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: 20170355981
    Abstract: A method and reagent for constructing a nucleic acid double-linker single-strand cyclic library.
    Type: Application
    Filed: November 26, 2014
    Publication date: December 14, 2017
    Applicants: BGI SHENZHEN, BGISHENZHEN CO., LIMITED
    Inventors: Yuan JIANG, Qiaoling LI, Andrei ALEXEEV, Evan HUROWITZ, Xia ZHAO, Tong WANG, Chao DONG, Dong LI, Radoje DRMANAC, Wenwei ZHANG, Hui JIANG
  • 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
  • Publication number: 20170349893
    Abstract: A method and reagent for constructing a nucleic acid double-joint single-strand cyclical library.
    Type: Application
    Filed: November 26, 2014
    Publication date: December 7, 2017
    Applicants: BGI SHENZHEN, BGI SHENZHENN CO., LIMITED
    Inventors: Yuan JIANG, Xia ZHAO, Andrei ALEXEEV, Radoje DRMANAC, Wenwei ZHANG, Hui JIANG
  • Publication number: 20170292157
    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: November 22, 2016
    Publication date: October 12, 2017
    Applicant: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Publication number: 20170240961
    Abstract: Nucleoside analogues and methods of using such nucleoside analogues for sequencing of nucleic acids are provided.
    Type: Application
    Filed: February 23, 2017
    Publication date: August 24, 2017
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Snezana Drmanac, Handong Li, Xun Xu
  • Publication number: 20170233728
    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: Application
    Filed: October 14, 2014
    Publication date: August 17, 2017
    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
  • Publication number: 20170226577
    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: September 16, 2016
    Publication date: August 10, 2017
    Applicant: Complete Genomics Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
  • Publication number: 20170175184
    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: Application
    Filed: February 25, 2017
    Publication date: June 22, 2017
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Patent number: 9679103
    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: Grant
    Filed: August 22, 2012
    Date of Patent: June 13, 2017
    Assignee: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac
  • Publication number: 20170152554
    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: Application
    Filed: February 6, 2017
    Publication date: June 1, 2017
    Applicant: Complete Genomics, Inc.
    Inventors: RADOJE DRMANAC, Matthew Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Patent number: 9650673
    Abstract: 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: Grant
    Filed: May 15, 2015
    Date of Patent: May 16, 2017
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
  • Publication number: 20170120213
    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: Application
    Filed: October 10, 2016
    Publication date: May 4, 2017
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
  • Patent number: 9637785
    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: May 2, 2017
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 9637784
    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: May 2, 2017
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Publication number: 20170022554
    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: April 22, 2016
    Publication date: January 26, 2017
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
  • Patent number: 9551026
    Abstract: Methods are provided for carrying out DNA sequencing on a device having upper and lower conductive layers separated by an insulative layer. Holes in the upper conductive layer create discrete attachment sites for DNA fragments. Voltage is applied to the surface to control affinity between the attachment sites and the DNA fragments, and to compact the DNA fragments for discrete optical detection.
    Type: Grant
    Filed: December 27, 2011
    Date of Patent: January 24, 2017
    Assignee: Complete Genomincs, Inc.
    Inventors: Andres Fernandez, Bryan Staker, Radoje Drmanac
  • Patent number: 9523125
    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: December 2, 2013
    Date of Patent: December 20, 2016
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 9524369
    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: Grant
    Filed: April 13, 2012
    Date of Patent: December 20, 2016
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Patent number: 9514272
    Abstract: Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations.
    Type: Grant
    Filed: October 11, 2012
    Date of Patent: December 6, 2016
    Assignee: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac, Oleg Alferov
  • Patent number: 9499863
    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: September 16, 2013
    Date of Patent: November 22, 2016
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong