Gene Sequence Determination Patents (Class 702/20)
  • Patent number: 9459196
    Abstract: Systems and methods for displaying measured values of a complete blood count (“CBC”) parameter include displaying the measured values of the CBC parameter obtained from a plurality of samples from a first lot of a quality control composition, where the displaying includes displaying a marker corresponding to each measured value from the first lot on a plot that includes a two dimensional coordinate system, and where the two dimensional coordinate system includes a first dimension corresponding to a time at which measured values of the CBC parameter were obtained, and a second dimension corresponding to a numerical value of the CBC parameter.
    Type: Grant
    Filed: July 13, 2012
    Date of Patent: October 4, 2016
    Assignee: Roche Diagnostics Hematology, Inc.
    Inventor: Russell Zahniser
  • Patent number: 9425951
    Abstract: Embodiments of a method and/or system of transmitting and/or receiving data is disclosed.
    Type: Grant
    Filed: May 29, 2015
    Date of Patent: August 23, 2016
    Assignee: Robert T. and Virginia T. Jenkins
    Inventor: Jack J. LeTourneau
  • Patent number: 9364567
    Abstract: Provided are fragments of human p97 (melanotransferrin) polypeptides having blood-brain barrier (BBB) transport activity, including variants and combinations thereof, conjugates comprising the p97 fragments, and related methods of use thereof, for instance, to facilitate delivery of therapeutic or diagnostic agents across the BBB.
    Type: Grant
    Filed: March 13, 2014
    Date of Patent: June 14, 2016
    Assignee: biOasis Technologies, Inc.
    Inventors: Timothy Z. Vitalis, Reinhard Gabathuler
  • Patent number: 9322752
    Abstract: The present disclosure relates to apparatus, systems, compositions, and methods for analyzing a sample containing particles. In some aspects the system comprises an analyzer which may be a visual analyzer. In one aspect, this disclosure relates to a particle imaging system comprising a flowcell through which a sample containing particles is caused to flow, and a high optical resolution imaging device which captures images for image analysis of samples. Other compositions, methods and features of this disclosure are disclosed herein.
    Type: Grant
    Filed: March 17, 2014
    Date of Patent: April 26, 2016
    Assignee: IRIS International, Inc.
    Inventors: Bart J. Wanders, Thomas H. Adams, Gregory A. Farrell, Warren Groner, Xiaodong Zhao
  • Patent number: 9255296
    Abstract: The present invention provides a method of diagnosing the existence of a kidney disorder in a feline comprising measuring the level of expression of one or more biomarkers selected from the group consisting of lumican; collagen alpha 1 (111) chain, variant 12; decorin; secreted frizzled-related protein 2; retinol binding protein 5; MMP-2; MMP-7; and MMP-19, in a biological sample from the feline, wherein differences in expression of the one or more biomarkers in the sample relative to a control value for expression in a sample from a normal animal indicate the existence of a kidney disorder; a method of treating a feline so diagnosed; and compositions, reagents and kits for carrying out the specified methods.
    Type: Grant
    Filed: February 24, 2011
    Date of Patent: February 9, 2016
    Assignee: HILL'S PET NUTRITION, INC.
    Inventors: Samer Waleed Al-Murrani, Xiangming Gao, Sukhaswami Malladi
  • Patent number: 9245050
    Abstract: Embodiments of methods, apparatuses, devices and/or systems for manipulating hierarchical sets of data are disclosed. In particular, methods, apparatus devices and or/or systems for analyzing hierarchical data are disclosed.
    Type: Grant
    Filed: February 17, 2011
    Date of Patent: January 26, 2016
    Assignee: Robert T. and Virginia T. Jenkins
    Inventors: Karl Schiffmann, Jack J. LeTourneau, Mark Andrews
  • Patent number: 9223930
    Abstract: Methods and systems for identifying a quantitation cycle (Cq) for a PCR reaction that includes fitting a line having a plurality of line segments to data points associated with a PCR amplification reaction. The data points include a cycle value associated with a PCR cycle and a product value associated with a PCR product. A baseline is identified and reaction segment associated with an exponential region of the PCR reaction is also identified. The reaction segment includes a subset of the plurality of line segments having a slope not less than a steepness criterion. A reaction line is fit to the data points associated with the reaction segment. The Cq is identified by calculating the cycle value for a data point defining the intersection of the baseline and reaction line.
