Patents Assigned to Affymetrix, Inc.
  • Methods for genotyping polymorphisms in humans
    Patent number: 7629164
    Abstract: The invention provides nucleic acid sequences that are complementary, in one embodiment, to a collection of human single nucleotide polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel by, for example, allele specific hybridization. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
    Type: Grant
    Filed: July 13, 2004
    Date of Patent: December 8, 2009
    Assignee: Affymetrix, Inc.
    Inventors: Hajime Matsuzaki, Rui Mei
  • Assays for determining telomere length and repeated sequence copy number
    Publication number: 20090298709
    Abstract: Methods of detecting copy number of a repeated sequence element, including methods of determining telomere length, are provided. The methods can be multiplexed for detection of repeated sequence element copy number on two or more nucleic acid targets simultaneously. Compositions, kits, and systems related to the methods are also described.
    Type: Application
    Filed: May 21, 2009
    Publication date: December 3, 2009
    Applicant: Affymetrix, Inc.
    Inventor: Yunqing Ma
  • Modified Nucleic Acid Probes
    Publication number: 20090286690
    Abstract: Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.
    Type: Application
    Filed: May 20, 2008
    Publication date: November 19, 2009
    Applicant: Affymetrix, INC.
    Inventors: Glenn Hugh McGall, Charles Garrett Miyada, Maureen T. Cronin, Jennifer Dee Tan, Mark S. Chee
  • ARRAY-BASED TRANSLOCATION AND REARRANGEMENT ASSAYS
    Publication number: 20090239764
    Abstract: Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.
    Type: Application
    Filed: March 11, 2009
    Publication date: September 24, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Andrew Sparks, Michael H. Shapero, Glenn K. Fu, Keith W. Jones
  • RESEQUENCING METHODS FOR IDENTIFICATION OF SEQUENCE VARIANTS
    Publication number: 20090233809
    Abstract: Methods for detection of variant alleles are disclosed. In preferred aspects variants are detected by hybridization patterns to arrays of probes that are contain a single mismatch to a reference sequence, thus reducing the number of probes needed for resequencing by hybridization. The target capture method used is Target Amplification by Capture and Ligation (TACL), and is capable of amplifying many thousands of loci together. Mismatch Repair Detection (MRD) is used as an allele enrichment method to efficiently sort variant and non-variant alleles in thousands of loci simultaneously.
    Type: Application
    Filed: March 4, 2009
    Publication date: September 17, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Malek Faham, Jianbiao Zheng
  • Silane Mixtures
    Publication number: 20090215652
    Abstract: 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 synthesis are useful in modulating the active site density and hydrolytic stability of a surface. These compositions are particularly useful in silanating a surface prior to preparation of a polymer array and provide for increased hybridization results.
    Type: Application
    Filed: January 23, 2009
    Publication date: August 27, 2009
    Applicant: Affymetrix, INC.
    Inventors: Glenn H. McGall, Robert G. Kuimemlis
  • PARALLEL PREPARATION OF HIGH FIDELITY PROBES IN AN ARRAY FORMAT
    Publication number: 20090192050
    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: January 28, 2009
    Publication date: July 30, 2009
    Applicant: Affymetrix, INC.
    Inventors: Robert G. Kuimelis, Glenn H. McGall
  • Parallel preparation of high fidelity probes in an array format
    Patent number: 7547775
    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: Grant
    Filed: January 3, 2006
    Date of Patent: June 16, 2009
    Assignee: Affymetrix, Inc.
    Inventors: Robert G. Kuimelis, Glenn H. McGall
  • BIOARRAY CHIP REACTION APPARATUS AND ITS MANUFACTURE
    Publication number: 20090143249
    Abstract: A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
    Type: Application
    Filed: November 5, 2008
    Publication date: June 4, 2009
    Applicant: Affymetrix, INC.
    Inventors: Donald M. Besemer, Virginia W. Goss, James L. Winkler
  • Sequencing of surface immobilized polymers utilizing microfluorescence detection
    Publication number: 20090137419
    Abstract: Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents which specifically recognize terminal monomers are used to label polymers at defined positions on a solid substrate.
    Type: Application
    Filed: December 1, 2008
    Publication date: May 28, 2009
    Applicant: Affymetrix, INC.
