael H. Shapero
  • Methods for synthesizing pools of probes
    Patent number: 9359640
    Abstract: Compositions, methods and kits are disclosed for synthesizing and amplifying pools of probes using precursor oligonucleotides. In some aspects the precursor is amplified and nicking enzymes are used to separate the full length probes from the amplification products. The methods enable the preparation of single stranded DNA probes of defined sequence and length that are suitable for use in target detection assays.
    Type: Grant
    Filed: May 7, 2014
    Date of Patent: June 7, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Yuker Wang, Keith W. Jones, Ronald J. Sapolsky
  • Method for detecting transcription factor-protein interactions
    Patent number: 9334537
    Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.
    Type: Grant
    Filed: April 8, 2013
    Date of Patent: May 10, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Xianqiang Li, Xin Jiang
  • Manufacturing and processing polymer arrays
    Patent number: 9290798
    Abstract: The invention provides methods to process multiple microarrays by providing a microarray plate and processing plates. In an embodiment of the invention, methods for assembling microarray plates by using wafers are described for high throughput microarray processing.
    Type: Grant
    Filed: July 2, 2013
    Date of Patent: March 22, 2016
    Assignee: Affymetrix, Inc.
    Inventor: Mohsen Shirazi
  • Detection of nucleic acids
    Patent number: 9273349
    Abstract: This invention provides compositions, methods, and systems for characterizing, resolving, and quantitating single stranded and double stranded DNA and RNA in-situ. Paired sense and anti-sense probes can signal the presence of double stranded nucleic acids. DNA and RNA can be distinguished in cell and tissue samples by hybridizing with probe sets adapted to highlight differences in these targets in-situ.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: March 1, 2016
    Assignee: Affymetrix, Inc.
    Inventors: Quan Nguyen, Yunqing Ma, Audrey Lin, Shauna Levinson, Chunfai Lai
  • Feature intensity reconstruction of biological probe array
    Patent number: 9147103
    Abstract: The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
    Type: Grant
    Filed: November 21, 2014
    Date of Patent: September 29, 2015
    Assignee: Affymetrix, Inc.
    Inventor: Earl A. Hubbell
  • Methods and compositions for amplification of nucleic acids
    Patent number: 9085761
    Abstract: The present invention provides methods, compositions, and kits for storing and enhancing the activity of polymerases and particularly thermostable polymerases. The methods comprise mixing a thermostable polymerase with at least one zwitterionic or ylide surfactant that has at least one PEO group. In another aspect the polymerase is mixed with a blocker such as PLURONIC® or TETRONIC® or an amine N-oxide derivative thereof. The thermostable polymerase may be reversibly inactivated by treatment with 2-(Methylsulfonyl)ethyl 4-nitrophenyl carbonate. Compositions and kits for performing the process according to the invention are also provided.
    Type: Grant
    Filed: March 8, 2013
    Date of Patent: July 21, 2015
    Assignee: AFFYMETRIX, INC.
    Inventors: Glenn H. McGall, Anthony D. Barone, Christopher J. Kubu
  • Array-based translocation and rearrangement assays
    Patent number: 9074244
    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: March 11, 2009
    Date of Patent: July 7, 2015
    Assignee: Affymetrix, Inc.
    Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
  • Multiplex branched-chain DNA assays
    Patent number: 8986931
    Abstract: Methods of detecting two or more nucleic acids in a multiplex branched-chain DNA assay are provided. Different nucleic acids are captured through cooperative hybridization events on different, identifiable subsets of particles or at different selected positions on a spatially addressable solid support. Compositions, kits, and systems related to the methods are also described.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: March 24, 2015
    Assignee: Affymetrix, Inc.
    Inventors: Yuling Luo, Wen Yang
  • Multiplex targeted amplification using flap nuclease
    Patent number: 8980563
    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: December 17, 2010
    Date of Patent: March 17, 2015
    Assignee: Affymetrix, Inc.
    Inventors: Jianbiao Zheng, Li Weng, Malek Faham
  • SYSTEM, METHOD, AND PRODUCT FOR IMAGING PROBE ARRAYS WITH SMALL FEATURE SIZES
    Publication number: 20150057167
    Abstract: An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.
    Type: Application
    Filed: August 23, 2013
    Publication date: February 26, 2015
    Applicant: Affymetrix, Inc.
    Inventors: Michael D. Kaiser, David R. Smith