    Type: Grant
    Filed: July 27, 2012
    Date of Patent: December 29, 2015
    Assignee: Thermo Fisher Scientific Oy
    Inventors: Jorma Mustola, Antti Koski
  • Patent number: 9175339
    Abstract: An object of the disclosure of the present specification is to provide a method for detection of a target nucleic acid which allows construction of an effective detection system of a target nucleic acid. For this purpose, in the disclosure of the present specification, a first primer comprising an identification sequence complementary to a target sequence in a target nucleic acid and a tag addition sequence, and a second primer having a label are prepared. The first primer and the second primer are used for the target nucleic acid in a sample to amplify a chimeric DNA having a tag sequence and the label. The chimeric DNA is hybridized with a detection probe on a solid phase to obtain signal intensity information based on the label, and the target nucleic acid is detected based on the signal intensity information.
    Type: Grant
    Filed: October 26, 2010
    Date of Patent: November 3, 2015
    Assignee: NGK Insulators, Ltd.
    Inventors: Mitsuo Kawase, Toshikazu Hirota, Kousuke Niwa
  • Patent number: 9169515
    Abstract: A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed.
    Type: Grant
    Filed: February 18, 2011
    Date of Patent: October 27, 2015
    Assignee: Life Technologies Corporation
    Inventors: Min-Yi Shen, Douglas Greiner
  • Patent number: 9170992
    Abstract: A method, software, database and system for determining an optimal treatment for an illness in an individual and for determining the impact (e.g., side effects and intended benefits) of the treatment in the individual are presented in which an attribute profile of the individual containing genetic and non-genetic attributes is compared against a database containing combinations genetic and non-genetic attributes that are statistically associated with successful treatment of the illness in other individuals.
    Type: Grant
    Filed: January 9, 2012
    Date of Patent: October 27, 2015
    Assignee: Expanse Bioinformatics, Inc.
    Inventors: Andrew Alexander Kenedy, Charles Anthony Eldering
  • Patent number: 9163238
    Abstract: The present invention is directed to the identification of a novel repressor located between ˜1.2 kb to ˜1.6 kb from the translation start site of the IFN-?1 promoter. The present invention provides a method of using siRNAs against ZEB1 (binds to the repressor region) and BLIMP-1 (binds outside the repressor region) and increases the promoter activity of IFN-?1 (i.e., increases the production of IFN-?1 protein). siRNAs against ZEB1 mRNA or BLIMP-1 mRNA increase IFN-?1 gene activity. There is provided a therapeutic application of siRNAs against ZEB1 and BLIMP-1 mRNAs in treating a mammal (including a human) by increasing the production of IFN-?1 protein that promotes an anti-viral response as well as treats asthma diseases.
    Type: Grant
    Filed: July 7, 2014
    Date of Patent: October 20, 2015
    Assignee: Medical Diagnostic Laboratories, LLC
    Inventors: Grant Gallagher, Rachael Siegel, Joyce Eskdale
  • Patent number: 9139860
    Abstract: The present invention relates to a self-amplifying folded oligonucleotide structure for sensitive oligonucleotide sensing without polymerase chain reaction (PCR). A self-amplifying folded oligonucleotide structure comprise a target sensing sequence having stem loop structure, a signaling molecule and signal modifying molecule labeled two stems wherein the two stems include oligonucleotide sequence that is complementary to a target sensing sequence of another self-amplifying folded oligonucleotide structure.
    Type: Grant
    Filed: April 11, 2011
    Date of Patent: September 22, 2015
    Assignee: Korea University Research and Business Foundation
    Inventor: Hong Gu Chun
  • Patent number: 9133461
    Abstract: The invention relates to double-stranded ribonucleic acid (dsRNA) compositions targeting the ALAS1 gene, and methods of using such dsRNA compositions to alter (e.g., inhibit) expression of ALAS1.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: September 15, 2015
    Assignees: Alnylam Pharmaceuticals, Inc., Icahn School of Medicine at Mount Sinai
    Inventors: Brian Bettencourt, Kevin Fitzgerald, William Querbes, Robert J. Desnick, Makiko Yasuda
  • Patent number: 9133525
    Abstract: A method for identifying a risk factor for diseases, disorders or conditions, such as those caused by human immunodeficiency virus, using the polymerase chain reaction and specific primers. Methods for treating patients having these diseases, disorders or conditions by antimicrobial treatment of the risk factor by combined antiviral and antibacterial treatment or by sustaining or stimulating the subject's immune system. Methods for screening biological products including red blood cell preparations. Primers and methods for detecting nucleic acids or microbial agents associated with red blood cells, such as those associated with red blood cells in subjects infected with HIV and undergoing antiretroviral therapy.