    Inventors: William J. Dower, Stephen P.A. Fodor
  • Methods for Genotyping Polymorphisms
    Publication number: 20090131268
    Abstract: The invention provides method for genotyping specific sets of polymorphisms in a single multiplex reaction. The polymorphisms are selected to be of interest in detecting genetic variation that alters individuals' metabolism, distribution, extretion and transport of pharmacological compounds. In preferred aspects the genotyping employs a multiplex hybridization-based assay. In some aspects combinations of methods are employed to allow the combination of polymorphisms to be interrogated. The invention also provides nucleic acid standards for validating the performance of such hybridization-based assays.
    Type: Application
    Filed: September 15, 2008
    Publication date: May 21, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Paul Hardenbol, Jonathan E. Forman, George Karlin-Neumann, Xin Miao
  • Locus specific amplification using array probes
    Publication number: 20090117573
    Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.
    Type: Application
    Filed: September 15, 2008
    Publication date: May 7, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Glenn K. Fu, Michael H. Shapero, Pei-Hua Wang
  • Methods for Identifying DNA Copy Number Changes Using Hidden Markov Model Based Estimations
    Publication number: 20090098547
    Abstract: Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.
    Type: Application
    Filed: June 23, 2008
    Publication date: April 16, 2009
    Applicant: Affymetrix, Inc.
    Inventor: Srinka Ghosh
  • Multiplex PCR
    Patent number: 7510829
    Abstract: Compositions and methods for nucleic acid amplification are provided that minimize the formation and amplification of spurious products, particularly in multiplex amplification reactions. Linear amplification molecules are provided. A first embodiment comprises a first common primer sequence, a first template homology region, a cleavable site, a second common primer sequence and a second template homology region. Methods employing the linear amplification molecules for nucleic acid amplification are also provided. A first embodiment comprises a template-specific hybridization, a linear amplification, a template-specific intramolecular hybridization, a strand cleavage, a second linear amplification and an exponential amplification using common primers.
    Type: Grant
    Filed: November 19, 2002
    Date of Patent: March 31, 2009
    Assignee: Affymetrix, Inc.
    Inventors: Malek Faham, Eugeni Anatolyevich Namsaraev, Thomas Daniel Willis
  • PHOTOCLEAVABLE PROTECTING GROUPS
    Publication number: 20090076295
    Abstract: Novel compounds are provided, which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.
    Type: Application
    Filed: September 19, 2008
    Publication date: March 19, 2009
    Applicant: Affymetrix, INC.
    Inventors: Anthony D. Barone, Glenn H. McGall
  • Methods for Genotyping with Selective Adaptor Ligation
    Publication number: 20090075345
    Abstract: 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 in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. This selective adaptor ligation allows for selective amplification of a subset of the fragments using primers complementary to the adaptor sequence. In another aspect primers that are complementary to a subset of the fragments after adaptor ligation are used for amplification. Amplified fragments may be analyzed to genotype polymorphisms by hybridization to an array of probes that are complementary to target sequences that will be amplified.
    Type: Application
    Filed: November 17, 2008
    Publication date: March 19, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Michael H. Shapero, Keith W. Jones
  • Nucleic acid labeling methods
    Patent number: 7504215
    Abstract: In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3?-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3?-AppN-3?-linker-detectable moiety is used as donor molecule.
    Type: Grant
    Filed: November 4, 2004
    Date of Patent: March 17, 2009
    Assignee: Affymetrix, Inc.
    Inventors: Kyle B. Cole, Vivi Truong, Glenn H. McGall, Anthony D. Barone
  • Substrate preparation process
    Publication number: 20090062148
    Abstract: 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 throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
    Type: Application
    Filed: August 8, 2006
    Publication date: March 5, 2009
    Applicant: Affymetrix, Inc.
    Inventors: Martin Goldberg, Martin Diggelman, Earl Hubbell, Glenn Mcgall, Nam Quoc Ngo, MacDonald Morris, Mel Yamamoto, Jennifer Tan, Richard P. Rava
  • PHOTOACID GENERATORS FOR THE SYNTHESIS OF OLIGO-DNA IN A POLYMER MATRIX
    Publication number: 20090062149
    Abstract: Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
    Type: Application
    Filed: November 3, 2008
    Publication date: March 5, 2009
    Applicant: Affymetrix, INC.
    Inventors: Glenn H. McGall, Andrea Cuppoletti
  • Nucleic Acid Labeling Methods
    Publication number: 20090054258
    Abstract: In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3?-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3?-AppN-3?-linker-detectable moiety is used as donor molecule.
    Type: Application
    Filed: October 22, 2008
    Publication date: February 26, 2009
    Applicant: Affymetrix, Inc
    Inventors: Kyle B. Cole, Vivi Truong, Glenn H. McGall, Anthony D. Barone