Patents Assigned to Complete Genomics AS
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Patent number: 11835437Abstract: 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: GrantFiled: November 10, 2020Date of Patent: December 5, 2023Assignee: Complete Genomics, Inc.Inventors: Norman Lee Burns, Jay Willis Shafto
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Patent number: 11692221Abstract: The present invention provides a method for sequencing a nucleic acid using an immersion reaction protocol. The immersion reaction protocol comprises sequentially immersing a solid support having nucleic acid molecules immobilized thereon in different reaction containers to realize nucleic acid sequencing.Type: GrantFiled: August 1, 2017Date of Patent: July 4, 2023Assignees: MGI TECH CO., LTD., COMPLETE GENOMICS, INC.Inventors: Jin Yang, Xun Xu, Hui Wang, Bin Xie, Zhuokun Li, Shengming Zhao, Ao Chen, Chongjun Xu, Wenwei Zhang, Ming Ni
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Publication number: 20220362735Abstract: This disclosure provides methods and compositions for long fragment read sequencing. Technology is described 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. Combinatorial oligonucleotide bar codes are used to label fragments from nearby portions of the genome, which facilitate computational assembly of sequence reads to obtain the genome sequence. This improves efficiency and accuracy of sequencing, whereby an entire sequence can be obtained from fragments that constitute a lower coverage amount of the genome.Type: ApplicationFiled: June 15, 2022Publication date: November 17, 2022Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
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Patent number: 11485966Abstract: The present invention provides a method for improving the loading of nucleic acid on a solid support by contacting the solid support with a poloxamer-containing reagent. The present invention also provides a method for improving the stability of a nucleic acid on a solid support, comprising contacting a nucleic acid molecule with a partially double-strand oligonucleotide before or after loading the nucleic acid molecule on a solid support, so as to cause the nucleic acid molecule to hybridize with the oligonucleotide. The present invention also provides a combined use of the two methods.Type: GrantFiled: October 11, 2017Date of Patent: November 1, 2022Assignees: MGI TECH CO., LTD., COMPLETE GENOMICS, INC.Inventors: Hui Wang, Xun Xu, Jin Yang, Ao Chen, Chongjun Xu, Wenwei Zhang
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Patent number: 11414702Abstract: 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: GrantFiled: December 30, 2019Date of Patent: August 16, 2022Assignee: Complete Genomics, Inc.Inventor: Radoje Drmanac
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Patent number: 11389779Abstract: 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: GrantFiled: October 10, 2016Date of Patent: July 19, 2022Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
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Patent number: 11214832Abstract: 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: GrantFiled: November 22, 2016Date of Patent: January 4, 2022Assignee: Complete Genomics, Inc.Inventor: Radoje Drmanac
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Patent number: 11098356Abstract: 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: GrantFiled: May 17, 2019Date of Patent: August 24, 2021Assignee: Complete Genomics, Inc.Inventor: Radoje Drmanac
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Patent number: 10837879Abstract: 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: GrantFiled: October 30, 2012Date of Patent: November 17, 2020Assignee: Complete Genomics, Inc.Inventors: Norman Lee Burns, Jay Willis Shafto
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Patent number: 10726942Abstract: 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: GrantFiled: August 25, 2014Date of Patent: July 28, 2020Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Bahram Ghaffarzadeh Kermani
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Patent number: 10662473Abstract: 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: GrantFiled: August 3, 2018Date of Patent: May 26, 2020Assignee: Complete Genomics, Inc.Inventor: Radoje Drmanac
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Patent number: 10557166Abstract: 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: GrantFiled: March 17, 2014Date of Patent: February 11, 2020Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev
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Patent number: 10468121Abstract: 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: GrantFiled: October 1, 2014Date of Patent: November 5, 2019Assignee: Complete Genomics, Inc.Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac, Brock A. Peters
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Publication number: 20190316190Abstract: 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: ApplicationFiled: November 13, 2018Publication date: October 17, 2019Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Brian K. Hauser, George Yeung
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Patent number: 10351909Abstract: 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: GrantFiled: February 25, 2017Date of Patent: July 16, 2019Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20190088463Abstract: 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: ApplicationFiled: September 11, 2018Publication date: March 21, 2019Applicant: Complete Genomics, Inc.Inventors: Shifeng Li, Jian Gong, Yan-You Lin, Cheng Frank Zhong
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Patent number: 10227647Abstract: 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: GrantFiled: February 10, 2016Date of Patent: March 12, 2019Assignee: Complete Genomics, Inc.Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
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Patent number: 10190162Abstract: 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: GrantFiled: October 23, 2015Date of Patent: January 29, 2019Assignee: Complete Genomics, Inc.Inventors: Snezana Drmanac, Handong Li, Radoje Drmanac, Eric Harness, Chongjun Xu
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Publication number: 20190010542Abstract: 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: ApplicationFiled: March 29, 2018Publication date: January 10, 2019Applicant: Complete Genomics Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Publication number: 20190002969Abstract: 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: ApplicationFiled: March 26, 2018Publication date: January 3, 2019Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev