Patents Assigned to Affymetrix, Inc.
  • Publication number: 20150038352
    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: Application
    Filed: October 2, 2013
    Publication date: February 5, 2015
    Applicant: AFFYMETRIX, INC.
    Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, Jonh E. Blume
  • Patent number: 8945811
    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: February 6, 2013
    Date of Patent: February 3, 2015
    Assignee: Affymetrix, Inc.
    Inventor: Randall J. True
  • Publication number: 20150017632
    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: December 3, 2013
    Publication date: January 15, 2015
    Applicant: Affymetrix, Inc.
    Inventors: Hajime Matsuzaki, Xing Su, Sean Walsh, Giulia Kennedy, Rui Mei
  • Patent number: 8934689
    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: October 30, 2012
    Date of Patent: January 13, 2015
    Assignee: Affymetrix, Inc.
    Inventor: Earl A. Hubbell
  • Patent number: 8932819
    Abstract: Methods, compositions and kits are disclosed for assays to determine the binding affinity of DNA-binding proteins or RNA-binding proteins for their corresponding recognition site(s). In particular, assays are disclosed for measuring binding affinities when either the binding protein, or the recognition sequence of the recognition site, or cofactor proteins, contain one or more mutations. The disclosed assays can thus be utilized to measure the effect on transcription factor binding caused by mutations within the recognition site, or mutations within the binding domain of the protein, and to provide binding affinity information that can be correlated with altered gene regulation and expression. The disclosed assays can be personalized to a specific person or organism, with the measured binding affinities based upon an individual's specific binding proteins and recognition sites.
    Type: Grant
    Filed: July 6, 2012
    Date of Patent: January 13, 2015
    Assignee: Affymetrix, Inc.
    Inventor: Philip Dickinson
  • Publication number: 20150004600
    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: May 7, 2014
    Publication date: January 1, 2015
    Applicant: Affymetrix, Inc.
    Inventors: Yuker Wang, Keith W. Jones, Ronald J. Sapolsky
  • Patent number: 8883691
    Abstract: Microparticles including spatially coded microparticles, systems for imaging and methods of detecting such microparticles as well as using the same in bioassays are provided.
    Type: Grant
    Filed: June 25, 2008
    Date of Patent: November 11, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Randall J. True
  • Patent number: 8859196
    Abstract: The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a solid support, derivatizing the first layer by contacting the first layer with a silanation reagent, and a second layer disposed on said first layer wherein the second layer includes functional groups protected with a photolabile protecting group.
    Type: Grant
    Filed: October 18, 2011
    Date of Patent: October 14, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Mark O. Trulson, Glenn H. McGall, Bei-Shen Sywe, Lisa T. Kajisa, Dana Truong, Richard P. Rava, Martin J. Goldberg
  • Patent number: 8855939
    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 18, 2012
    Date of Patent: October 7, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Alan J. Williams, Charles W. Sugnet, James H. Gorrell
  • Publication number: 20140274756
    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: Application
    Filed: March 14, 2013
    Publication date: September 18, 2014
    Applicant: Affymetrix, Inc.
    Inventors: Quan Nguyen, Yunqing Ma, Audrey Lin, Shauna Levinson, Steve Lai
  • Publication number: 20140274728
    Abstract: Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.
    Type: Application
    Filed: March 15, 2013
    Publication date: September 18, 2014
    Applicant: AFFYMETRIX, INC.
    Inventor: AFFYMETRIX, INC.
  • Patent number: 8835116
    Abstract: Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors.
    Type: Grant
    Filed: November 2, 2012
    Date of Patent: September 16, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Giulia Kennedy
  • Patent number: 8835125
    Abstract: Disclosed are compositions and methods for the labeling of two or more targets with different labels. Specifically, disclosed are compositions for biotin and the protection of biotin within multilabel assays which employ the biotin-biotin binding protein binding relationship for each distinct label in relation to targets such as nucleic acids, polypeptides, antibodies or cells. These multilabel assays are enabled through the use of biotin with desthiobiotin, orthogonal protecting schemes for biotin, or a combination of the approaches.
    Type: Grant
    Filed: December 16, 2011
    Date of Patent: September 16, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Robert G. Kuimelis, Glenn H. McGall, Stephen P. A. Fodor
  • Patent number: 8828688
    Abstract: Compositions and methods for amplifying selected polynucleotides, including DNA and RNA, particularly in multiplex amplification reactions using common primers amplification. Generally, methods of the invention employ multiple steps such as template-specific hybridization, a linear amplification, partial degradation of nucleic acid, and ligation. At the end of the process the sequences of selected polynucleotides are flanked by the common sequences which can be used for exponential amplification using common primers. In some aspects the polynucleotides are associated with a barcode and the presence of the barcode is detected to measure the amount of the polynucleotide.
    Type: Grant
    Filed: May 27, 2011
    Date of Patent: September 9, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Eugeni A. Namsaraev
  • Patent number: 8815510
    Abstract: In one aspect of the invention, methods for analyzing nucleic acid sample are provided. In a preferred embodiment, nucleic acids are selected using affinity matrices prior hybridization with a microarray.
    Type: Grant
    Filed: February 17, 2012
    Date of Patent: August 26, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Stephen P. A. Fodor
  • Patent number: 8808995
    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: January 11, 2012
    Date of Patent: August 19, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Ketih W. Jones, Michael H. Shapero, Stephen P. A. Fodor
  • Patent number: 8796186
    Abstract: A system and method for processing biological sensors. The system includes a support component configured to support a fluidic component. The fluidic component includes at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the system includes a hybridization component configured to perform a hybridization process on a first sensor and a second sensor. Moreover, the system includes a transport component configured to move the first sensor, directly or indirectly, from the hybridization component into the first container and in contact with the first volume of the first fluid.
    Type: Grant
    Filed: June 10, 2009
    Date of Patent: August 5, 2014
    Assignee: Affymetrix, Inc.
    Inventor: Mohsen Shirazi
  • Patent number: 8790873
    Abstract: Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.
    Type: Grant
    Filed: January 19, 2010
    Date of Patent: July 29, 2014
    Assignee: Affymetrix, Inc.
    Inventors: Eugeni A. Namsaraev, Xin Miao, John E. Blume
  • Publication number: 20140194296
    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: Application
    Filed: December 12, 2013
    Publication date: July 10, 2014
    Applicant: Affymetrix, Inc.
    Inventors: Yuling Luo, Yunqing Ma, Gary McMaster, Quan Ngoc Nguyen, Frank Witney, Wen Yang
  • Publication number: 20140187434
    Abstract: Nucleic acid labeling compounds are disclosed. The compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
    Type: Application
    Filed: June 27, 2013
    Publication date: July 3, 2014
    Applicant: Affymetrix, Inc.
    Inventors: Glenn Hugh McGall, Anthony Dale Barone