Patents Assigned to Complete Genomics, Inc.
  • Patent number: 11098356
    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: Grant
    Filed: May 17, 2019
    Date of Patent: August 24, 2021
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 10837879
    Abstract: The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein.
    Type: Grant
    Filed: October 30, 2012
    Date of Patent: November 17, 2020
    Assignee: Complete Genomics, Inc.
    Inventors: Norman Lee Burns, Jay Willis Shafto
  • 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
  • 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: 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: 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
  • 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
  • Publication number: 20190088463
    Abstract: A method for forming sequencing flow cells can include providing a semiconductor wafer covered with a dielectric layer, and forming a patterned layer on the dielectric layer. The patterned layer has a differential surface that includes alternating first surface regions and second surface regions. The method can also include attaching a cover wafer to the semiconductor wafer to form a composite wafer structure including a plurality of flow cells. The composite wafer structure can then be singulated to form a plurality of dies. Each die forms a sequencing flow cell. The sequencing flow cell can include a flow channel between a portion of the patterned layer and a portion of the cover wafer, an inlet, and an outlet. Further, the method can include functionalizing the sequencing flow cell to create differential surfaces.
    Type: Application
    Filed: September 11, 2018
    Publication date: March 21, 2019
    Applicant: Complete Genomics, Inc.
    Inventors: Shifeng Li, Jian Gong, Yan-You Lin, Cheng Frank Zhong
  • 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: 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
  • 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
  • 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
  • Patent number: 10017815
    Abstract: A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis.
    Type: Grant
    Filed: August 28, 2015
    Date of Patent: July 10, 2018
    Assignee: Complete Genomics, Inc.
    Inventor: Arnold Oliphant