Patents Assigned to Affymetrix, Inc.
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Publication number: 20130230221Abstract: 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: ApplicationFiled: November 29, 2012Publication date: September 5, 2013Applicant: Affymetrix, Inc.Inventors: Benjamin M. Bolstad, Harry Zuzan
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Patent number: 8518479Abstract: 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: GrantFiled: October 5, 2007Date of Patent: August 27, 2013Assignee: Affymetrix, Inc.Inventors: Chuan Gao, Tianyue Yu
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Patent number: 8520976Abstract: 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: GrantFiled: September 23, 2011Date of Patent: August 27, 2013Assignee: Affymetrix, Inc.Inventors: Michael D. Kaiser, David R. Smith
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Publication number: 20130210028Abstract: 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: ApplicationFiled: December 19, 2012Publication date: August 15, 2013Applicant: Affymetrix, Inc.Inventor: Affymetrix, Inc.
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Patent number: 8501122Abstract: 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: GrantFiled: December 8, 2010Date of Patent: August 6, 2013Assignee: Affymetrix, Inc.Inventor: Mohsen Shirazi
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Publication number: 20130197208Abstract: 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: ApplicationFiled: November 20, 2012Publication date: August 1, 2013Applicant: Affymetrix, Inc.Inventor: Affymetrix, Inc.
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Patent number: 8497064Abstract: 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: GrantFiled: November 1, 2011Date of Patent: July 30, 2013Assignee: Affymetrix, Inc.Inventors: Glenn H. McGall, Anthony D. Barone
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Patent number: 8498825Abstract: 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: GrantFiled: June 23, 2011Date of Patent: July 30, 2013Assignee: Affymetrix, Inc.Inventors: Jing Huang, Keith W. Jones
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Publication number: 20130190199Abstract: 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: ApplicationFiled: November 2, 2012Publication date: July 25, 2013Applicant: Affymetrix, Inc.Inventor: Affymetrix, Inc.
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Publication number: 20130190213Abstract: 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: ApplicationFiled: March 6, 2013Publication date: July 25, 2013Applicant: AFFYMETRIX, INC.Inventor: AFFYMETRIX, INC.
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Patent number: 8492121Abstract: 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: GrantFiled: June 29, 2011Date of Patent: July 23, 2013Assignee: Affymetrix, Inc.Inventor: Shoulian Dong
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Patent number: 8486665Abstract: 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: GrantFiled: January 23, 2012Date of Patent: July 16, 2013Assignee: Affymetrix, Inc.Inventors: Jeannine C. Muller-Greven, Marc A. Post, Christopher J. Kubu
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Publication number: 20130169645Abstract: 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: ApplicationFiled: September 25, 2012Publication date: July 4, 2013Applicant: AFFYMETRIX, INC.Inventor: Affymetrix, Inc.
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Publication number: 20130165350Abstract: 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: ApplicationFiled: December 22, 2011Publication date: June 27, 2013Applicant: Affymetrix, Inc.Inventors: Robert Kuimelis, Glenn McGall, Dexter Pao, Zihui Chen, Trevor Axelrod
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Patent number: 8470535Abstract: 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: GrantFiled: April 21, 2011Date of Patent: June 25, 2013Assignee: Affymetrix, Inc.Inventors: Gary McMaster, Yunqing Ma
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Patent number: 8467974Abstract: 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: GrantFiled: June 15, 2011Date of Patent: June 18, 2013Assignee: Affymetrix, Inc.Inventors: Shantanu V. Kaushikkar, Teresa A. Webster, Rui Mei, Linda McAllister
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Publication number: 20130150248Abstract: 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: ApplicationFiled: December 2, 2010Publication date: June 13, 2013Applicant: 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
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Patent number: 8460854Abstract: 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: GrantFiled: December 29, 2011Date of Patent: June 11, 2013Assignee: Affymetrix, Inc.Inventor: Randall J. True
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Patent number: 8460876Abstract: 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: GrantFiled: November 3, 2011Date of Patent: June 11, 2013Assignee: Affymetrix, Inc.Inventors: Xianqiang Li, Xin Jiang
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Publication number: 20130142408Abstract: 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: ApplicationFiled: October 30, 2012Publication date: June 6, 2013Applicant: AFFYMETRIX, INC.Inventor: AFFYMETRIX, INC.
