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Affymetrix, Inc. Patents
Assignee:
Affymetrix, Inc.
Address:
Santa Clara, CA
No. of patents:
436
Patents:


1 2 3 4 5 6 7 8 9










Patent Number Title Of Patent Date Issued
H2136 Nucleic acids encoding G protein-coupled receptors December 6, 2005
The present invention provides novel GPCR polynucleotides, GPCR polypeptides, gene delivery vehicles comprising and/or expressing the GPCR polynucleotides, antibodies and fragments capable of specifically binding to the GPCR polypeptides, and modulators of the GPCR. Also provided by the
D430024 Chip packaging device August 29, 2000
8586312 Methods of using an array of pooled probes in genetic analysis November 19, 2013
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 f
8288522 Detection of nucleic acids through amplification of surrogate nucleic acids October 16, 2012
Methods for detecting and optionally quantitating one or more target nucleic acids are provided, in which a surrogate nucleic acid is captured to each target nucleic acid, amplified, and detected. Compositions, kit, and systems related to the methods are also described.
8273304 Analytical biochemistry system with robotically carried bioarray September 25, 2012
An analytical biochemistry system featuring a substrate with reactants immobilized thereon at fixed, known locations, a holder supporting the substrate and a manipulator for transporting the holder to a fixed sample and to an inspection station. The reactants are binding agents for a
8258199 Photoacid generators for the synthesis of oligo-DNA in a polymer matrix September 4, 2012
Compounds represented by the following structural formulas can be used as photoacid generators: ##STR00001## Such compounds are useful, for example, in fabricating arrays of polymers.
8242081 Cell penetrating peptides for intracellular delivery of molecules August 14, 2012
The present invention concerns cell-penetrating peptides which comprise an amino acid sequence consisting of GLX.sub.9RALX.sub.9RX.sub.1LX.sub.2RSLX.sub.9X.sub.3X.sub.4X.sub.5X.sub.6- X.sub.7X.sub.8 (SEQ ID No: 1), wherein X.sub.1 is A, L or G, X.sub.2 is W or none, X.sub.3 is R or K,
8236493 Methods of enzymatic discrimination enhancement and surface-bound double-stranded DNA August 7, 2012
Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to
8233735 Methods and apparatus for detection of fluorescently labeled materials July 31, 2012
Fluorescently marked targets bind to a substrate 230 synthesized with polymer sequences at known locations. The targets are detected by exposing selected regions of the substrate 230 to light from a light source 100 and detecting the photons from the light fluoresced therefrom, and r
8227253 Oxide layers on silicon substrates for effective confocal laser microscopy July 24, 2012
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 oxide coating to pro
8224586 System, method, and computer product for exon array analysis July 17, 2012
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 iterativel
8208710 System, method, and product for scanning of biological materials June 26, 2012
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
8204695 Techniques for identifying, confirming, mapping, and categorizing polymers June 19, 2012
Systems and methods for identifying, confirming, mapping, and categorizing sample polymers, such as nucleic acid sequences, are provided. An estimation of the fraction of first and second polymers in a sample of polymers can be calculated by inputting a first hybridization value indi
8200440 System, method, and computer software product for genotype determination using probe array data June 12, 2012
An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in
8190373 Methods for identifying DNA copy number changes May 29, 2012
Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disc
8178278 Miniaturized microparticles May 15, 2012
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 segments, wherein the
8170808 Methods and computer software for detecting splice variants May 1, 2012
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 splicing events.
8168368 Miniaturized microparticles May 1, 2012
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 first portion of a code
8133987 Primer array synthesis and validation March 13, 2012
Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.
8133667 Methods for genotyping with selective adaptor ligation March 13, 2012
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
8129168 Recombinant colwellia psychrerythraea alkaline phosphatase and uses thereof March 6, 2012
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 psychreryt
8114978 Methods for genotyping selected polymorphism February 14, 2012
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 differen
8114681 Highly multiplexed particle-based assays February 14, 2012
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.
8114584 Antireflective coatings for high-resolution photolithographic synthesis of DNA array February 14, 2012
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
8105821 Silane mixtures January 31, 2012
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 supporting polymer sy
8101737 Parallel preparation of high fidelity probes in an array format January 24, 2012
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 10.sup.1 to about 10.sup.5 different sequences, generally between 25-160 bases in l
8095323 Polymorphism detection January 10, 2012
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 complementary to target nucleic
8088555 Multiple step printing methods for microbarcodes January 3, 2012
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 microparticles, each microparticle
8084197 Identification of molecular sequence signatures and methods involving the same December 27, 2011
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 useful data about
8076083 Screening methods involving the detection of short-lived proteins December 13, 2011
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
8076072 Nucleic acid labeling compounds December 13, 2011
Nucleic acid labeling compounds including the following are disclosed: ##STR00001## These compounds are useful for attaching a detectable label to a nucleic acid.
8075852 System and method for bubble removal December 13, 2011
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.
8071759 Water soluble cholesterol derivatives December 6, 2011
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 derivatives disclose
8067578 Substrate preparation process November 29, 2011
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 throug
8062844 Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays November 22, 2011
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 activatable deprotecting
8055098 System, method, and product for imaging probe arrays with small feature sizes November 8, 2011
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
8034912 Parallel preparation of high fidelity probes in an array format October 11, 2011
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 10.sup.1 to about 10.sup.5 different sequences, generally between 25-160 bases in l
8029999 Complexity management of genomic DNA October 4, 2011
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 furt
8029997 Methods of analysis of allelic imbalance October 4, 2011
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 m
8026057 Nucleic acid labeling compounds September 27, 2011
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,
8009889 Feature intensity reconstruction of biological probe array August 30, 2011
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
8007267 System and method for making lab card by embossing August 30, 2011
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.
7993883 Complexity management of genomic DNA August 9, 2011
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
7992098 System, method, and computer software product for linked window interfaces August 2, 2011
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 one or more charact
7991564 Methods for high throughput genotyping August 2, 2011
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 an
7991560 System, method, and computer software for the presentation and storage of analysis results August 2, 2011
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 expres
7985547 Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping July 26, 2011
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 sequences located adjacent
7983467 System, method, and product for scanning of biological materials July 19, 2011
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
7964654 Photoacid generators for the synthesis of oligo-DNA in a polymer matrix June 21, 2011
Compounds represented by the following structural formulas can be used as photoacid generators: ##STR00001## Such compounds are useful, for example, in fabricating arrays of polymers.
7962291 Methods and computer software for detecting splice variants June 14, 2011
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 splicing events.
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