    Type: Grant
    Filed: January 28, 2013
    Date of Patent: September 15, 2015
    Inventor: Luc Montagnier
  • Patent number: 9115401
    Abstract: Methods are disclosed for resolving measurement problems such problems in measuring chromosomal copy number. Some disclosed methods involve first selecting a primary assay element characteristic to partition. Such characteristic may be a source of experimental variability such as the GC content of measured DNA sequences. Additionally, the disclosed methods may employ an abundance or copy number function to transform the assay element frequencies into an abundance, dose, copy number score, or the like. In some cases, the disclosed methods estimate an amount of certain fetal DNA in a sample. The methods can further compare the estimated amount to a measured amount of fetal DNA in the sample. The comparison can be used to determine the fetal sex or aneuploidy.
    Type: Grant
    Filed: February 21, 2014
    Date of Patent: August 25, 2015
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Brian K. Rhees, John P. Burke
  • Patent number: 9116866
    Abstract: The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.
    Type: Grant
    Filed: September 30, 2013
    Date of Patent: August 25, 2015
    Assignee: Seven Bridges Genomics Inc.
    Inventor: Deniz Kural
  • Patent number: 9104656
    Abstract: Provided are techniques for locating one or more genome patterns. One or more lexical annotators that each identifies a sequence of nucleotides are created. One or more parsing rule annotators are created using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators. The one or more parsing rule annotators are used to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.
    Type: Grant
    Filed: July 3, 2012
    Date of Patent: August 11, 2015
    Assignee: International Business Machines Corporation
    Inventors: Stephen D. Bowman, Dandala V. Reddy, David B. Werts
  • Patent number: 9104657
    Abstract: Provided are techniques for locating one or more genome patterns. One or more lexical annotators that each identifies a sequence of nucleotides are created. One or more parsing rule annotators are created using at least one of (1) one or more of the lexical annotators, (2) one or more dictionary entries, and (3) one or more previously-defined parsing rule annotators. The one or more parsing rule annotators are used to discover the one or more genome patterns comprising a combination of the lexical annotators and the parsing rule annotators.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: August 11, 2015
    Assignee: International Business Machines Corporation
    Inventors: Stephen D. Bowman, Dandala V. Reddy, David B. Werts
  • Patent number: 9085775
    Abstract: A nucleotide leader sequence 5?-UTR comprises elements favorable to gene expression, such as repeated CAA trinucleotide elements in combination with repeated CT dinucleotide elements.
    Type: Grant
    Filed: December 27, 2007
    Date of Patent: July 21, 2015
    Assignee: RODINA HOLDINGS S.A.
    Inventors: Stefano Marchetti, Francesca De Amicis, Tamara Patti
  • Patent number: 9081883
    Abstract: A dynamic diagnostic plan generator arranges diagnostic test procedures related to a vehicle/power tool/patient symptom or operational problem in a sequence based on a probabilistic Failure Mode and Effects Analysis (FMEA). The diagnostic plan generator also tracks a vehicle/power tool/patient state, and provides instructions for test preparation steps and instructions for performing the diagnostic test procedures. The plan generator further generates schematic illustrations of the diagnostic test procedures, and creates a diagnostic data structure containing information related to the diagnostic test procedures. In addition, the diagnostic plan generator sends and receives information regarding actual failure mode occurrences, for example, to and from a central database. Furthermore, the diagnostic plan generator facilitates the creation of failure mode tests by an expert diagnostics author.
    Type: Grant
    Filed: March 5, 2013
    Date of Patent: July 14, 2015
    Assignee: Bosch Automotive Service Solutions Inc.
    Inventors: William W. Wittliff, III, Olav M. Underdal, Harry M. Gilbert, Alex Portyanko
  • Patent number: 9077515
    Abstract: Embodiments of a method and/or system of transmitting and/or receiving data is disclosed.
