Patents Assigned to Complete Genomics, Inc.
  • Patent number: 8660421
    Abstract: A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.
    Type: Grant
    Filed: April 3, 2013
    Date of Patent: February 25, 2014
    Assignee: Complete Genomics, Inc.
    Inventors: Bryan P. Staker, Craig E. Uhrich
  • Publication number: 20140051588
    Abstract: The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.
    Type: Application
    Filed: April 16, 2012
    Publication date: February 20, 2014
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Publication number: 20140005056
    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: September 16, 2013
    Publication date: January 2, 2014
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
  • Patent number: 8617811
    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: January 28, 2009
    Date of Patent: December 31, 2013
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 8615365
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: December 24, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20130323652
    Abstract: Methods of preparing organosilane-functionalized regions on a substrate surface and more specifically fabricating patterned functionalized substrates suitable to be optically read, the methods generally comprising employing a vapor deposition process of an organosilane gas onto a lithographically patterned silicon surface followed by removal of the patterning media in a bath of organic solvents and ultrasonic excitation. The inventive methods provide optimized surface density of functional species while avoiding deleterious effects that can occur when lithographically patterned substrates are exposed to various gaseous species during the functionalization process.
    Type: Application
    Filed: June 5, 2012
    Publication date: December 5, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Andres Fernandez, Shaunak Roy, Jay Shafto, Norman L. Burns, Claudia Richter, Pierre F. Indermuhle
  • Patent number: 8592150
    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: June 15, 2010
    Date of Patent: November 26, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Andrei Alexeev, Peter Hong
  • Patent number: 8551702
    Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
    Type: Grant
    Filed: December 15, 2008
    Date of Patent: October 8, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Publication number: 20130222570
    Abstract: A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.
    Type: Application
    Filed: April 3, 2013
    Publication date: August 29, 2013
    Applicant: Complete Genomics, Inc.
    Inventor: Complete Genomics, Inc.
  • Patent number: 8518640
    Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
    Type: Grant
    Filed: October 5, 2009
    Date of Patent: August 27, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Publication number: 20130178369
    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: Application
    Filed: October 30, 2012
    Publication date: July 11, 2013
    Applicant: Complete Genomics, Inc.
    Inventor: Complete Genomics, Inc.
  • Publication number: 20130124100
    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: Application
    Filed: April 13, 2012
    Publication date: May 16, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Publication number: 20130110407
    Abstract: After DNA fragments are sequenced and mapped to a reference, various hypotheses for the sequences in a variant region can be scored to find which sequence hypotheses are more likely. A hypothesis can include a specific variable fraction for the plurality of alleles that comprise the sequence hypothesis in the region. A likelihood of each hypothesis can be determined using a probability that accounts for the fraction of the alleles specified in the respective sequence hypothesis. Thus, other hypotheses besides standard homozygous and equal heterozygous (i.e., one chromosome with A and one with B in a cell) can be explored by explicitly including the variable fractions of the alleles as a parameter in the optimization. Also, a variant score can be determined for a variant relative to a reference. The variant score can be used to determine a variant calibrated score indicating a likelihood that the variant call is correct.
    Type: Application
    Filed: September 17, 2012
    Publication date: May 2, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Jonathan Baccash, Aaron Halpern, Chao Tian, Krishna Pant, Paolo Carnevali
  • Patent number: 8428454
    Abstract: A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.
    Type: Grant
    Filed: April 20, 2012
    Date of Patent: April 23, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Bryan P. Staker, Craig E. Uhrich
  • Publication number: 20130096841
    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: Application
    Filed: October 11, 2012
    Publication date: April 18, 2013
    Applicant: Complete Genomics, Inc.
    Inventor: Complete Genomics, Inc.
  • Patent number: 8415099
    Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
    Type: Grant
    Filed: December 5, 2008
    Date of Patent: April 9, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Matthew Callow
  • Patent number: 8407554
    Abstract: Data extracted from fluorosphore responses of fluorophore labeled bases in genetic material used in sequencing of unknown fragments from a defined set of for example a model system are converted into a class of block codes that are then employed in a computer-based process to compare and correct preliminary calls of calls of the categorically known genetic material. In a specific embodiment, the Reed-Solomon codes are employed to identify one or more errors as may occur in a finite block of codes. The methodology is also useful to identify elements of a real system containing known elements in the form of a tag. Reed-Solomon sensors may be employed with and in addition to other types of genome sensors.
    Type: Grant
    Filed: February 1, 2010
    Date of Patent: March 26, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Karen W. Shannon
  • Publication number: 20130059737
    Abstract: Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes).
    Type: Application
    Filed: October 8, 2012
    Publication date: March 7, 2013
    Applicant: Complete Genomics, Inc.
    Inventor: Complete Genomics, Inc.
  • Publication number: 20130059740
    Abstract: The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.
    Type: Application
    Filed: April 16, 2012
    Publication date: March 7, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
  • Publication number: 20130054508
    Abstract: Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength.
    Type: Application
    Filed: August 22, 2012
    Publication date: February 28, 2013
    Applicant: Complete Genomics, Inc.
    Inventors: Bahram Ghaffarzadeh Kermani, Radoje Drmanac