Patents Assigned to Complete Genomics AS
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Publication number: 20090155781Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: June 18, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090155793Abstract: A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis.Type: ApplicationFiled: October 30, 2008Publication date: June 18, 2009Applicant: Complete Genomics, Inc.Inventor: Arnold Oliphant
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Publication number: 20090143235Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.Type: ApplicationFiled: October 29, 2007Publication date: June 4, 2009Applicant: COMPLETE GENOMICS, INC.Inventors: Radoje Drmanac, Matthew Callow
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Publication number: 20090137414Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: October 31, 2007Publication date: May 28, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20090137404Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: October 31, 2007Publication date: May 28, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20090118488Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: May 7, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090117006Abstract: Substrates are provided for use in the detection, identification and analysis of biologic or chemical samples that are labeled with a fluorescent label, in which the plane of maximum fluorescence is displaced from a reflective substrate surface so that the intensity maximum of the standing wave interference pattern of incident and reflected probe radiation is enhanced. The format of the substrates includes substantially planar surfaces as well as substrates with introduced variations to the substrate surface, e.g., depressions, wells, pedestals and the like, disposed in arrays or other similar structures such that one or more fluorophore-comprising objects can be attached thereto.Type: ApplicationFiled: October 30, 2008Publication date: May 7, 2009Applicant: Complete Genomics, Inc.Inventor: Andres Fernandez
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Publication number: 20090111115Abstract: The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information.Type: ApplicationFiled: October 15, 2008Publication date: April 30, 2009Applicant: COMPLETE GENOMICS, INC.Inventors: Radoje Drmanac, Snezana Drmanac
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Publication number: 20090111705Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing selective capture of defined molecules. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.Type: ApplicationFiled: November 2, 2007Publication date: April 30, 2009Applicant: Complete Genomics, Inc.Inventors: Andrew Sparks, Arnold Oliphant, George Yeung
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Publication number: 20090111706Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing amplification procedures. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.Type: ApplicationFiled: November 2, 2007Publication date: April 30, 2009Applicant: Complete Genomics, Inc.Inventors: Andrew Sparks, Arnold Oliphant, Radoje Drmanac
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Publication number: 20090105961Abstract: The present invention provides methods for determining a base probability in a target nucleic acid within an experimental data set. The methods of the invention provide specific methods of improving accuracy of base calling for experimental sequencing data compared to conventional methods. The experimental base values used in the methods of the present invention provide relative base probabilities within an experimental data set that are robust and uniformly optimal regardless of the experimental conditions.Type: ApplicationFiled: November 9, 2007Publication date: April 23, 2009Applicant: COMPLETE GENOMICS, INC.Inventor: Radoje Drmanac
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Publication number: 20090075343Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another using nicking reactions. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.Type: ApplicationFiled: November 2, 2007Publication date: March 19, 2009Applicant: COMPLETE GENOMICS, INC.Inventors: Andrew Sparks, Steven Huang, Radoje Drmanac, Arnold Oliphant
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Publication number: 20090036316Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: ApplicationFiled: October 31, 2007Publication date: February 5, 2009Applicant: Complete Genomics, Inc.Inventor: Radoje T. Drmanac
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Publication number: 20090011416Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: ApplicationFiled: October 31, 2007Publication date: January 8, 2009Applicant: Complete Genomics, Inc.Inventor: Radoje T. Drmanac
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Publication number: 20090011943Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: January 8, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090005252Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: January 1, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Publication number: 20090005259Abstract: The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.Type: ApplicationFiled: October 31, 2007Publication date: January 1, 2009Applicant: Complete Genomics, Inc.Inventor: Radoje T. Drmanac
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Publication number: 20080318796Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.Type: ApplicationFiled: October 29, 2007Publication date: December 25, 2008Applicant: Complete Genomics,Inc.Inventors: Radoje T. DRMANAC, Matthew Callow
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Publication number: 20080234136Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: October 31, 2007Publication date: September 25, 2008Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20080221832Abstract: Aspects of the various embodiments of the invention relate generally to computing relative base value probabilities using discrete experimental base values to calculate distributions of relative base probabilities. This information can be used with associated experimental measurements to increase the accuracy of the data analysis.Type: ApplicationFiled: November 9, 2007Publication date: September 11, 2008Applicant: COMPLETE GENOMICS, INC.Inventor: Radoje Drmanac