    Type: Grant
    Filed: January 7, 2014
    Date of Patent: July 7, 2015
    Assignee: Robert T. and Virginia T. Jenkins
    Inventor: Jack J. LeTourneau
  • Patent number: 9065469
    Abstract: In embodiments of compression match enumeration, a trie structure can be searched to enumerate data sequence matches after the trie structure is generated. The trie structure can be generated by overwriting a suffix array of data sequences stored in a memory buffer, where the suffix array includes an array of buffer positions sorted alphabetically by a data string that begins a data sequence at a respective buffer position. The trie structure can then be traversed to determine the data sequence matches from nodes in the trie structure. The trie structure can also be updated while being traversed to bypass multiple enumerations of the data sequence matches that have the same match length.
    Type: Grant
    Filed: July 19, 2013
    Date of Patent: June 23, 2015
    Assignee: Microsoft Technology Licensing, LLC
    Inventor: Benjamin A. Mickle
  • Patent number: 9043160
    Abstract: The invention is directed to methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect, the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence tree representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated.
    Type: Grant
    Filed: August 2, 2011
    Date of Patent: May 26, 2015
    Assignee: SEQUENTA, INC.
    Inventors: Martin Moorhead, Malek Faham, Thomas Willis
  • Publication number: 20150142334
    Abstract: RNA sequencing techniques provide rapid base-calling and resequencing for improved bio-informatics. Exemplary embodiments of computer-implemented systems and methods can be provided, as applied to RNA sequence interpretation, enumeration and classification, etc.
    Type: Application
    Filed: November 17, 2014
    Publication date: May 21, 2015
    Inventor: BHUBANESWAR MISHRA
  • Publication number: 20150133318
    Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.
    Type: Application
    Filed: April 24, 2014
    Publication date: May 14, 2015
    Applicant: UNIVERSITY OF MASSACHUSETTS
    Inventors: Craig C. MELLO, Weifeng GU
  • Publication number: 20150120210
    Abstract: Disclosed are a method and a device for labelling single nucleotide polymorphism site in a genome. The above-mentioned method comprises: the single-end RAD sequences from the genomes of two individuals are obtained; the single-end RAD sequences are filtered to remove unqualified sequences; the sequencing depth of the sequences from the genomes of two individuals is aligned in pairs and without gaps to determine the SNP sites.
    Type: Application
    Filed: December 29, 2011
    Publication date: April 30, 2015
    Applicant: BGI TECH SOLUTIONS CO., LTD.
    Inventors: Ye Tao, Zequn Zheng, Zihao Feng, Yingrui Li, Huanming Yang, Jun Wang, Jian Wang
  • Publication number: 20150120209
    Abstract: Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).
    Type: Application
    Filed: May 5, 2014
    Publication date: April 30, 2015
    Applicant: New York University
    Inventors: Bhubaneswar Mishra, Thomas Anantharaman, Sang Lim
  • Publication number: 20150110754
    Abstract: Provided herein are methods for accurately determining the alleles present at a locus that is broadly applicable to any locus, including highly polymorphic loci such as HLA loci, BGA loci and HV loci. Embodiments of the disclosed methods are useful in a wide range of applications, including, for example, organ transplantation, personalized medicine, diagnostics, forensics and anthropology.
    Type: Application
    Filed: October 14, 2014
    Publication date: April 23, 2015
    Inventors: Yu Bai, Wen Fury
  • Publication number: 20150111762
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases.
    Type: Application
    Filed: May 2, 2013
    Publication date: April 23, 2015
    Inventor: Mark W. Eshoo
  • Publication number: 20150111763
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases.
    Type: Application
    Filed: May 2, 2013
    Publication date: April 23, 2015
    Inventor: Mark W. Eshoo
  • Patent number: 9014989
    Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.
    Type: Grant
    Filed: February 13, 2014
    Date of Patent: April 21, 2015
    Assignee: Edico Genome, Corp.
    Inventors: Robert McMillen, Michael Ruehle
  • Patent number: 9012150
    Abstract: Methods for identifying ribonucleotide sequences, in vitro, using the ribosome-mediated translation, are provided.
