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).

  • Publication number: 20160237488
    Abstract: This application discloses methods of producing a DNA strand for sequencing, as well as genetic constructs, libraries, and arrays using DNA strands produced according to these methods. The application also discloses methods of sequencing using the DNA strands, genetic constructs, libraries, and arrays produced. In certain aspects, DNA being sequenced includes a target sequence and at least one adaptor sequence.
    Type: Application
    Filed: February 10, 2016
    Publication date: August 18, 2016
    Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
  • Publication number: 20160222441
    Abstract: The invention relates to novel methods and materials for encoding and decoding information on individual molecules through the use of nano-tags, nano-barcodes, or modifications of a native molecule.
    Type: Application
    Filed: August 27, 2015
    Publication date: August 4, 2016
    Inventors: Radoje Drmanac, Brian Hauser, Joseph Komoski
  • Publication number: 20160168629
    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: Application
    Filed: January 29, 2016
    Publication date: June 16, 2016
    Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
  • Publication number: 20160130647
    Abstract: Novel fluorescent nucleotide analogues are provided herein. Also provided herein are methods of using the nucleotide analogues in sequencing-by-synthesis and signal confinement methods.
    Type: Application
    Filed: October 23, 2015
    Publication date: May 12, 2016
    Inventors: Snezana Drmanac, Handong Li, Radoje Drmanac, Eric Harness, Chongjun Xu
  • Patent number: 9328382
    Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.
    Type: Grant
    Filed: March 11, 2014
    Date of Patent: May 3, 2016
    Assignee: COMPLETE GENOMICS, INC.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Patent number: 9267172
    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: August 12, 2013
    Date of Patent: February 23, 2016
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow
  • Publication number: 20160046985
    Abstract: The present invention provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.
    Type: Application
    Filed: March 17, 2014
    Publication date: February 18, 2016
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Publication number: 20160023180
    Abstract: 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: Application
    Filed: October 7, 2015
    Publication date: January 28, 2016
    Inventor: Radoje Drmanac
  • Publication number: 20160017414
    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: Application
    Filed: May 15, 2015
    Publication date: January 21, 2016
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20150379192
    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: December 31, 2015
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Patent number: 9222132
    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.
    Type: Grant
    Filed: August 25, 2014
    Date of Patent: December 29, 2015
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Publication number: 20150169824
    Abstract: Methods, systems, and apparatuses are provided for creating and using a machine-leaning model to call a base at a position of a nucleic acid based on intensity values measured during a production sequencing run. The model can be trained using training data from training sequencing runs performed earlier. The model is trained using intensity values and assumed sequences that are determined as the correct output. The training data can be filtered to improve accuracy. The training data can be selected in a specific manner to be representative of the type of organism to be sequenced. The model can be trained to use intensity signals from multiple cycles and from neighboring nucleic acids to improve accuracy in the base calls.
    Type: Application
    Filed: December 15, 2014
    Publication date: June 18, 2015
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac
  • Publication number: 20150159204
    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: Application
    Filed: December 24, 2014
    Publication date: June 11, 2015
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Patent number: 9023769
    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: November 30, 2010
    Date of Patent: May 5, 2015
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Fredrik Dahl, Evan Hurowitz, Fredrie Dahl
  • Publication number: 20150094961
    Abstract: Long fragment read techniques can be used to identify deletions and resolve base calls by utilizing shared labels (e.g., shared aliquots) of a read with any reads corresponding to heterozygous loci (hets) of a haplotype. For example, the linking of a locus to a haplotype of multiple hets can increase the reads available at the locus for determining a base call for a particular haplotype. For a hemizygous deletion, a region can be linked to one or more hets, and the labels for a particular haplotype can be used to identify which reads in the region correspond to which haplotype. In this manner, since the reads for a particular haplotype can be identified, a hemizygous deletion can be determined. Further, a phasing rate of pulses can be used to identify large deletions. A deletion can be identified with the phasing rate is sufficiently low, and other criteria can be used.
    Type: Application
    Filed: October 1, 2014
    Publication date: April 2, 2015
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac, Brock A. Peters
  • Publication number: 20150057947
    Abstract: Techniques perform de novo assembly. The assembly can use labels that indicate origins of the nucleic acid molecules. For example, a representative set of labels identified from initial reads that overlap with a seed can be used. Mate pair information can be used. A sequence read that aligns to an end of a contig can lead to using the other sequence read of a mate pair, and the other sequence read can be used to determine which branch to use to extend, e.g., in an external cloud or helper contig. A kmer index can include labels indicating an origin of each of the nucleic acid molecules that include each kmer, memory addresses of the reads that correspond to each kmer in the index, and a position in each of the mate pairs that includes the kmer. Haploid seeds can also be determined using polymorphic loci identified in a population.
    Type: Application
    Filed: August 25, 2014
    Publication date: February 26, 2015
    Inventors: Radoje Drmanac, Bahram Ghaffarzadeh Kermani
  • Patent number: 8951731
    Abstract: 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: Grant
    Filed: October 15, 2008
    Date of Patent: February 10, 2015
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Snezana Drmanac
  • Publication number: 20150038345
    Abstract: 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: Application
    Filed: July 18, 2014
    Publication date: February 5, 2015
    Inventor: Radoje Drmanac
  • Publication number: 20140378321
    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.
    Type: Application
    Filed: August 25, 2014
    Publication date: December 25, 2014
    Inventor: Radoje Drmanac
  • Publication number: 20140356865
    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.
    Type: Application
    Filed: December 2, 2013
    Publication date: December 4, 2014
    Applicant: Complete Genomics, Inc.
    Inventor: Radoje Drmanac