Patents Assigned to Affymetrix, Inc.
  • Methods for synthesizing pools of probes
    Patent number: 8759036
    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: March 21, 2012
    Date of Patent: June 24, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Yuker Wang, Keith Jones, Ronald J. Sapolsky
  • Multiple step printing methods for microbarcodes
    Patent number: 8748079
    Abstract: A system and method for forming encoded microparticles is described. One embodiment includes a method for forming a microparticle, the method comprising providing a pattern, wherein the pattern defines a code element, printing the pattern on a substrate to form a first code element within a microparticle region, printing the pattern on the substrate to form at least one successive code element, such that the first code element and the at least one successive code element are within the same microparticle region, wherein a code is formed by the first code element and any successive code elements.
    Type: Grant
    Filed: January 11, 2013
    Date of Patent: June 10, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Randall True
  • Method of oligonucleotide synthesis
    Patent number: 8728767
    Abstract: Methods and kits for synthesizing a plurality of oligonucleotides are provided. Methods for providing a plurality of oligonucleotides enriched for full length oligonucleotides are provided. Truncated oligonucleotides are preferentially removed from the sample by digestion. Methods are also provided for amplification of a plurality of oligonucleotides.
    Type: Grant
    Filed: December 21, 2007
    Date of Patent: May 20, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Michael Shapero
  • Parallel preparation of high fidelity probes in an array format
    Patent number: 8729251
    Abstract: The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
    Type: Grant
    Filed: November 20, 2012
    Date of Patent: May 20, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Robert G. Kuimelis, Glenn H. McGall
  • Amplification and analysis of selected targets on solid supports
    Patent number: 8716190
    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: October 6, 2010
    Date of Patent: May 6, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Glenn K. Fu, Glenn H. McGall, Robert G. Kuimelis, Jing Hu, Pei-Hua Wang
  • Method for Detecting Transcription Factor-Protein Interactions
    Publication number: 20140121122
    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: Application
    Filed: April 8, 2013
    Publication date: May 1, 2014
    Applicant: Affymetrix, Inc.
    Inventor: Xianqiang Li
  • Analysis of methylation using nucleic acid arrays
    Patent number: 8709716
    Abstract: Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.
    Type: Grant
    Filed: January 27, 2011
    Date of Patent: April 29, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J Williams, Eric B. Schell, John E. Blume
  • Miniaturized microparticles
    Patent number: 8697334
    Abstract: An encoded microparticle having a spatial code is provided; and a set of encoded microparticles possessing subsets each provided with a distinguishable spatial code, wherein the codes comply with a pre-determined coding scheme. Presented are also methods of using the encoded microparticles in various biological assays, such as various multiplex assays and visualizing them by creating a digital image of the encoded microparticles and determining whether false positives are present. Further are provided methods of manufacture of the encoded microparticles which employ ferromagnetic nanoparticles applied using spin-on-glass techniques.
    Type: Grant
    Filed: December 23, 2011
    Date of Patent: April 15, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Randall J. True, Martin J. Goldberg, Michael Ru, Michael P. Mittmann
  • Highly multiplexed particle-based assays
    Patent number: 8685753
    Abstract: Methods are provided for detecting and optionally quantitating multiple analytes, including nucleic acid and/or polypeptide analytes, in particle-based assays that can be highly multiplexed. Compositions, systems, and kits related to the methods are also featured.
    Type: Grant
    Filed: January 10, 2012
    Date of Patent: April 1, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Jason Martin, Quan Ngoc Nguyen
  • Complexity management of genomic DNA
    Patent number: 8679758
    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: August 6, 2012
    Date of Patent: March 25, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
  • Miniaturized microparticles
    Publication number: 20140057809
    Abstract: A system and method for forming encoded microparticles is described. One embodiment includes an encoded microparticle, the microparticle comprising a plurality of segments aligned along an axis, wherein the plurality of segments define a code for the microparticle; and an outer cuboid encapsulating the plurality of segments, wherein the plurality of segments are detectable through the outer cuboid.
    Type: Application
    Filed: February 6, 2013
    Publication date: February 27, 2014
    Applicant: AFFYMETRIX, INC.
    Inventor: AFFYMETRIX, INC.
  • Multiple Step Printing Methods for Microbarcodes
    Publication number: 20140051027
    Abstract: A system and method for forming encoded microparticles is described. One embodiment includes a method for forming a microparticle, the method comprising providing a pattern, wherein the pattern defines a code element, printing the pattern on a substrate to form a first code element within a microparticle region, printing the pattern on the substrate to form at least one successive code element, such that the first code element and the at least one successive code element are within the same microparticle region, wherein a code is formed by the first code element and any successive code elements.
    Type: Application
    Filed: January 11, 2013
    Publication date: February 20, 2014
    Applicant: AFFYMETRIX, INC.
    Inventor: AFFYMETRIX, INC.
  • Automated method of manufacturing polyer arrays
    Patent number: 8652774
    Abstract: The present invention provides methods to process multiple sensors by providing a sensor plate and HT plates. In a preferred embodiment of the invention, methods for assembling microarray pegs and microarray plates are described for high throughput microarray processing.
    Type: Grant
    Filed: October 4, 2005
    Date of Patent: February 18, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Melvin Yamamoto, Clifford A. Oostman, Jr., John S. Sze, Keith S. Pearson, Philip C. Trenholme, Dan Liu, Chi Sou Yu
  • System for photolithographic synthesis of polymer arrays
    Patent number: 8637434
    Abstract: The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Grant
    Filed: September 28, 2012
    Date of Patent: January 28, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Martin J. Goldberg, Martin Diggelman, Earl A. Hubbell, Glenn H. McGall, Ngo Nam, MacDonald S. Morris, Melvin Yamamoto, Jennifer Tan, Richard Rava
  • Multiplex capture of nucleic acids
    Patent number: 8632970
    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 23, 2010
    Date of Patent: January 21, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Yuling Luo, Wen Yang
  • MANUFACTURING AND PROCESSING POLYMER ARRAYS
    Publication number: 20140018266
    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: Application
    Filed: July 2, 2013
    Publication date: January 16, 2014
    Applicant: Affymetrix, Inc.
    Inventor: Mohsen Shirazi
  • Multiplex capture of nucleic acids
    Patent number: 8628918
    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. Compositions, kits, and systems related to the methods are also described.
    Type: Grant
    Filed: May 8, 2006
    Date of Patent: January 14, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Yuling Luo, Wen Yang
  • Recombinant Colwellia Psychrerythraea Alkaline Phosphatase and Uses Thereof
    Publication number: 20130344493
    Abstract: A heat labile alkaline phosphatase enzyme and methods of using the same and kits including the same are disclosed. Specifically, a nucleotide sequence of, peptide sequence of, methods of using, and kits comprising, a heat labile alkaline phosphatase isolated from Colwellia psychrerythraea are provided. Methods of over-expression and purification of the recombinant alkaline phosphatase and mutants thereof are also disclosed. Methods of over-expressing and purifying commercially useful quantities of active recombinant heat labile alkaline phosphatase fusion enzymes from C. psychrerythraea, wherein the fusion enzymes comprise one or more heterologous leader sequences are disclosed. The disclosed C. psychrerythraea heat labile alkaline phosphatase has properties similar to shrimp alkaline phosphatase and can be substituted for shrimp alkaline phosphatase in assays involving the same.
    Type: Application
    Filed: June 13, 2013
    Publication date: December 26, 2013
    Applicant: Affymetrix, Inc.
    Inventors: Jeannine C. Muller-Greven, Marc A. Post, Christopher J. Kubu
  • Methods for producing codes for microparticles
    Patent number: 8592136
    Abstract: Methods and apparatus are provided for forming a plurality of encoded microparticles with a printing process to define a code for identifying the microparticles. In some embodiments the printing process includes printing steps performed with photolithography.
    Type: Grant
    Filed: September 13, 2006
    Date of Patent: November 26, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Randall J. True
  • Methods of using an array of pooled probes in genetic analysis
    Patent number: 8586312
    Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provides methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.
    Type: Grant
    Filed: August 17, 2010
    Date of Patent: November 19, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Erik Gentalen, Mark Chee