Patents Assigned to Affymetrix, Inc.
  • 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
  • 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
  • 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
  • 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
  • Publication number: 20130230221
    Abstract: Disclosed are methods and software for biological data analysis. Specifically, provided are methods, computer programs and systems for analyzing data in the form of various intensity measurements obtained from an oligonucleotides microarray experiment. Such data may be microarray data obtained from an experiment conducted to determine copy number of a human genetic sample. The data are corrected by application of one or more covariate adjusters which may be applied simultaneously and which may be selected by a user. Further, the present application provides methods of filtering image data and signal restoration of image data using log2 ratio data.
    Type: Application
    Filed: November 29, 2012
    Publication date: September 5, 2013
    Applicant: Affymetrix, Inc.
    Inventors: Benjamin M. Bolstad, Harry Zuzan
  • Patent number: 8520976
    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: September 23, 2011
    Date of Patent: August 27, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Michael D. Kaiser, David R. Smith
  • Patent number: 8518479
    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: Grant
    Filed: October 5, 2007
    Date of Patent: August 27, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Chuan Gao, Tianyue Yu
  • Publication number: 20130210028
    Abstract: Encoded microparticles described are useful in the study of many different biological agents in multiplex assays. For instance, the encoded microparticles may be employed in various co-precipitation assays to purify and/or isolate various analytes of interest. Encoded microparticles may also be used as real-time detectors in many different situations whereby binding of a secreted analyte or contaminating analyte may be detected using various labeling techniques. Further, encoded microparticles may be attached in a specific manner to particular cell types, for instance in a heterogeneous mixture of cells, either fixed in tissue or circulating, to allow identification, localization and/or sorting of the cells in the context of various biological events under various environments or conditions.
    Type: Application
    Filed: December 19, 2012
    Publication date: August 15, 2013
    Applicant: Affymetrix, Inc.
    Inventor: Affymetrix, Inc.
  • Patent number: 8501122
    Abstract: The invention provides sensor plates, particularly plates having a plurality of sensors, and related methods for assembling such plates. The sensors can be arrays of probes, such as microarrays, including high density oligonucleotide microarrays. The methods include the steps of selecting a substrate having a plurality of sensors, aligning the substrate to a support plate, and attaching the substrate to the support plate. Moduled sensor plates, and methods of assembling such plates, are also provided. The moduled sensor plates can include a plurality of sensor plates, such as sensor or microarray strip plates, with each strip plate having an attachment feature that is used to attach the strip plate to a frame. The sensor plates and moduled sensor plates can be inserted into processing plates, including hybridization plates, washing plates, staining plates, and detection plates.
    Type: Grant
    Filed: December 8, 2010
    Date of Patent: August 6, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Mohsen Shirazi
  • Publication number: 20130197208
    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 20, 2012
    Publication date: August 1, 2013
    Applicant: Affymetrix, Inc.
    Inventor: Affymetrix, Inc.
  • Patent number: 8497064
    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: Grant
    Filed: November 1, 2011
    Date of Patent: July 30, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Glenn H. McGall, Anthony D. Barone
  • Patent number: 8498825
    Abstract: Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.
    Type: Grant
    Filed: June 23, 2011
    Date of Patent: July 30, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Jing Huang, Keith W. Jones
  • Publication number: 20130190213
    Abstract: In one aspect of the invention, systems, methods, and devices are provided for handling liquid. In some embodiments, such systems, methods, and devices are used to process reagent biochemical reactions.
    Type: Application
    Filed: March 6, 2013
    Publication date: July 25, 2013
    Applicant: AFFYMETRIX, INC.
    Inventor: AFFYMETRIX, INC.
  • Publication number: 20130190199
    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: Application
    Filed: November 2, 2012
    Publication date: July 25, 2013
    Applicant: Affymetrix, Inc.
    Inventor: Affymetrix, Inc.
  • Patent number: 8492121
    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 presence or absence of a polymorphism.
    Type: Grant
    Filed: June 29, 2011
    Date of Patent: July 23, 2013
    Assignee: Affymetrix, Inc.
    Inventor: Shoulian Dong
  • Patent number: 8486665
    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: Grant
    Filed: January 23, 2012
    Date of Patent: July 16, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Jeannine C. Muller-Greven, Marc A. Post, Christopher J. Kubu
  • Publication number: 20130169645
    Abstract: Innovative systems and methods for visualizing information collected from analyzing samples are provided. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is significant to a characteristic such as disease or resistance to disease. Additionally, the computer system may facilitate display of further information about relevant genes once they are identified.
    Type: Application
    Filed: September 25, 2012
    Publication date: July 4, 2013
    Applicant: AFFYMETRIX, INC.
    Inventor: Affymetrix, Inc.
  • Publication number: 20130165350
    Abstract: The present invention provide several methods of derivatizing a surface of a support with one or more linkers thus providing a suitable platform for synthesis of a polymer array, particular a nucleic acid array. Some methods derivatize a surface with a self-assembled monolayer (SAM) of a linker. The SAM confers advantages of hydrolytic stability, broad compatibility with synthesis and detection chemistries, and reduced emergence of latent functional groups during polymer array synthesis. Substrates can also be derivatized with multi-layers of SAMs providing greater hydrolytic stability. Substrates can also be derivatized by synthesizing a linker in situ on the substrate by atom transfer radical polymerization of functional and functional monomers. Appropriate selection of monomers reduces emergence of latent functional groups in subsequent array synthesis.
    Type: Application
    Filed: December 22, 2011
    Publication date: June 27, 2013
    Applicant: Affymetrix, Inc.
    Inventors: Robert Kuimelis, Glenn McGall, Dexter Pao, Zihui Chen, Trevor Axelrod
  • Patent number: 8470535
    Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.
    Type: Grant
    Filed: April 21, 2011
    Date of Patent: June 25, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Gary McMaster, Yunqing Ma
  • Patent number: 8467974
    Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
    Type: Grant
    Filed: June 15, 2011
    Date of Patent: June 18, 2013
    Assignee: Affymetrix, Inc.
    Inventors: Shantanu V. Kaushikkar, Teresa A. Webster, Rui Mei, Linda McAllister