Patents by Inventor Radoje Drmanac

Radoje Drmanac 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).

  • Patent number: 8609335
    Abstract: 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: Grant
    Filed: May 2, 2011
    Date of Patent: December 17, 2013
    Assignee: Callida Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
  • Publication number: 20130316920
    Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.
    Type: Application
    Filed: August 8, 2013
    Publication date: November 28, 2013
    Applicant: Callida Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 8592150
    Abstract: The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.
    Type: Grant
    Filed: June 15, 2010
    Date of Patent: November 26, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
  • Publication number: 20130310264
    Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.
    Type: Application
    Filed: July 30, 2013
    Publication date: November 21, 2013
    Applicant: Callida Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 8551702
    Abstract: 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: Grant
    Filed: December 15, 2008
    Date of Patent: October 8, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Patent number: 8518640
    Abstract: 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: Grant
    Filed: October 5, 2009
    Date of Patent: August 27, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Patent number: 8445197
    Abstract: 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: Grant
    Filed: October 31, 2007
    Date of Patent: May 21, 2013
    Assignee: Callida Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Patent number: 8445194
    Abstract: 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: Grant
    Filed: June 13, 2006
    Date of Patent: May 21, 2013
    Assignee: Callida Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20130124100
    Abstract: The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process.
    Type: Application
    Filed: April 13, 2012
    Publication date: May 16, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Patent number: 8440397
    Abstract: 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: Grant
    Filed: October 31, 2007
    Date of Patent: May 14, 2013
    Assignee: Callida Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
  • Patent number: 8415099
    Abstract: 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: Grant
    Filed: December 5, 2008
    Date of Patent: April 9, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Publication number: 20130059740
    Abstract: The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.
    Type: Application
    Filed: April 16, 2012
    Publication date: March 7, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Publication number: 20130054508
    Abstract: Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength.
    Type: Application
    Filed: August 22, 2012
    Publication date: February 28, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac
  • Publication number: 20130054151
    Abstract: Haplotypes of one or more portions of a chromosome of an organism from sequencing information of DNA or RNA fragments can be determined. Heterozygous loci (hets) can be used to determine haplotypes. One allele on a first het can be connected (likely to be on the same haplotype) to an allele on a second het, thereby defining a particular orientation between the hets. Haplotypes can be assembled through these connections. Errors can be identified through redundant connection information, particularly using a confidence value (strength) for a particular connection. The connections among a set of hets can be analyzed to determine likely haplotypes for that set, e.g., an optimal tree of a graph containing the hets. Furthermore, haplotypes of different contiguous sections (contig) of the chromosome can be matched to a particular chromosome copy (e.g., to a particular parental copy). Thus, the phase of an entire chromosome can be determined.
    Type: Application
    Filed: August 22, 2012
    Publication date: February 28, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac
  • Patent number: 8298768
    Abstract: Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure.
    Type: Grant
    Filed: December 1, 2008
    Date of Patent: October 30, 2012
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Clifford Reid
  • Publication number: 20120122699
    Abstract: 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. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.
    Type: Application
    Filed: February 4, 2011
    Publication date: May 17, 2012
    Applicant: COMPLETE GENOMICS, INC.
    Inventors: Fredrik DAHL, Radoje Drmanac, Andrew Sparks
  • Publication number: 20120122721
    Abstract: Methods are provided for carrying out nucleic acid analysis, including sequence identification, employing voltage and/or controlled electric charge to enhance operation. A device comprises substrates for nucleic acid analysis, a first electrically conductive layer, a first electrically insulative layer of dielectric material on the first conductive layer, a second electrically conductive layer disposed upon the first insulative layer in a pattern to define discrete attachment sites for macromolecules on the first insulative layer, the second conductive layer provided with means for resisting affinity for the macromolecules to impede their attachment to sites on the second conductive layer, and terminals for the first and second conductive layers for applying a voltage pattern between the first and the second conductive layers to control affinity between the macromolecules and the discrete attachment sites.
    Type: Application
    Filed: December 27, 2011
    Publication date: May 17, 2012
    Applicant: Complete Genomics, Inc.
    Inventors: Andres Fernandez, Bryan Staker, Radoje Drmanac
  • Publication number: 20120100534
    Abstract: 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: Application
    Filed: December 5, 2008
    Publication date: April 26, 2012
    Applicant: COMPLETE GENOMICS, INC.
    Inventors: Radoje Drmanac, Andrew Sparks, Fredrik Dahl, Matthew J. Callow, Clifford Reid
  • Patent number: 8133719
    Abstract: 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: Grant
    Filed: October 31, 2007
    Date of Patent: March 13, 2012
    Assignee: Callida Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20110319281
    Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.
    Type: Application
    Filed: January 31, 2011
    Publication date: December 29, 2011
    Applicant: CALLIDA GENOMICS, INC.
    Inventor: Radoje DRMANAC