Patents by Inventor Matthew J. Callow
Matthew J. Callow has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20180002735Abstract: 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: March 13, 2017Publication date: January 4, 2018Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow
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Publication number: 20170226577Abstract: 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: September 16, 2016Publication date: August 10, 2017Applicant: Complete Genomics Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Publication number: 20170175184Abstract: The invention relates to an automated method for high-throughput DNA sequencing from high density DNA arrays by (a) initiating a first sequencing reaction on a first high density DNA array; and imaging said first high density DNA array using a detector, and (b) initiating a first sequencing reaction on a second high density DNA array; and imaging said second high density DNA array using the detector, wherein the first sequencing reaction in (a) is initiated before the first sequencing reaction in (b) is initiated such that the sequencing reactions in (a) and (b) are staggered. By using asynchronous sequencing reactions and imaging two separate arrays using one detector, imaging can be carried out on one array while sequencing reactions are carried out on one the other, substrate, the other substrate is imaged, reducing the idle time of the imaging system.Type: ApplicationFiled: February 25, 2017Publication date: June 22, 2017Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 9650673Abstract: Random arrays of single molecules are provided for carrying out large scale analyzes, 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: GrantFiled: May 15, 2015Date of Patent: May 16, 2017Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20160194686Abstract: 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: December 7, 2015Publication date: July 7, 2016Inventors: Radoje T. Drmanac, Matthew J. Callow
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Publication number: 20160168629Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: ApplicationFiled: January 29, 2016Publication date: June 16, 2016Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 9267172Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.Type: GrantFiled: August 12, 2013Date of Patent: February 23, 2016Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow
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Publication number: 20160017414Abstract: 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: May 15, 2015Publication date: January 21, 2016Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20150159204Abstract: 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: December 24, 2014Publication date: June 11, 2015Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20140213461Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.Type: ApplicationFiled: August 12, 2013Publication date: July 31, 2014Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow
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Publication number: 20140073513Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: ApplicationFiled: November 13, 2013Publication date: March 13, 2014Applicant: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 8609335Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: GrantFiled: May 2, 2011Date of Patent: December 17, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 8445197Abstract: 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: GrantFiled: October 31, 2007Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8445194Abstract: 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: GrantFiled: June 13, 2006Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8445196Abstract: 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: GrantFiled: October 31, 2007Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8440397Abstract: 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: GrantFiled: October 31, 2007Date of Patent: May 14, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Publication number: 20120100534Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.Type: ApplicationFiled: December 5, 2008Publication date: April 26, 2012Applicant: COMPLETE GENOMICS, INC.Inventors: Radoje Drmanac, Andrew Sparks, Fredrik Dahl, Matthew J. Callow, Clifford Reid
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Patent number: 8133719Abstract: 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: GrantFiled: October 31, 2007Date of Patent: March 13, 2012Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20110281738Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: ApplicationFiled: May 2, 2011Publication date: November 17, 2011Applicant: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 7960104Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.Type: GrantFiled: September 29, 2006Date of Patent: June 14, 2011Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung