Patents Assigned to Affymetrix, Inc.
  • Publication number: 20130150248
    Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.
    Type: Application
    Filed: December 2, 2010
    Publication date: June 13, 2013
    Applicant: AFFYMETRIX, INC.
    Inventors: Maureen T. Cronin, Charles G. Miyada, Earl A. Hubbell, Mark Chee, Stephen P.A. Fodor, Xiaohua C. Huang, Robert J. Lipshutz, Peter E. Lobban, MacDonald S. Morris, Edward L. Sheldon
  • Patent number: 8460854
    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: December 29, 2011
    Date of Patent: June 11, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Randall J. True
  • Patent number: 8460876
    Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.
    Type: Grant
    Filed: November 3, 2011
    Date of Patent: June 11, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Xianqiang Li, Xin Jiang
  • Publication number: 20130142408
    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: Application
    Filed: October 30, 2012
    Publication date: June 6, 2013
    Applicant: AFFYMETRIX, INC.
    Inventor: AFFYMETRIX, INC.
  • Publication number: 20130137583
    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: Application
    Filed: August 6, 2012
    Publication date: May 30, 2013
    Applicant: Affymetrix, Inc.
    Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
  • Publication number: 20130126757
    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: Application
    Filed: October 12, 2012
    Publication date: May 23, 2013
    Applicant: Affymetrix, Inc.
    Inventor: Affymetrix, Inc.
  • Patent number: 8445201
    Abstract: A method, device and system for hybridizing a target oligonucleotide to at least one array comprising a plurality of mixing beads are provided. A target solution is mixed by agitating the mixing beads while the target oligonucleotides are hybridizing to the complementary probes on the array. In another embodiment, a permeable barrier contains the mixing beads, thereby preventing them from contacting the array surface.
    Type: Grant
    Filed: July 30, 2010
    Date of Patent: May 21, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Bellon Laurent, Martin J. Goldberg, Robert J. Lipshutz, Kaliyur Narasimhan
  • Publication number: 20130116130
    Abstract: Compositions, methods and kits are disclosed for high-sensitivity counting of individual molecules by stochastic labeling of a identical molecules in mixtures of molecules by attachment of a unique label-tags from a diverse pool of label tags to confer uniqueness to otherwise identical or indistinguishable events. Individual occurrences of target molecules randomly choose from a non-depleting reservoir of diverse label-tags. Labeled molecules may be detected by hybridization or sequencing based methods. Molecules that would otherwise be identical in information content are labeled to create a separately detectable product that can be distinctly detected. The disclosed stochastic transformation methods reduce the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed label-tags are present. The methods may be used, for example, to count a given species of molecule within a sample.
    Type: Application
    Filed: December 15, 2011
    Publication date: May 9, 2013
    Applicant: AFFYMETRIX, INC.
    Inventors: Glenn K. Fu, Stephen P.A. Fodor
  • Patent number: 8426578
    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: July 29, 2010
    Date of Patent: April 23, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Yuling Luo, Wen Yang
  • Publication number: 20130096295
    Abstract: Disclosed are saccharide and phosphocholine derivatives. The derivatives include azide and alkyne derivatives which form one end of a variable length carbon chain. The opposite end of the variable length carbon chain is covalently linked to the saccharide or phosphocholine. The saccharide may be, for instance, a maltoside. The alkyne and azide derivatives of the saccharides and phosphocholine may be reacted together to form amphiphilic molecules useful in cellular membrane studies and applications. By adjusting the length of the carbon chain, the biochemical and biophysical properties of the resultant 1,4-disubstituted 1,2,3-triazole compounds may be custom tailored for the intended application. Resultant molecules may form micelles, bicelle, lipid bilayers and other like structures useful in the isolation and purification of membrane bound or membrane associated proteins and biochemical components.
    Type: Application
    Filed: October 12, 2011
    Publication date: April 18, 2013
    Applicant: AFFYMETRIX, INC.
    Inventors: Benjamin R. Travis, Ritesh Mittal, Lijun Huang, Liang Tang
  • Patent number: 8404443
    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: March 29, 2011
    Date of Patent: March 26, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Christopher James Kubu, Jeannine Catherine Muller-Greven, Robert Bruce Moffett
  • Publication number: 20130072390
    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: Application
    Filed: March 21, 2012
    Publication date: March 21, 2013
    Applicant: AFFYMETRIX, INC.
    Inventors: Yuker Wang, Keith Jones, Ronald J. Sapolsky
  • Publication number: 20130059763
    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: Application
    Filed: September 28, 2012
    Publication date: March 7, 2013
    Applicant: Affymetrix, Inc.
    Inventor: Affymetrix, Inc..
  • Patent number: 8391582
    Abstract: An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.
    Type: Grant
    Filed: May 25, 2012
    Date of Patent: March 5, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Nathan K. Weiner, Patrick J. Odoy, Eric Schultz, Mark Jones, James T. Overbeck, Herman DeWeerd, David A. Stura, Albert K. Bukys, Tim J. Woolaver, Thomas P. Regan, David Bradbury, Eric E. McKenzie, Roger DiPaolo, Christopher Miles, Joel M. Katz, Oleinik-Ovod Ksenia
  • Patent number: 8392355
    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: Grant
    Filed: September 10, 2010
    Date of Patent: March 5, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Giulia C Kennedy, Yaron Turpaz, Chun Zhang
  • Patent number: 8372576
    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: Grant
    Filed: April 30, 2012
    Date of Patent: February 12, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Randall True
  • Patent number: 8374818
    Abstract: The present invention relates to systems and methods for examining a number of components that have been assembled onto a substrate. In general, the invention relates to the calibration of inspection tools for inspecting components on the substrate. In particular, the invention relates to the calibration of inspection tools for detecting the accuracy of the array pegs positions on an assembled HTA plate.
    Type: Grant
    Filed: December 21, 2009
    Date of Patent: February 12, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Peter Meijles
  • Patent number: 8369596
    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: July 19, 2011
    Date of Patent: February 5, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Earl A. Hubbell
  • Publication number: 20130029273
    Abstract: In one aspect of the invention, methods, and devices are provided for creating microfluidic and nanofluidic features. In some embodiments, such methods and devices are used to create at least one channel of a desired volume within a channel in a plastic substrate.
    Type: Application
    Filed: October 5, 2007
    Publication date: January 31, 2013
    Applicant: Affymetrix, INC.
    Inventors: Chuan Gao, Tianyue Yu
  • Publication number: 20130017966
    Abstract: The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. This selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Amplified fragments may be analyzed to genotype polymorphisms by hybridization to an array of probes that are complementary to target sequences that will be amplified.
    Type: Application
    Filed: February 3, 2012
    Publication date: January 17, 2013
    Applicant: Affymetrix, Inc.
    Inventors: Michael H. Shapero, Keith W. Jones