Patents Represented by Attorney Deana A. Arnold
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Patent number: 8309330Abstract: Methods, substrates, and systems for diagnostic sequencing are provided. Small circles of nucleic acids from about 10 bases to about 200 bases can be sequenced, for example using template dependent sequencing by synthesis. The use of small circles of nucleic acids allows for repeated sequencing of the same portions of the nucleic acid, providing for higher accuracy sequence determinations.Type: GrantFiled: February 1, 2011Date of Patent: November 13, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
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Patent number: 8274040Abstract: This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.Type: GrantFiled: October 17, 2011Date of Patent: September 25, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foquet, Jonas Korlach, Hovig Bayandorian
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Patent number: 8252910Abstract: Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.Type: GrantFiled: November 18, 2009Date of Patent: August 28, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Jonas Korlach, Jeffrey Wegener
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Patent number: 8236499Abstract: Provided are methods and compositions for the production of linear single-stranded nucleic acids, which can be used as templates in high-throughput sequencing systems. Also provided are methods and compositions for the production of closed single-stranded nucleic acid loops, which can be used as templates in high-throughput sequencing systems.Type: GrantFiled: March 27, 2009Date of Patent: August 7, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Pranav Patel, Keith Bjornson, Kevin Travers, Cheryl Heiner
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Patent number: 8207509Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.Type: GrantFiled: September 26, 2011Date of Patent: June 26, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Paul Lundquist, Stephen Turner
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Patent number: 8198023Abstract: The present invention provides compositions and methods for reducing steric hindrance in the product of nucleic acid polymerase reaction. Methods and compositions of the invention encompass application of exonucleases, endonucleases, and uracil-DNA glycosylases to a nucleic acid polymerase reaction such that newly formed nucleic acid strands are modified (e.g., cleaved) while the polymerase reaction continues to proceed.Type: GrantFiled: August 4, 2009Date of Patent: June 12, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Congcong Ma, Paul Wyatt
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Patent number: 8153375Abstract: Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.Type: GrantFiled: March 27, 2009Date of Patent: April 10, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
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Patent number: 8143030Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.Type: GrantFiled: March 27, 2009Date of Patent: March 27, 2012Assignee: Pacific Biosciences of California, Inc.Inventors: Kenneth Mark Maxham, Jon Sorenson, John Eid, Patrick Marks, Kevin Travers
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Patent number: 8071346Abstract: Compositions, devices, systems and methods for reducing and/or preventing photodamage of one or more reactants in illuminated analytical reactions by one or more of incorporating photodamage mitigating agents within the reaction mixture and/or interrogating different observation regions of the reaction mixture for a period that is less than a photodamage threshold period.Type: GrantFiled: October 31, 2007Date of Patent: December 6, 2011Assignee: Pacific Bioscience of California, Inc.Inventors: John Eid, Devon Murphy, Geoffrey Otto, Stephen Turner
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Patent number: 8053742Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.Type: GrantFiled: October 1, 2010Date of Patent: November 8, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: Paul Lundquist, Stephen Turner
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Patent number: 7998717Abstract: Compositions, devices, systems and methods for reducing and/or preventing photodamage of one or more reactants in illuminated analytical reactions by one or more of incorporating photodamage mitigating agents within the reaction mixture and/or interrogating different observation regions of the reaction mixture for a period that is less than a photodamage threshold period.Type: GrantFiled: December 2, 2005Date of Patent: August 16, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: John Eid, Devon Murphy, Geoffrey Otto, Stephen Turner
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Patent number: 7993895Abstract: Compositions, devices, systems and methods for reducing and/or preventing photodamage of one or more reactants in illuminated analytical reactions by one or more of incorporating photodamage mitigating agents within the reaction mixture and/or interrogating different observation regions of the reaction mixture for a period that is less than a photodamage threshold period.Type: GrantFiled: December 1, 2006Date of Patent: August 9, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: John Eid, Devon Murphy, Geoffrey Otto, Stephen Turner
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Patent number: 7906284Abstract: The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.Type: GrantFiled: October 26, 2007Date of Patent: March 15, 2011Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jonas Korlach
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Patent number: 7838847Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.Type: GrantFiled: October 31, 2007Date of Patent: November 23, 2010Assignee: Pacific Biosciences of California, Inc.Inventors: Paul Lundquist, Stephen Turner
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Patent number: 7834329Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.Type: GrantFiled: October 31, 2007Date of Patent: November 16, 2010Assignee: Pacific Biosciences of California, Inc.Inventors: Paul Lundquist, Stephen Turner
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Patent number: 7820983Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyzes, cellular analyzes and other molecular analyzes.Type: GrantFiled: August 31, 2007Date of Patent: October 26, 2010Assignee: Pacific Biosciences of California, Inc.Inventors: Paul Lundquist, Stephen Turner
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Patent number: 7767394Abstract: The present invention relates to preparation of nucleotide compositions and uses thereof for conducting nucleic acid analyses. The compositions and methods embodied in the present invention are particularly useful for nucleic acid analyses that require high-resolution detection of labeled nucleotides or labeled nucleic acid targets.Type: GrantFiled: February 9, 2006Date of Patent: August 3, 2010Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jonas Korlach
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Patent number: 7476503Abstract: The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.Type: GrantFiled: September 16, 2005Date of Patent: January 13, 2009Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jonas Korlach
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Patent number: 7427480Abstract: Improved life sciences business systems and methods are disclosed. One or more genomes are scanned for single nucleotide polymorphisms. The polymorphisms are assigned to haplotype blocks, and representative SNPs from the haplotype blocks are used in association studies for pharmaceutical and diagnostic developments.Type: GrantFiled: July 13, 2005Date of Patent: September 23, 2008Assignee: Perlegen Sciences, Inc.Inventors: Bradley A Margus, David R Cox
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Patent number: 7335474Abstract: Methods and systems for identifying biological marker-placebo effect correlations are provided. Clinical trial design and data analysis of clinical trial data is modified to accommodate marker-placebo effect correlations.Type: GrantFiled: September 13, 2004Date of Patent: February 26, 2008Assignee: Perlegen Sciences, Inc.Inventors: Bradley Margus, David Cox, Jesse Hsu