AU2017223600B2 - Generation of phased read-sets for genome assembly and haplotype phasing - Google Patents

Generation of phased read-sets for genome assembly and haplotype phasing Download PDF

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AU2017223600B2
AU2017223600B2 AU2017223600A AU2017223600A AU2017223600B2 AU 2017223600 B2 AU2017223600 B2 AU 2017223600B2 AU 2017223600 A AU2017223600 A AU 2017223600A AU 2017223600 A AU2017223600 A AU 2017223600A AU 2017223600 B2 AU2017223600 B2 AU 2017223600B2
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nucleic acid
segment
sequence
dna
molecule
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AU2017223600A1 (en
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Marco BLANCHETTE
Richard E. Green Jr.
Paul Hartley
Daniel S. ROKHSAR
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Dovetail Genomics LLC
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C40B40/08—Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2522/00—Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10—Nucleic acid binding proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2533/00—Reactions characterised by the enzymatic reaction principle used
    • C12Q2533/10—Reactions characterised by the enzymatic reaction principle used the purpose being to increase the length of an oligonucleotide strand
    • C12Q2533/107—Probe or oligonucleotide ligation

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
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  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
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  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • General Chemical & Material Sciences (AREA)
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  • Urology & Nephrology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
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AU2017223600A 2016-02-23 2017-02-23 Generation of phased read-sets for genome assembly and haplotype phasing Active AU2017223600B2 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201662298966P 2016-02-23 2016-02-23
US201662298906P 2016-02-23 2016-02-23
US62/298,906 2016-02-23
US62/298,966 2016-02-23
US201662305957P 2016-03-09 2016-03-09
US62/305,957 2016-03-09
PCT/US2017/019099 WO2017147279A1 (en) 2016-02-23 2017-02-23 Generation of phased read-sets for genome assembly and haplotype phasing

Publications (2)

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AU2017223600A1 AU2017223600A1 (en) 2018-09-27
AU2017223600B2 true AU2017223600B2 (en) 2023-08-03

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AU2017223600A Active AU2017223600B2 (en) 2016-02-23 2017-02-23 Generation of phased read-sets for genome assembly and haplotype phasing

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US (2) US10975417B2 (OSRAM)
EP (1) EP3420108A4 (OSRAM)
JP (2) JP7441003B2 (OSRAM)
KR (1) KR102744506B1 (OSRAM)
CN (1) CN109072298B (OSRAM)
AU (1) AU2017223600B2 (OSRAM)
CA (1) CA3014911A1 (OSRAM)
IL (1) IL261180B (OSRAM)
SG (1) SG11201807117WA (OSRAM)
WO (1) WO2017147279A1 (OSRAM)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016019360A1 (en) 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly
EP3420108A4 (en) * 2016-02-23 2019-11-06 Dovetail Genomics LLC GENERATION OF LIVE PHASES FOR THE GENERATION ARRANGEMENT AND HAPLOTYPE PHASE RULES
KR102412442B1 (ko) 2016-05-13 2022-06-22 더브테일 제노믹스 엘엘씨 보존된 샘플로부터의 장범위 링키지 정보의 회수
US20210371918A1 (en) * 2017-04-18 2021-12-02 Dovetail Genomics, Llc Nucleic acid characteristics as guides for sequence assembly
CN112367988A (zh) * 2018-05-08 2021-02-12 芝加哥大学 涉及乙氧二羟丁酮衍生物的组合物和方法
JP2022515221A (ja) 2018-12-21 2022-02-17 エピサイファー，インコーポレイテッド クロマチンマッピングアッセイ用のｄｎａバーコード化ヌクレオソーム
WO2020264185A1 (en) 2019-06-27 2020-12-30 Dovetail Genomics, Llc Methods and compositions for proximity ligation
CN115349128A (zh) 2020-02-13 2022-11-15 齐默尔根公司 宏基因组文库和天然产物发现平台
JP2024502028A (ja) * 2020-12-30 2024-01-17 ダブテイル ゲノミクス エルエルシー 配列決定ライブラリー調製のための方法および組成物

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150363550A1 (en) * 2013-02-01 2015-12-17 The Regents Of The University Of California Methods for genome assembly and haplotype phasing

Family Cites Families (176)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US1007228A (en) 1911-03-03 1911-10-31 William R Munden Door-hanger.
US1045793A (en) 1911-03-07 1912-11-26 Adolphe Houdard Bed-pan.
NL154598B (nl) 1970-11-10 1977-09-15 Organon Nv Werkwijze voor het aantonen en bepalen van laagmoleculire verbindingen en van eiwitten die deze verbindingen specifiek kunnen binden, alsmede testverpakking.
US3817837A (en) 1971-05-14 1974-06-18 Syva Corp Enzyme amplification assay
US3939350A (en) 1974-04-29 1976-02-17 Board Of Trustees Of The Leland Stanford Junior University Fluorescent immunoassay employing total reflection for activation
US3996345A (en) 1974-08-12 1976-12-07 Syva Company Fluorescence quenching with immunological pairs in immunoassays
US4275149A (en) 1978-11-24 1981-06-23 Syva Company Macromolecular environment control in specific receptor assays
US4277437A (en) 1978-04-05 1981-07-07 Syva Company Kit for carrying out chemically induced fluorescence immunoassay
US4366241A (en) 1980-08-07 1982-12-28 Syva Company Concentrating zone method in heterogeneous immunoassays
US5242794A (en) 1984-12-13 1993-09-07 Applied Biosystems, Inc. Detection of specific sequences in nucleic acids
US4988617A (en) 1988-03-25 1991-01-29 California Institute Of Technology Method of detecting a nucleotide change in nucleic acids
US5681726A (en) * 1988-09-19 1997-10-28 Stratagene Method of double stranded DNA synthesis
US5234809A (en) 1989-03-23 1993-08-10 Akzo N.V. Process for isolating nucleic acid
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5494810A (en) 1990-05-03 1996-02-27 Cornell Research Foundation, Inc. Thermostable ligase-mediated DNA amplifications system for the detection of genetic disease
EP0562025B1 (en) 1990-12-06 2001-02-07 Affymetrix, Inc. (a Delaware Corporation) Compounds and their use in a binary synthesis strategy
US5994056A (en) 1991-05-02 1999-11-30 Roche Molecular Systems, Inc. Homogeneous methods for nucleic acid amplification and detection
WO1993009668A1 (en) 1991-11-22 1993-05-27 Affymax Technology N.V. Combinatorial strategies for polymer synthesis
US6033854A (en) 1991-12-16 2000-03-07 Biotronics Corporation Quantitative PCR using blocking oligonucleotides
US5567583A (en) 1991-12-16 1996-10-22 Biotronics Corporation Methods for reducing non-specific priming in DNA detection
US5348853A (en) 1991-12-16 1994-09-20 Biotronics Corporation Method for reducing non-specific priming in DNA amplification
WO1994024143A1 (en) 1993-04-12 1994-10-27 Northwestern University Method of forming oligonucleotides
US5837832A (en) 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
JPH09507121A (ja) 1993-10-26 1997-07-22 アフィマックス テクノロジーズ ナームロゼ ベノートスハップ 生物学的チップ上の核酸プローブアレー
US6110709A (en) 1994-03-18 2000-08-29 The General Hospital Corporation Cleaved amplified modified polymorphic sequence detection methods
US5571639A (en) 1994-05-24 1996-11-05 Affymax Technologies N.V. Computer-aided engineering system for design of sequence arrays and lithographic masks
US5705628A (en) 1994-09-20 1998-01-06 Whitehead Institute For Biomedical Research DNA purification and isolation using magnetic particles
US5795716A (en) 1994-10-21 1998-08-18 Chee; Mark S. Computer-aided visualization and analysis system for sequence evaluation
US5599695A (en) 1995-02-27 1997-02-04 Affymetrix, Inc. Printing molecular library arrays using deprotection agents solely in the vapor phase
US5780613A (en) 1995-08-01 1998-07-14 Northwestern University Covalent lock for self-assembled oligonucleotide constructs
EP0937159A4 (en) 1996-02-08 2004-10-20 Affymetrix Inc SPECIATION OF MICROORGANISMS FROM MICROPLATES AND CHARACTERIZATION OF THE PHENOTYPES THEREOF
US5786146A (en) 1996-06-03 1998-07-28 The Johns Hopkins University School Of Medicine Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguishing modified methylated and non-methylated nucleic acids
DE69739357D1 (de) 1996-06-04 2009-05-28 Univ Utah Res Found Überwachung der hybridisierung während pcr
US6117635A (en) 1996-07-16 2000-09-12 Intergen Company Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon
US6582921B2 (en) * 1996-07-29 2003-06-24 Nanosphere, Inc. Nanoparticles having oligonucleotides attached thereto and uses thereof
US6449562B1 (en) 1996-10-10 2002-09-10 Luminex Corporation Multiplexed analysis of clinical specimens apparatus and method
WO1998041651A1 (en) 1997-03-18 1998-09-24 Hsc Research & Development Limited Partnership Method for preparing chromatin
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
CA2306907A1 (en) 1997-10-28 1999-05-06 The Regents Of The University Of California Dna base mismatch detection using flow cytometry
US5989823A (en) 1998-09-18 1999-11-23 Nexstar Pharmaceuticals, Inc. Homogeneous detection of a target through nucleic acid ligand-ligand beacon interaction
GB9812768D0 (en) 1998-06-13 1998-08-12 Zeneca Ltd Methods
US20040106110A1 (en) 1998-07-30 2004-06-03 Solexa, Ltd. Preparation of polynucleotide arrays
US20030022207A1 (en) 1998-10-16 2003-01-30 Solexa, Ltd. Arrayed polynucleotides and their use in genome analysis
US6787308B2 (en) 1998-07-30 2004-09-07 Solexa Ltd. Arrayed biomolecules and their use in sequencing
WO2000014281A2 (en) 1998-08-21 2000-03-16 Naxcor Assays using crosslinkable immobilized nucleic acids
ES2280131T3 (es) 1998-12-02 2007-09-01 Adnexus Therapeutics, Inc. Fusiones de adn-proteina y utilizaciones de las mismas.
US8367322B2 (en) 1999-01-06 2013-02-05 Cornell Research Foundation, Inc. Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing
US6994969B1 (en) 1999-04-30 2006-02-07 Methexis Genomics, N.V. Diagnostic sequencing by a combination of specific cleavage and mass spectrometry
US7056661B2 (en) 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
US6225109B1 (en) 1999-05-27 2001-05-01 Orchid Biosciences, Inc. Genetic analysis device
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7211390B2 (en) 1999-09-16 2007-05-01 454 Life Sciences Corporation Method of sequencing a nucleic acid
EP1218543A2 (en) 1999-09-29 2002-07-03 Solexa Ltd. Polynucleotide sequencing
US6582938B1 (en) 2001-05-11 2003-06-24 Affymetrix, Inc. Amplification of nucleic acids
GB0002389D0 (en) 2000-02-02 2000-03-22 Solexa Ltd Molecular arrays
US6291187B1 (en) * 2000-05-12 2001-09-18 Molecular Staging, Inc. Poly-primed amplification of nucleic acid sequences
US6448717B1 (en) 2000-07-17 2002-09-10 Micron Technology, Inc. Method and apparatuses for providing uniform electron beams from field emission displays
WO2002027029A2 (en) 2000-09-27 2002-04-04 Lynx Therapeutics, Inc. Method for determining relative abundance of nucleic acid sequences
US7001724B1 (en) 2000-11-28 2006-02-21 Applera Corporation Compositions, methods, and kits for isolating nucleic acids using surfactants and proteases
DE10120797B4 (de) 2001-04-27 2005-12-22 Genovoxx Gmbh Verfahren zur Analyse von Nukleinsäureketten