    Type: Grant
    Filed: May 26, 2005
    Date of Patent: April 21, 2015
    Assignee: Anima Cell Metrology
    Inventor: Ze'ev Smilansky
  • Patent number: 9009039
    Abstract: Technologies are described herein for noise adaptive training to achieve robust automatic speech recognition. Through the use of these technologies, a noise adaptive training (NAT) approach may use both clean and corrupted speech for training. The NAT approach may normalize the environmental distortion as part of the model training. A set of underlying “pseudo-clean” model parameters may be estimated directly. This may be done without point estimation of clean speech features as an intermediate step. The pseudo-clean model parameters learned from the NAT technique may be used with a Vector Taylor Series (VTS) adaptation. Such adaptation may support decoding noisy utterances during the operating phase of a automatic voice recognition system.
    Type: Grant
    Filed: June 12, 2009
    Date of Patent: April 14, 2015
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Michael Lewis Seltzer, James Garnet Droppo, Ozlem Kalinli, Alejandro Acero
  • Publication number: 20150100247
    Abstract: A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.
    Type: Application
    Filed: October 3, 2014
    Publication date: April 9, 2015
    Inventors: Christian KOLLER, Marcin SIKORA, Peter VANDER HORN
  • Patent number: 9002888
    Abstract: A method, computer program product and system of minimizing epigenetic surprisal data either by comparing epigenetic surprisal data to a fixed baseline epigenetic data, so that all of the comparisons were made to the same baseline epigenetic data or by comparing epigenetic surprisal data to a rolling baseline of epigenetic surprisal data—that is, after each comparison the baseline is changed to the data from the time point which had been compared previously.
    Type: Grant
    Filed: June 29, 2012
    Date of Patent: April 7, 2015
    Assignee: International Business Machines Corporation
    Inventors: Robert R. Friedlander, James R. Kraemer
  • Publication number: 20150094963
    Abstract: A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.
    Type: Application
    Filed: December 11, 2014
    Publication date: April 2, 2015
    Inventors: John Z. Sanborn, David Haussler
  • Publication number: 20150094223
    Abstract: A method and apparatus for diagnosing cancer by using genetic information, the method comprising acquiring first gene expression data of a subject, for whom cancer is to be diagnosed, for a gene marker set including at least one gene marker; and determining a possibility of a presence of the cancer of the subject by using the acquired first gene expression data and pre-stored second gene expression data of a normal person group and a cancer patient group, wherein the gene marker set includes gene markers such as pyrroline-5-carboxylate reductase 1 (PYCR1), phosphoglycerate dehydrogenase (PHGDH), glutaminase 2 (liver, mitochondrial) (GLS2), and glutaminase (GLS) among others.
    Type: Application
    Filed: September 3, 2014
    Publication date: April 2, 2015
    Inventors: Eunjin Lee, Taejin Ahn
  • Publication number: 20150094212
    Abstract: Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant.
    Type: Application
    Filed: October 1, 2014
    Publication date: April 2, 2015
    Inventors: Rajesh Gottimukkala, Fiona Hyland, Sowmi Utiramerur, Jeoffrey Schageman, Susan Magdaleno
  • Patent number: 8996318
    Abstract: A novel method for prediction of the degree of heterotic phenotypes in plants is disclosed. Structural variation analyzes of the genome are used to predict the degree of a heterotic phenotype in plants. In some examples, copy number variation is used to predict the degree of heterotic phenotype. In some methods copy number variation is detected using competitive genomic hybridization arrays. Further, methods for optimizing the arrays are disclosed, together with kits for producing such arrays, as well as hybrid plants selected for development based on the predicted results.
    Type: Grant
    Filed: December 29, 2008
    Date of Patent: March 31, 2015
    Assignees: Pioneer Hi-Bred International, Inc., E. I. du Pont de Nemours and Company
    Inventors: Mary Beatty, James A. Janni, Jonathan E. Lightner, J. Antoni Rafalski
  • Publication number: 20150087537
    Abstract: A method for sequencing a polynucleotide sample having a barcode sequence includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined order of nucleotide flows; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-correcting code that is (i) designed based on and adapted for use with the predetermined order of nucleotide flows, and (ii) capable of distinguishing any codeword in the error-correcting code from the other codewords in the error-correcting code in the presence of zero, one, and two errors.
    Type: Application
    Filed: October 3, 2014
    Publication date: March 26, 2015
    Inventor: Earl Hubbell
  • Publication number: 20150087526
    Abstract: The present disclosure provides peptide amino acid sequencing and identification methods and kits for performing such methods. For example, single-molecule detection of fluorophore-labeled peptides is disclosed using multiple rounds of standard Edman degradation or using digestion by chemicals or enzymes. Different fluorophores covalently attached to each of a specific type of amino acid side chain of a peptide provide for the derivation of the peptide's encoded amino acid sequence following image alignments of multiple Edman cycles or following digestion by chemicals or enzymes. The amino acid sequence of a peptide and/or the identity of the peptide can be determined by bioinformatic analysis based on the encoded amino acid sequence. The present disclosure further provides peptide derivatization and immobilization strategies to enable the sequencing and identification of a single peptide or a plurality of peptides.
    Type: Application
    Filed: January 24, 2013
    Publication date: March 26, 2015
    Inventor: Jay R. Hesselberth
  • Publication number: 20150088432
    Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.
    Type: Application
    Filed: September 26, 2014
    Publication date: March 26, 2015
    Inventors: John Zachary Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Shahrooz Rabizadeh, Nicole Hensley, Patrick Soon-Shiong
  • Publication number: 20150073724
    Abstract: Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.
    Type: Application
    Filed: May 27, 2014
    Publication date: March 12, 2015
    Inventors: Ashutosh, Devendra Joshi, Christian A. Le Cocq
  • Patent number: 8976049
    Abstract: The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.
    Type: Grant
    Filed: August 22, 2014
    Date of Patent: March 10, 2015
    Assignee: Good Start Genetics, Inc.
    Inventors: Caleb Kennedy, Niru Chennagiri
  • Publication number: 20150066384
    Abstract: Provided are a system and method for sequence alignment. The system for sequence alignment includes an exact matching module configured to perform exact matching of an input read to a reference sequence, a secondary matching module configured to map the read to the reference sequence in consideration of mismatches between the read and the reference sequence when the read does not exactly match the reference sequence, and a global alignment module configured to perform global alignment operation of the read with the reference sequence when the read is not mapped to the reference sequence by the secondary matching module.
    Type: Application
    Filed: May 8, 2014
    Publication date: March 5, 2015
    Applicant: SAMSUNG SDS CO., LTD.
    Inventor: Min Seo PARK
  • Publication number: 20150066385
    Abstract: The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.
    Type: Application
    Filed: August 27, 2014
    Publication date: March 5, 2015
    Inventors: Michael SCHNALL-LEVIN, Mirna JAROSZ, Serge SAXONOV, Kevin NESS, Benjamin HINDSON
  • Publication number: 20150066383
    Abstract: The invention generally relates to tools for genomic analysis and particularly to a pipeline editor that can turn pipelines into standalone tools for use in other pipelines. The invention provides systems and methods for genomic analysis in which individual analytical tools can be arranged into analytical pipelines that can then be “collapsed” into standalone tools, which themselves can be put into the pool of individual tools for use in further building of pipelines. Aspects of the invention provide a system that includes a server computer system operable to present to a user a plurality of genomic tools, receive input from the user arranging the tools into a pipeline, create a new tool that includes the pipeline, and offer the new tool along with the plurality of genomic tools.
    Type: Application
    Filed: September 3, 2013
    Publication date: March 5, 2015
    Applicant: Seven Bridges Genomics Inc.
    Inventor: Sebastian Wernicke
  • Patent number: 8972874
    Abstract: A graphical user interface (GUI) type model helps application designers create error free graphical user interface applications (GAPs). The GUI type model provides a reference set of GUI element types. The application designer assigns a selected GUI element type to each GUI element in a GAP design. The GUI element types help ensure consistent and proper treatment of the GUI element types at every stage in the development of the application, from initial planning and design, to compilation and execution.
    Type: Grant
    Filed: January 23, 2012
    Date of Patent: March 3, 2015
    Assignee: Accenture Global Services Limited
    Inventors: Mark Grechanik, Qing Xie, Chen Fu
  • Publication number: 20150057946
    Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.
    Type: Application
    Filed: September 3, 2013
    Publication date: February 26, 2015
    Applicant: SEVEN BRIDGES GENOMICS INC.
    Inventor: Deniz Kural
  • Publication number: 20150057947
    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: Application
    Filed: August 25, 2014
    Publication date: February 26, 2015
    Inventors: Radoje Drmanac, Bahram Ghaffarzadeh Kermani