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: 10227647
    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: Grant
    Filed: February 10, 2016
    Date of Patent: March 12, 2019
    Assignee: Complete Genomics, Inc.
    Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
  • Patent number: 10190162
    Abstract: Novel fluorescent nucleotide analogs are provided herein. Also provided herein are methods of using the nucleotide analogs in sequencing-by-synthesis and signal confinement methods.
    Type: Grant
    Filed: October 23, 2015
    Date of Patent: January 29, 2019
    Assignee: Complete Genomics, Inc.
    Inventors: Snezana Drmanac, Handong Li, Radoje Drmanac, Eric Harness, Chongjun Xu
  • Publication number: 20190010542
    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: Application
    Filed: March 29, 2018
    Publication date: January 10, 2019
    Applicant: Complete Genomics Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
  • Publication number: 20190002969
    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 26, 2018
    Publication date: January 3, 2019
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Publication number: 20190002970
    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: Application
    Filed: May 30, 2018
    Publication date: January 3, 2019
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Publication number: 20180355421
    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: December 13, 2018
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Publication number: 20180346980
    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 3, 2018
    Publication date: December 6, 2018
    Applicant: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 10125392
    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: Grant
    Filed: August 20, 2013
    Date of Patent: November 13, 2018
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Publication number: 20180291371
    Abstract: Provided are a method for constructing a nucleic acid single-stranded cyclic library and the reagents used therein. By the combination of interruption via a transposase with a restricted nick translation reaction, the method realizes a simple and rapid nucleic acid single-stranded cyclic library construction.
    Type: Application
    Filed: November 26, 2014
    Publication date: October 11, 2018
    Applicant: BGI Shenzhen Co., Ltd.
    Inventors: Chunyu Geng, Ruoying Chen, Yuan Jiang, Xia Zhao, Rongrong Guo, Lingyu He, Yaqiao Li, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Patent number: 10068053
    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: Grant
    Filed: December 15, 2014
    Date of Patent: September 4, 2018
    Assignee: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac
  • Publication number: 20180245132
    Abstract: Provided herein are compositions, methods, and kits for enriching for one or more nucleic acid sequences of interest in a sample. The methods include providing a circular ligase, one or more 5? hook probes and/or one or more 3? hook probes and contacting the sample comprising the nucleic acids with the circular ligase and one or more 5? hook probes and/or one or more 3? hook probes under conditions to allow the hook probes to selectively bind to the one or more nucleic acid sequences of interest, and under conditions to form one or more hook products, each hook product comprising the hook probes and the one or more nucleic acid sequences of interest.
    Type: Application
    Filed: February 23, 2018
    Publication date: August 30, 2018
    Applicant: Complete Genomics, Inc.
    Inventors: Yuan Jiang, Radoje Drmanac
  • Publication number: 20180223358
    Abstract: The invention provides compositions and methods for sequencing nucleic acids and other applications. In sequencing by synthesis, unlabeled reversible terminators are incorporated by a polymerase in each cycle, then labeled after incorporation by binding to the reversible terminator a directly or indirectly labeled antibody or other affinity reagent.
    Type: Application
    Filed: January 4, 2018
    Publication date: August 9, 2018
    Inventors: Radoje Drmanac, Snezana Drmanac, Handong Li, Xun Xu, Matthew J. Callow, Leon Eckhardt, Naibo Yang, Quan Ding
  • Patent number: 10023910
    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: April 22, 2016
    Date of Patent: July 17, 2018
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Publication number: 20180180567
    Abstract: Provided is a microwell electrode, comprising one or more first electrodes (301); one or more second electrodes (303) each arranged opposite to one first electrode (301), wherein a channel (601) is provided between each first electrode and the second electrode opposite thereto, and the channel (601) has at least one end in communication with a chamber; and one or more guiding electrodes (501) located in the chamber (401). The microwell electrode electrode can sensitively detect a signal and improve the read length of a sequencer greatly. The invention further relates to a method for manufacturing the micro-porous electrode, a microwell electrode array, a sensor chip, a sequencing system, and a method for analysis of a chemical substance and a nucleic acid molecule based on the microwell electrode.
    Type: Application
    Filed: June 23, 2016
    Publication date: June 28, 2018
    Inventors: Handong LI, Jianxun LIN, Quanxin YUN, Shaohua XIANG, Radoje DRMANAC, Snezana DRMANAC, Yongwei ZHANG
  • Patent number: 9944984
    Abstract: A high density DNA array comprising a patterned surface, said surface comprising a pattern of small DNA binding regions separated by a non-DNA binding surface, wherein the DNA binding regions comprise DNA capture chemistry and the non-DNA binding surface does not have the DNA capture chemistry wherein more than 50% of the DNA binding regions in the array have single informative DNA species.
    Type: Grant
    Filed: February 6, 2017
    Date of Patent: April 17, 2018
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20180051333
    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: September 26, 2017
    Publication date: February 22, 2018
    Inventor: Radoje Drmanac
  • Publication number: 20180044668
    Abstract: The present invention provides a novel method for ligating an adapter to a target polynucleotide and methods of generating a library of mate-pair polynucleotide constructs that employ such a ligation method. Libraries and arrays comprising mate-pair polynucleotide constructs, and methods of sequencing libraries and arrays comprising mate-pair polynucleotide constructs, are also provided.
    Type: Application
    Filed: October 13, 2015
    Publication date: February 15, 2018
    Applicant: BGI SHENZHEN CO., LIMITED
    Inventors: Yuan JIANG, Radoje DRMANAC, Evan HUROWITZ, Andrei ALEXEEV, Xia ZHAO, Jie RUAN
  • Publication number: 20180030532
    Abstract: Provided are an adaptor element in a bubble shape, a method of constructing a sequencing library with such an adapter element. The adaptor element is a hybrid formed with a long-chain nucleic acid A and a short-chain nucleic acid B. The hybrid is in the bubble shape with paired regions at two terminals and a non-paired region in the middle.
    Type: Application
    Filed: November 21, 2014
    Publication date: February 1, 2018
    Inventors: Yuan Jiang, Xia Zhao, Qiaoling Li, Shengmao Liu, Bo Wang, Li Chen, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Publication number: 20180016628
    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: February 7, 2017
    Publication date: January 18, 2018
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
  • Publication number: 20170356039
    Abstract: Provided are a vesicular linker and a single-chain cyclic library constructed by using the linker. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantages of high throughput sequencing, high accuracy and simple operations.
    Type: Application
    Filed: November 21, 2014
    Publication date: December 14, 2017
    Inventors: Yuan Jiang, Jing Guo, Xiaojun Ji, Chunyu Geng, Kai Tian, Xia Zhao, Huaiqian Xu, Wenwei Zhang, Hui Jiang, Radoje Drmanac