WO2003095608A2 (en) 2001-05-11 2003-11-20 Stamatoyannopoulos, John, A. Dna microarrays comprising active chromatin elements and comprehensive profiling therewith
GB0114853D0 (en) 2001-06-18 2001-08-08 Medical Res Council Happier Mapping
AU2002337030A1 (en) 2001-08-29 2003-03-18 Genovoxx Gmbh Method for analyzing nucleic acid sequences and gene expression
AU2002350485A1 (en) 2001-10-04 2003-04-22 Genovoxx Gmbh Device for sequencing nucleic acid molecules
DE10149786B4 (de) 2001-10-09 2013-04-25 Dmitry Cherkasov Oberfläche für Untersuchungen aus Populationen von Einzelmolekülen
US20050124022A1 (en) 2001-10-30 2005-06-09 Maithreyan Srinivasan Novel sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
AU2002360344A1 (en) 2001-11-09 2003-05-26 Monogram Biosciences, Inc. Detection of nucleic acid sequences by cleavage and separation of tag-containing structures
EP1483587A2 (en) 2002-03-08 2004-12-08 The Babraham Institute Tagging and recovery of elements associated with target molecules
US20030228627A1 (en) 2002-03-22 2003-12-11 Emerson Beverly M. Assay for p53 function in cells
DE10214395A1 (de) 2002-03-30 2003-10-23 Dmitri Tcherkassov Verfahren zur Analyse von Einzelnukleotidpolymorphismen
CA2490864C (en) 2002-06-28 2012-09-11 Sention, Inc. Methods of detecting sequence differences
US7563600B2 (en) 2002-09-12 2009-07-21 Combimatrix Corporation Microarray synthesis and assembly of gene-length polynucleotides
US7414117B2 (en) 2002-12-26 2008-08-19 Ngk Insulators, Ltd. Nucleotide derivative and DNA microarray
EP1594950A4 (en) 2003-01-29 2007-07-25 454 Corp PRODUCT FOR THE PREPARATION OF SIMPLE STRANDED DNA BANKS
US20040197779A1 (en) 2003-04-03 2004-10-07 Apffel James Alexander Methods for analyzing mixtures of proteins
US8741577B2 (en) 2003-04-07 2014-06-03 Bio-Rad Laboratories Inc. Surface immobilised multilayer structure of vesicles
FI20030778A0 (fi) 2003-05-22 2003-05-22 Licentia Oy Taudin määrittäminen tai ennustaminen
US20070111204A1 (en) 2003-06-27 2007-05-17 Kathleen Delgrosso Methods for detecting nucleic acid variations
ATE422554T1 (de) 2003-07-02 2009-02-15 Dsm Ip Assets Bv Verbessertes testsystem zur bestimmung des vorhandenseins eines antibiotikums in einer flüssigkeit
GB0316075D0 (en) 2003-07-09 2003-08-13 Molecular Sensing Plc Protease detection assay
EP1725572B1 (de) 2003-11-05 2017-05-31 AGCT GmbH Makromolekulare nukleotidverbindungen und methoden zu deren anwendung
DE10356837A1 (de) 2003-12-05 2005-06-30 Dmitry Cherkasov Modifizierte Nukleotide und Nukleoside
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
DE102004009704A1 (de) 2004-02-27 2005-09-15 Dmitry Cherkasov Makromolekulare Nukleotidverbindungen und Methoden zu deren Anwendung
BRPI0508100A (pt) 2004-02-28 2007-07-17 Chang Ning J Wang complexos de ácido nucléico bem como processo para detecção e sistema multifásico
DE102004025746A1 (de) 2004-05-26 2005-12-15 Dmitry Cherkasov Verfahren, Oberfläche und Substrate zur hochparallelen Sequenzierung von Nukleinsäureketten
DE102004025694A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren und Oberfläche zu hochparallelen Analysen von Nukleinsäureketten
DE102004025695A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren und Oberfläche zur parallelen Sequenzierung von Nukleinsäureketten
DE102004025745A1 (de) 2004-05-26 2005-12-15 Cherkasov, Dmitry Oberfläche für die Analysen an einzelnen Molekülen
DE102004025696A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren, Oberfläche und Substrate zu hochparallelen Analysen von Nukleinsäureketten
DE102004025744A1 (de) 2004-05-26 2005-12-29 Dmitry Cherkasov Oberfläche für die Analysen an einzelnen Nukleinsäuremolekülen
GB0413688D0 (en) * 2004-06-18 2004-07-21 Novartis Forschungsstiftung Analysis of methylated nucleic acid
US20060024711A1 (en) 2004-07-02 2006-02-02 Helicos Biosciences Corporation Methods for nucleic acid amplification and sequence determination
US7361468B2 (en) 2004-07-02 2008-04-22 Affymetrix, Inc. Methods for genotyping polymorphisms in humans
US7276720B2 (en) 2004-07-19 2007-10-02 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
US20060012793A1 (en) 2004-07-19 2006-01-19 Helicos Biosciences Corporation Apparatus and methods for analyzing samples
US20060024678A1 (en) 2004-07-28 2006-02-02 Helicos Biosciences Corporation Use of single-stranded nucleic acid binding proteins in sequencing
GB0422730D0 (en) 2004-10-13 2004-11-17 Lingvitae As Method
WO2006097320A2 (de) 2005-03-17 2006-09-21 Genovoxx Gmbh Makromolekulare nukleotidverbindungen und methoden zu deren anwendung
US7425415B2 (en) 2005-04-06 2008-09-16 City Of Hope Method for detecting methylated CpG islands
JP2006301289A (ja) 2005-04-20 2006-11-02 Tokyo Ohka Kogyo Co Ltd ネガ型レジスト組成物およびレジストパターン形成方法
US20090233291A1 (en) 2005-06-06 2009-09-17 454 Life Sciences Corporation Paired end sequencing
CA2611671C (en) 2005-06-15 2013-10-08 Callida Genomics, Inc. Single molecule arrays for genetic and chemical analysis
PL1899488T3 (pl) 2005-07-04 2016-03-31 Erasmus Univ Medical Center Test uchwytu konformacji chromosomu na czipie (4C)
JPWO2007074747A1 (ja) 2005-12-26 2009-06-04 株式会社クラレ 細胞培養用材料
US20070172839A1 (en) 2006-01-24 2007-07-26 Smith Douglas R Asymmetrical adapters and methods of use thereof
GB0603251D0 (en) 2006-02-17 2006-03-29 Isis Innovation DNA conformation
US8071296B2 (en) 2006-03-13 2011-12-06 Agency For Science, Technology And Research Nucleic acid interaction analysis
WO2007136874A2 (en) 2006-05-18 2007-11-29 President And Fellows Of Harvard College Genomic library construction
EP2057282A4 (en) 2006-08-24 2010-10-27 Univ Massachusetts Medical MAPPING GENOMIC INTERACTIONS
AU2007351524B2 (en) 2006-10-04 2013-08-15 Brookhaven Science Associates DNA-guided nanoparticle assemblies
US8278112B2 (en) 2006-12-21 2012-10-02 The Regents Of The University Of California Site-specific installation of methyl-lysine analogues into recombinant histones
PT2121977T (pt) 2007-01-11 2017-08-18 Erasmus Univ Medical Center Captura da conformação cromossómica circular (4c)
WO2008097887A2 (en) 2007-02-02 2008-08-14 Emory University Methods of direct genomic selection using high density oligonucleotide microarrays
CN101743326A (zh) 2007-05-14 2010-06-16 因赛特遗传学公司 筛选核酸中的单核苷酸变异的方法
US8951731B2 (en) 2007-10-15 2015-02-10 Complete Genomics, Inc. Sequence analysis using decorated nucleic acids
EP2053132A1 (en) 2007-10-23 2009-04-29 Roche Diagnostics GmbH Enrichment and sequence analysis of geomic regions
US8592150B2 (en) 2007-12-05 2013-11-26 Complete Genomics, Inc. Methods and compositions for long fragment read sequencing
US8263367B2 (en) 2008-01-25 2012-09-11 Agency For Science, Technology And Research Nucleic acid interaction analysis
WO2009132315A1 (en) 2008-04-24 2009-10-29 Life Technologies Corporation Method of sequencing and mapping target nucleic acids
US20090298064A1 (en) 2008-05-29 2009-12-03 Serafim Batzoglou Genomic Sequencing
GB0810051D0 (en) 2008-06-02 2008-07-09 Oxford Biodynamics Ltd Method of diagnosis
US8076070B2 (en) 2008-08-06 2011-12-13 University Of Southern California Genome-wide chromosome conformation capture
US9434985B2 (en) 2008-09-25 2016-09-06 University Of Massachusetts Methods of identifying interactions between genomic loci
SG171325A1 (en) 2008-11-18 2011-07-28 Bionanomatrix Inc Polynucleotide mapping and sequencing
EP2393940B1 (en) 2009-02-03 2014-12-17 New England Biolabs, Inc. Generation of random double-strand breaks in dna using enzymes
US9524369B2 (en) 2009-06-15 2016-12-20 Complete Genomics, Inc. Processing and analysis of complex nucleic acid sequence data
WO2011028334A2 (en) 2009-08-26 2011-03-10 The Regents Of The University Of Michigan Synthesis and isolation of dendrimer systems
US10072287B2 (en) 2009-09-10 2018-09-11 Centrillion Technology Holdings Corporation Methods of targeted sequencing
WO2011056872A2 (en) 2009-11-03 2011-05-12 Gen9, Inc. Methods and microfluidic devices for the manipulation of droplets in high fidelity polynucleotide assembly
US8841075B1 (en) 2010-04-13 2014-09-23 Cleveland State University Homologous pairing capture assay and related methods and applications
US20110287947A1 (en) 2010-05-18 2011-11-24 University Of Southern California Tethered Conformation Capture
BR112013000552B8 (pt) 2010-07-09 2023-01-17 Cergentis B V Estratégias de sequenciamento de região de interesse genômica em 3d
WO2012047726A1 (en) 2010-09-29 2012-04-12 The Broad Institute, Inc. Methods for chromatin immuno-precipitations
WO2012045012A2 (en) 2010-09-30 2012-04-05 Raindance Technologies, Inc. Sandwich assays in droplets
US20120197533A1 (en) 2010-10-11 2012-08-02 Complete Genomics, Inc. Identifying rearrangements in a sequenced genome
EP2630263B2 (en) 2010-10-22 2021-11-10 Cold Spring Harbor Laboratory Varietal counting of nucleic acids for obtaining genomic copy number information
KR101173257B1 (ko) 2010-10-27 2012-08-10 삼성에스디에스 주식회사 하플로타입 페이징 방법 및 장치
US20140057799A1 (en) 2010-12-16 2014-02-27 Gigagen System and Methods for Massively Parallel Analysis of Nucleic Acids in Single Cells
EP2668294B1 (en) 2011-01-28 2021-04-07 The Broad Institute, Inc. Paired end bead amplification and high throughput sequencing
AU2012212148B8 (en) 2011-02-02 2017-07-06 University Of Washington Through Its Center For Commercialization Massively parallel contiguity mapping
CN103492588A (zh) 2011-02-25 2014-01-01 伊路敏纳公司 用于单体型测定的方法和系统
CN103843001B (zh) 2011-04-14 2017-06-09 考利达基因组股份有限公司 复杂核酸序列数据的处理和分析
EP2705156B1 (en) 2011-05-05 2015-08-26 Institut National de la Santé et de la Recherche Médicale (INSERM) Linear dna amplification
WO2012159025A2 (en) 2011-05-18 2012-11-22 Life Technologies Corporation Chromosome conformation analysis
EP2710172B1 (en) 2011-05-20 2017-03-29 Fluidigm Corporation Nucleic acid encoding reactions
US20120330559A1 (en) 2011-06-21 2012-12-27 Life Technologies Corporation Systems and methods for hybrid assembly of nucleic acid sequences
WO2013078470A2 (en) 2011-11-22 2013-05-30 MOTIF, Active Multiplex isolation of protein-associated nucleic acids
JP6168722B2 (ja) 2012-01-31 2017-07-26 ブラザー工業株式会社 画像形成装置
AU2013251701A1 (en) 2012-04-24 2014-10-30 Gen9, Inc. Methods for sorting nucleic acids and multiplexed preparative in vitro cloning
KR101974577B1 (ko) 2012-05-21 2019-05-02 삼성전자주식회사 나노입자 제작용 주형 및 이를 이용한 나노입자의 제조 방법
ES2675167T3 (es) 2012-07-13 2018-07-09 X-Chem, Inc. Bibliotecas codificadas por ADN que tienen enlaces oligonucleotídicos codificantes no legibles por polimerasas
WO2014047561A1 (en) 2012-09-21 2014-03-27 The Broad Institute Inc. Compositions and methods for labeling of agents
US9411930B2 (en) 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
US11618923B2 (en) 2013-03-15 2023-04-04 The Broad Institute, Inc. Methods of determining multiple interactions between nucleic acids in a cell
WO2015010051A1 (en) * 2013-07-19 2015-01-22 Ludwig Institute For Cancer Research Whole-genome and targeted haplotype reconstruction
CA2933387C (en) * 2013-12-11 2023-05-02 The Regents Of The University Of California Methods for labeling dna fragments to reconstruct physical linkage and phase
WO2015123588A1 (en) 2014-02-13 2015-08-20 Bio-Rad Laboratories, Inc. Chromosome conformation capture in partitions
WO2016019360A1 (en) * 2014-08-01 2016-02-04 Dovetail Genomics Llc Tagging nucleic acids for sequence assembly
US20170283860A1 (en) 2014-09-16 2017-10-05 The Board Of Trustees Of The Leland Stanford Junio University Methods and compositions for the removal of aldehyde adducts and crosslinks from biomolecules
WO2016061517A2 (en) 2014-10-17 2016-04-21 Illumina Cambridge Limited Contiguity preserving transposition
WO2016134034A1 (en) 2015-02-17 2016-08-25 Dovetail Genomics Llc Nucleic acid sequence assembly
WO2016154540A1 (en) * 2015-03-26 2016-09-29 Dovetail Genomics Llc Physical linkage preservation in dna storage
US11326159B2 (en) 2015-04-06 2022-05-10 The Regents Of The University Of California Methods and compositions for long-range haplotype phasing
DK3109324T5 (en) 2015-06-23 2019-02-11 Zytovision Gmbh PROCEDURE FOR THE DETECTION OF CHROMOSOMA DIFFERENCES
EP3822367A1 (en) 2015-06-24 2021-05-19 Oxford BioDynamics PLC Detection processes using sites of chromosome interaction
WO2017007847A1 (en) * 2015-07-07 2017-01-12 The Regents Of The University Of California Method for detecting protein-specific glycosylation
EP3337908A4 (en) 2015-08-18 2019-01-23 The Broad Institute, Inc. METHOD AND COMPOSITIONS FOR CHANGING THE FUNCTION AND STRUCTURE OF CHROMATIN GRINDING AND / OR DOMAINS
CN108368542B (zh) * 2015-10-19 2022-04-08 多弗泰尔基因组学有限责任公司 用于基因组组装、单元型定相以及独立于靶标的核酸检测的方法
EP3420108A4 (en) * 2016-02-23 2019-11-06 Dovetail Genomics LLC GENERATION OF LIVE PHASES FOR THE GENERATION ARRANGEMENT AND HAPLOTYPE PHASE RULES
KR102412442B1 (ko) * 2016-05-13 2022-06-22 더브테일 제노믹스 엘엘씨 보존된 샘플로부터의 장범위 링키지 정보의 회수
AU2019214956B2 (en) 2018-01-31 2025-06-26 Dovetail Genomics, Llc Sample prep for DNA linkage recovery
CN114729400A (zh) 2019-09-23 2022-07-08 元素生物科学公司 用于细胞可寻址核酸测序的方法
WO2021064463A1 (en) 2019-10-04 2021-04-08 Santersus Ag Method for isolating and analyzing cell free dna
WO2023091592A1 (en) 2021-11-19 2023-05-25 Dovetail Genomics, Llc Dendrimers for genomic analysis methods and compositions

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150363550A1 (en) * 2013-02-01 2015-12-17 The Regents Of The University Of California Methods for genome assembly and haplotype phasing

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
NICHOLAS H PUTNAM ET AL: "Chromosome-scale shotgun assembly using an in vitro method for long-range linkage", ARXIV.ORG, CORNELL UNIVERSITY LIBRARY, 18 February 2015, DOI: 1048550/arXiv.1502.05331 *

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