Patents Assigned to Affymetrix, Inc.
  • Methods for Selecting a Collection of Single Nucleotide Polymorphisms
    Publication number: 20110160092
    Abstract: 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: Application
    Filed: January 14, 2011
    Publication date: June 30, 2011
    Applicant: Affymetrix, INC.
    Inventors: Teresa A. Webster, Hajime Matsuzaki, Xiaojun Di, Earl A. Hubbell, Rui Mei, Simon Cawley, Gregory Marcus, Keith W. Jones
  • Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels
    Publication number: 20110160078
    Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.
    Type: Application
    Filed: December 15, 2010
    Publication date: June 30, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: Stephen P.A. Fodor, Glenn K. Fu
  • Methods of Analysis of Methylation
    Publication number: 20110151438
    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: Application
    Filed: October 24, 2007
    Publication date: June 23, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: Shivani Nautiyal, Malek Faham
  • Photoacid generators for the synthesis of oligo-DNA in a polymer matrix
    Patent number: 7964654
    Abstract: Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
    Type: Grant
    Filed: September 14, 2010
    Date of Patent: June 21, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Glenn H. McGall, Andrea Cuppoletti
  • Surface Modifications and Methods for their Synthesis and Use
    Publication number: 20110143966
    Abstract: Novel processes are disclosed for forming an array of polymers by functionalizing the surface of particles by methods that include covalently attaching a functionalized silicon compound. Substrates such as microparticles having functionalized silicon compounds attached thereto are produced by introducing at least one carboxyl group directly by silanating a carboxylated silane compound to the surface of a microparticle. In a further aspect of the invention, the silane compound is a dipodal carboxylated silane.
    Type: Application
    Filed: August 2, 2010
    Publication date: June 16, 2011
    Applicant: Affymetrix, INC.
    Inventors: Glenn H. McGall, Anthony D. Barone
  • System, method, and computer product for exon array analysis
    Patent number: 7962289
    Abstract: In one embodiment, a method for analyzing data generated by probe arrays is described that comprises receiving user selections of two or more data files and an identification of one or more subsets of intensity values acquired from a biological probe array. The method includes iteratively opening each data file, identifying the selected subset of intensity values associated with each open data file, determining parameters for processing, storing the parameters and the identified intensity values, and closing the open data file prior to the subsequent iteration. The method then includes processing the stored intensity values using the parameters to identify one or more biological events.
    Type: Grant
    Filed: June 2, 2006
    Date of Patent: June 14, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Alan J. Williams, Charles W. Sugnet, James H. Gorrell
  • Methods and computer software for detecting splice variants
    Patent number: 7962291
    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: October 2, 2006
    Date of Patent: June 14, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Alan Williams, Simon Cawley, John E. Blume, Hui Wang, Tyson Clark
  • MANUFACTURING AND PROCESSING POLYMER ARRAYS
    Publication number: 20110136699
    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: December 8, 2010
    Publication date: June 9, 2011
    Applicant: Affymetrix, INC.
    Inventor: Mohsen Shirazi
  • Oxide layers on silicon substrates for effective confocal laser microscopy
    Patent number: 7951601
    Abstract: Methods of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, the method comprising the steps of providing a silicon wafer substrate having a top side and a bottom side, coating the top side of the silicon wafer with an oxide coating to provide an oxide coated wafer, covalently coupling a plurality of probes to the top side of the coated wafer to provide a fixed polymer array, hybridizing the fixed polymer array with a plurality of labeled ligands, and assaying for one or more hybridized ligands using confocal laser fluorescence microscopy to detect hybridization are provided.
    Type: Grant
    Filed: December 21, 2006
    Date of Patent: May 31, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Robert G. Kuimelis, Zihui Chen, Glenn H. McGall
  • Hot start nucleic acid amplification
    Patent number: 7951534
    Abstract: Methods and compositions for performing nucleic acid duplication and amplification reactions are provided. A single-stranded nucleic acid binding protein is selected and provided in the reaction mixture which is assembled at a low, nonstringent temperature to include all of the necessary reagents for successful nucleic acid duplication or amplification reactions. By incorporating a single-stranded nucleic acid binding protein into the reaction mixture at low temperature, the generation of nonspecific products such as amplification products is improved despite the reaction mixture having been fully assembled at a nonstringent temperature.
    Type: Grant
    Filed: November 14, 2007
    Date of Patent: May 31, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Christopher James Kubu, Jeannine Catherine Muller-Greven, Robert Bruce Moffett
  • Multiplex Targeted Amplification Using Flap Nuclease
    Publication number: 20110124052
    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: Application
    Filed: December 17, 2010
    Publication date: May 26, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: Jianbiao Zheng, Li Weng, Malek Faham
  • USE OF ACID SCAVENGERS FOR THE SYNTHESIS OF STANDARD LENGTH AND LONG-MER POLYER ARRAYS
    Publication number: 20110124526
    Abstract: Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.
    Type: Application
    Filed: January 21, 2011
    Publication date: May 26, 2011
    Applicant: Affymetrix, INC.
    Inventors: Robert G. Kuimelis, Glenn H. McGall, Martin J. Goldberg, Guangyu Xu
  • Cell penetrating peptides for intracellular delivery of molecules
    Patent number: 7943581
    Abstract: The present invention concerns cell-penetrating peptides which comprise an amino acid sequence consisting of GLX9WRAX9WRX1LX2RSLX9WX3X4X5X6X7X8(SEQ ID No: 1), wherein X1 is A, L or G, X2 is W or none, X3 is R or K, X4 is K, L or S, X5 is L or K, X6 is R or W, X7 is K or S, and X8 is A, V or Q, and X9 is W, F or Y. These CPPs can be used as vectors for delivering nucleic acids and/or proteins and/or peptides to cells, in vitro or in vivo.
    Type: Grant
    Filed: December 30, 2008
    Date of Patent: May 17, 2011
    Assignees: Centre National de laRecherche de la Recherche, AFFYMETRIX, Inc.
    Inventors: Gilles Divita, Frederic Heitz, Catherine May Morris, Gudrun Aldrian-Herrada
  • Modified Nucleic Acid Probes
    Publication number: 20110092382
    Abstract: Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.
    Type: Application
    Filed: September 9, 2010
    Publication date: April 21, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: GLENN HUGH MCGALL, CHARLES GARRETT MIYADA, MAUREEN T. CRONIN, JENNIFER DEE TAN, MARK S. CHEE
  • Use of acid scavengers for the synthesis of standard length and long-mer polymer arrays
    Patent number: 7910312
    Abstract: Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.
    Type: Grant
    Filed: July 16, 2010
    Date of Patent: March 22, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Robert G. Kuimelis, Glenn H. McGall, Martin J. Goldberg, Guangyu Xu
  • Computer Software for Visualizing Genotyping Data
    Publication number: 20110060768
    Abstract: A computer system for visualizing recombination events in a group of individuals is provided. According to one aspect of the invention, high-density SNP genotype data is obtained from related individuals in a family. A pedigree is created, haplotypes are reconstructed and likely recombination breakpoints are identified with the use of publicly available computer programs. A software tool is then used facilitate the visualization of the recombination events in the family.
    Type: Application
    Filed: September 10, 2010
    Publication date: March 10, 2011
    Applicant: Affymetrix, INC.
    Inventors: Giulia Kennedy, Yaron Turpaz, Chun Zhang
  • Poly(A) Tail Length Measurement by PCR
    Publication number: 20110059453
    Abstract: Methods and kits for measuring the length of the poly(A) tail of selected target mRNA are disclosed herein. In preferred aspects the mRNA population is modified by addition of a tail comprising guanosine and inosine (G/I tailing). The added tail is used as a priming site for reverse transcription. The resulting cDNA is then amplified using one or more target specific primers and a universal primer that recognizes the tailed region. The products are separated according to size and the size is used to estimate the polyA tail length.
    Type: Application
    Filed: August 23, 2010
    Publication date: March 10, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: Sangpen Chamnongpol, Christopher J. Kubu
  • Analysis of methylation using nucleic acid arrays
    Patent number: 7901882
    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: April 2, 2007
    Date of Patent: March 8, 2011
    Assignee: Affymetrix, Inc.
    Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, John E. Blume
  • PARALLEL PREPARATION OF HIGH FIDELITY PROBES IN AN ARRAY FORMAT
    Publication number: 20110046344
    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: Application
    Filed: November 2, 2010
    Publication date: February 24, 2011
    Applicant: Affymetrix, INC.
    Inventors: Robert G. Kuimelis, Glenn H. McGall
  • Primer Array Synthesis and Validation
    Publication number: 20110046343
    Abstract: Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.
    Type: Application
    Filed: November 2, 2010
    Publication date: February 24, 2011
    Applicant: Affymetrix, INC.
    Inventors: Robert G. Kuimelis, Glenn H. McGall