Assignee: Affymetrix, Inc.

Location: Santa Clara, CA
No. of patents: 217

Number	Title	Issue Date
8178278	Miniaturized microparticles A system and method for encoded microparticles is described. One embodiment includes an encoded microparticle comprising a plurality of segments, wherein the plurality of segments form a spatial code; contrast coating on at least one segment of the plurality of segm...	05/15/2012
8168368	Miniaturized microparticles A system and method for forming encoded microparticles is described. One embodiment includes a system for forming encoded microparticles, the system comprising a step and repeat exposure system capable of performing a method comprising: printing at a first time a fi...	05/01/2012
8133987	Primer array synthesis and validation Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array. ...	03/13/2012
8133667	Methods for genotyping with selective adaptor ligation 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 o...	03/13/2012
8129168	Recombinant colwellia psychrerythraea alkaline phosphatase and uses thereof 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	03/06/2012
8114978	Methods for genotyping selected polymorphism 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...	02/14/2012
8114681	Highly multiplexed particle-based assays Methods are provided for detecting and optionally quantitating multiple analytes, including nucleic acid and/or polypeptide analytes, in particle-based assays that can be highly multiplexed. Compositions, systems, and kits related to the methods are also featured.	02/14/2012
8114584	Antireflective coatings for high-resolution photolithographic synthesis of DNA array 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 ...	02/14/2012
8105821	Silane mixtures Silanation compositions containing a mixture of two or more silanation reagents, where at least one silanation reagent includes a functional group capable of supporting polymer synthesis and at least one silanation reagent includes no functional group capable of sup...	01/31/2012
8101737	Parallel preparation of high fidelity probes in an array format 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, gener...	01/24/2012
8095323	Polymorphism detection The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complement...	01/10/2012
8088555	Multiple step printing methods for microbarcodes A system and method for forming encoded microparticles is described. One embodiment includes a method of forming an encoded microparticle, the method comprising: depositing and patterning a plurality of layers on a substrate so as to form a plurality of microparticl...	01/03/2012
8084197	Identification of molecular sequence signatures and methods involving the same Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving...	12/27/2011
8076083	Screening methods involving the detection of short-lived proteins 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...	12/13/2011
8076072	Nucleic acid labeling compounds Nucleic acid labeling compounds including the following are disclosed: These compounds are useful for attaching a detectable label to a nucleic acid. ...	12/13/2011
8075852	System and method for bubble removal 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 combine fluids while removing gaseous bubbles. ...	12/13/2011
8071759	Water soluble cholesterol derivatives Four novel water soluble cholesterol derivative compounds are disclosed. These compounds have various applications in studies of membrane proteins, including drug screening and studies of receptor stability and folding. In one aspect the water soluble cholesterol de...	12/06/2011
8067578	Substrate preparation process 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 c...	11/29/2011
8062844	Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays 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 activa...	11/22/2011
8055098	System, method, and product for imaging probe arrays with small feature sizes 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 intensi...	11/08/2011
8034912	Parallel preparation of high fidelity probes in an array format 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, gener...	10/11/2011
8029999	Complexity management of genomic DNA 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. ...	10/04/2011
8029997	Methods of analysis of allelic imbalance 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 ...	10/04/2011
8026057	Nucleic acid labeling compounds 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 terminal...	09/27/2011
8009889	Feature intensity reconstruction of biological probe array 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 iterative...	08/30/2011
8007267	System and method for making lab card by embossing In one aspect of the invention, systems, methods, and devices are provided for creating microfluidic and nanofluidic structures. In some embodiments, such systems, methods, and devices are used to create features with high aspect ratios in lab cards. ...	08/30/2011
7993883	Complexity management of genomic DNA 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 subs...	08/09/2011
7992098	System, method, and computer software product for linked window interfaces Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have o...	08/02/2011
7991564	Methods for high throughput genotyping 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...	08/02/2011
7991560	System, method, and computer software for the presentation and storage of analysis results 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 ...	08/02/2011
7985547	Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide s...	07/26/2011
7983467	System, method, and product for scanning of biological materials 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 focus...	07/19/2011
7964654	Photoacid generators for the synthesis of oligo-DNA in a polymer matrix Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers. ...	06/21/2011
7962291	Methods and computer software for detecting splice variants 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 s...	06/14/2011
7962289	System, method, and computer product for exon array analysis 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 meth...	06/14/2011
7951601	Oxide layers on silicon substrates for effective confocal laser microscopy 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 ox...	05/31/2011
7951534	Hot start nucleic acid amplification 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 includ...	05/31/2011
7943581	Cell penetrating peptides for intracellular delivery of molecules The present invention concerns cell-penetrating peptides which comprise an amino acid sequence consisting of GLX9WRAX9WRX1LX2RSLX9WX3X4X5X6X7X8(S...	05/17/2011
7910312	Use of acid scavengers for the synthesis of standard length and long-mer polymer arrays 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 activa...	03/22/2011
7901882	Analysis of methylation using nucleic acid arrays 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 meth...	03/08/2011

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Assignee: Affymetrix, Inc.