KR102412442B1 - 보존된 샘플로부터의 장범위 링키지 정보의 회수 - Google Patents

보존된 샘플로부터의 장범위 링키지 정보의 회수 Download PDF

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KR102412442B1
KR102412442B1 KR1020187036302A KR20187036302A KR102412442B1 KR 102412442 B1 KR102412442 B1 KR 102412442B1 KR 1020187036302 A KR1020187036302 A KR 1020187036302A KR 20187036302 A KR20187036302 A KR 20187036302A KR 102412442 B1 KR102412442 B1 KR 102412442B1
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dna
sample
nucleic acid
preserved
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KR20190037201A (ko
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크리스토퍼 존 트롤
마틴 피 파워스
니콜라스 에이치 퍼트넘
마르코 블란쳇
폴 하틀리
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더브테일 제노믹스 엘엘씨
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    • 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
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    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
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    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/101—Crosslinking agents, e.g. psoralen
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/161—Modifications characterised by incorporating target specific and non-target specific sites
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    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid
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    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/514—Detection characterised by immobilisation to a surface characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array

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  • Chemical & Material Sciences (AREA)
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  • Wood Science & Technology (AREA)
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  • General Chemical & Material Sciences (AREA)
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  • Biomedical Technology (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Transition And Organic Metals Composition Catalysts For Addition Polymerization (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
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KR1020187036302A 2016-05-13 2017-05-12 보존된 샘플로부터의 장범위 링키지 정보의 회수 Active KR102412442B1 (ko)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662336252P 2016-05-13 2016-05-13
US62/336,252 2016-05-13
US201662410599P 2016-10-20 2016-10-20
US62/410,599 2016-10-20
PCT/US2017/032466 WO2017197300A1 (en) 2016-05-13 2017-05-12 Recovering long-range linkage information from preserved samples

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KR20190037201A KR20190037201A (ko) 2019-04-05
KR102412442B1 true KR102412442B1 (ko) 2022-06-22

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US (3) US10947579B2 (cg-RX-API-DMAC7.html)
EP (2) EP3455356B1 (cg-RX-API-DMAC7.html)
JP (2) JP7497976B2 (cg-RX-API-DMAC7.html)
KR (1) KR102412442B1 (cg-RX-API-DMAC7.html)
CN (1) CN109477101B (cg-RX-API-DMAC7.html)
AU (1) AU2017263810B2 (cg-RX-API-DMAC7.html)
CA (1) CA3023990C (cg-RX-API-DMAC7.html)
DK (1) DK3455356T3 (cg-RX-API-DMAC7.html)
IL (1) IL262946B2 (cg-RX-API-DMAC7.html)
SG (1) SG11201810088SA (cg-RX-API-DMAC7.html)
WO (1) WO2017197300A1 (cg-RX-API-DMAC7.html)

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4219710A3 (en) 2014-08-01 2023-08-16 Dovetail Genomics, LLC Tagging nucleic acids for sequence assembly
GB2554572B (en) 2015-03-26 2021-06-23 Dovetail Genomics Llc Physical linkage preservation in DNA storage
CN107922959A (zh) 2015-07-02 2018-04-17 阿瑞玛基因组学公司 混合物样品的精确分子去卷积
KR102744506B1 (ko) * 2016-02-23 2024-12-18 더브테일 제노믹스 엘엘씨 게놈 어셈블리를 위한 페이징된 판독 세트의 생성 및 반수체형 페이징
SG11201810088SA (en) * 2016-05-13 2018-12-28 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
US11873481B2 (en) 2017-11-21 2024-01-16 Arima Genomics, Inc. Preserving spatial-proximal contiguity and molecular contiguity in nucleic acid templates
CA3090102A1 (en) * 2018-01-31 2019-08-08 Dovetail Genomics, Llc Sample prep for dna linkage recovery
WO2019217819A1 (en) * 2018-05-10 2019-11-14 The University Of North Carolina At Chapel Hill Method to extract chromatin from formalin fixed, paraffin embedded (ffpe) tissue
CN113272441A (zh) * 2018-11-20 2021-08-17 阿瑞玛基因组学公司 保留空间邻近连续性信息的制备核酸的方法和组合物
US20220267826A1 (en) * 2019-06-27 2022-08-25 Dovetail Genomics, Llc Methods and compositions for proximity ligation
AU2020381516A1 (en) * 2019-11-15 2022-06-02 Phase Genomics Inc. Chromosome conformation capture from tissue samples
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
WO2025059045A1 (en) * 2023-09-12 2025-03-20 Illumina, Inc. Systems and methods for determining linkage of sequence reads on a flow cell
WO2025072119A1 (en) * 2023-09-26 2025-04-03 10X Genomics, Inc. Methods, compositions, and kits for detecting spatial chromosomal interactions
WO2025155628A1 (en) * 2024-01-16 2025-07-24 The Regents Of The University Of California Interpretable deep learning predicts chemoresistance

