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: 10726942
    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: Grant
    Filed: August 25, 2014
    Date of Patent: July 28, 2020
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Bahram Ghaffarzadeh Kermani
  • Patent number: 10662473
    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 3, 2018
    Date of Patent: May 26, 2020
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Publication number: 20200115748
    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.
    Type: Application
    Filed: May 29, 2019
    Publication date: April 16, 2020
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20200080140
    Abstract: Provided are a vesicular adaptor and a single-chain cyclic library constructed by using the adaptor. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantage of high throughput sequencing, high accuracy and simple operations.
    Type: Application
    Filed: September 19, 2019
    Publication date: March 12, 2020
    Inventors: Yuan Jiang, Jing Guo, Xiaojun Ji, Chunyu Geng, Kai Tian, Xia Zhao, Huaiqian Xu, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Patent number: 10557166
    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: Grant
    Filed: March 17, 2014
    Date of Patent: February 11, 2020
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Patent number: 10544451
    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: Grant
    Filed: November 21, 2014
    Date of Patent: January 28, 2020
    Assignee: MGI TECH CO., LTD.
    Inventors: Yuan Jiang, Jing Guo, Xiaojun Ji, Chunyu Geng, Kai Tian, Xia Zhao, Huaiqian Xu, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Patent number: 10494630
    Abstract: Provided is a linker element and a method of using the linker element to construct a sequencing library, wherein the linker element consists of a linker A and a linker B, the linker A is obtained through the complementary pairing of a long nucleic acid strand and a short nucleic acid strand, the 5? end of the long strand has a phosphoric acid modification, and the 3? end of the short strand has an enclosed modification, with enzyme sites in the short strand; and the linker B is a nucleic acid single strand, and the 3? end thereof can be in a complementary pairing with the 5? end of the long strand of the linker A. Using the linker element of the present invention for constructing a sequencing library ensures the linking directionality of the linkers while solving the problems of fragment interlinking, linker self-linking and low linking efficiency, and reducing the purification reaction between steps, shortening the linking time and reducing costs.
    Type: Grant
    Filed: October 14, 2014
    Date of Patent: December 3, 2019
    Assignee: MGI TECH CO., LTD.
    Inventors: Yuan Jiang, Chunyu Geng, Xia Zhao, Shujin Fu, Lingyu He, Yaqiao Li, Xiaoshan Su, Fanzi Wu, Wenwei Zhang, Hui Jiang, Andrei Alexeev, Radoje Drmanac
  • Patent number: 10479991
    Abstract: A method and reagent for constructing a nucleic acid double-linker single-strand cyclic library.
    Type: Grant
    Filed: November 26, 2014
    Date of Patent: November 19, 2019
    Assignee: MGI TECH CO., LTD
    Inventors: Yuan Jiang, Qiaoling Li, Andrei Alexeev, Evan Hurowitz, Xia Zhao, Tong Wang, Chao Dong, Dong Li, Radoje Drmanac, Wenwei Zhang, Hui Jiang
  • Patent number: 10468121
    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: Grant
    Filed: October 1, 2014
    Date of Patent: November 5, 2019
    Assignee: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac, Brock A. Peters
  • Publication number: 20190323079
    Abstract: The present disclosure provided methods and compositions for nucleic acid sequencing. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and using two imaging events per sequencing cycle.
    Type: Application
    Filed: May 17, 2019
    Publication date: October 24, 2019
    Inventor: Radoje Drmanac
  • Publication number: 20190316190
    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: November 13, 2018
    Publication date: October 17, 2019
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
  • Publication number: 20190271037
    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: March 8, 2019
    Publication date: September 5, 2019
    Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
  • Patent number: 10351848
    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: Grant
    Filed: November 26, 2014
    Date of Patent: July 16, 2019
    Assignee: MGI TECH 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: 10351909
    Abstract: 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: Grant
    Filed: February 25, 2017
    Date of Patent: July 16, 2019
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Patent number: 10316356
    Abstract: Provided is a method of constructing a sequencing library using an adaptor element in a bubble shape. The bubble-shaped adaptor is ligated to a DNA fragment respectively at the 3?-terminal and the 5?-terminal i.e., two bubble-shaped adaptors with same sequences are ligated in one step. The bubble-shaped adaptor-ligated product is then amplified with a primer complementary to the 3?-terminal of the long-chain nucleic acid of the bubble-shaped adaptor, so as to replace the non-paired sequence in the short-chain nucleic acid.
    Type: Grant
    Filed: November 21, 2014
    Date of Patent: June 11, 2019
    Assignee: MGI TECH CO., LTD.
    Inventors: Yuan Jiang, Kai Tian, Xia Zhao, Wenwei Zhang, Huaiqian Xu, Hui Jiang, Radoje Drmanac, Chunyu Geng
  • Publication number: 20190144482
    Abstract: Reversibly blocked nucleoside analogues and methods of using such nucleoside analogues for sequencing of nucleic acids are provided.
    Type: Application
    Filed: April 21, 2017
    Publication date: May 16, 2019
    Inventors: Handong Li, Snezana Drmanac, Radoje Drmanac, Xun Xu, Lingling Peng, Scott Gablenz
  • 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