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016044313A1 (en) * 2014-09-16 2016-03-24 The Board Of Trustees Of The Leland Stanford Junior University Methods and compositions for the removal of aldehyde adducts and crosslinks from biomolecules

Family Cites Families (188)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
US4277437A (en) 1978-04-05 1981-07-07 Syva Company Kit for carrying out chemically induced fluorescence immunoassay
US4275149A (en) 1978-11-24 1981-06-23 Syva Company Macromolecular environment control in specific receptor assays
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
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
EP1046421B8 (en) 1990-12-06 2006-01-11 Affymetrix, Inc. (a Delaware Corporation) Methods and reagents for very large scale immobilized polymer synthesis
US5994056A (en) 1991-05-02 1999-11-30 Roche Molecular Systems, Inc. Homogeneous methods for nucleic acid amplification and detection
ATE262374T1 (de) 1991-11-22 2004-04-15 Affymetrix Inc Kombinatorische strategien für polymersynthese
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
ATE246702T1 (de) 1993-04-12 2003-08-15 Univ Northwestern Verfahren zur darstellung von oligonukleotiden
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
US6632598B1 (en) * 1994-03-11 2003-10-14 Biogenex Laboratories Deparaffinization compositions and methods for their use
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
US6228575B1 (en) 1996-02-08 2001-05-08 Affymetrix, Inc. Chip-based species identification and phenotypic characterization of microorganisms
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
CA2591550C (en) 1996-06-04 2009-04-28 University Of Utah Research Foundation Monitoring hybridization during pcr
US6117635A (en) 1996-07-16 2000-09-12 Intergen Company Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon
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
EP2034031A1 (en) 1997-10-28 2009-03-11 Los Alamos National Security, LLC DNA polymorphism identity determination 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
US20030022207A1 (en) 1998-10-16 2003-01-30 Solexa, Ltd. Arrayed polynucleotides and their use in genome analysis
US20040106110A1 (en) 1998-07-30 2004-06-03 Solexa, Ltd. Preparation of polynucleotide arrays
US6787308B2 (en) 1998-07-30 2004-09-07 Solexa Ltd. Arrayed biomolecules and their use in sequencing
CN1313908A (zh) 1998-08-21 2001-09-19 纳克斯科尔公司 使用可交联的固定的核酸的检测法
HK1039355B (en) 1998-12-02 2007-09-21 Bristol-Myers Squibb Company Dna-protein fusions and uses thereof
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
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
JP2005519635A (ja) 2001-05-11 2005-07-07 レギュローム コーポレーション 活性クロマチンエレメントを含むｄｎａマイクロアレイおよびそれを用いた包括的プロファイリング
GB0114853D0 (en) 2001-06-18 2001-08-08 Medical Res Council Happier Mapping
WO2003020968A2 (de) 2001-08-29 2003-03-13 Genovoxx Gmbh Verfahren zur analyse von nukleinsäurekettensequenzen und der genexpression
DE10246005A1 (de) 2001-10-04 2003-04-30 Genovoxx Gmbh Gerät zur Sequenzierung von Nukleinsäuremolekülen
DE10149786B4 (de) 2001-10-09 2013-04-25 Dmitry Cherkasov Oberfläche für Untersuchungen aus Populationen von Einzelmolekülen
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US20050124022A1 (en) 2001-10-30 2005-06-09 Maithreyan Srinivasan Novel sulfurylase-luciferase fusion proteins and thermostable sulfurylase
CA2465588A1 (en) 2001-11-09 2003-05-22 Aclara Biosciences, Inc. Detection of nucleic acid sequences by cleavage and separation of tag-containing structures
AU2003214395A1 (en) 2002-03-08 2003-09-22 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
CN1665938B (zh) 2002-06-28 2012-10-10 普里梅拉蒂斯有限公司 检测序列差异的方法
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
CN102212614B (zh) 2003-01-29 2013-12-25 454生命科学公司 核酸扩增和测序的方法
CA2515424A1 (en) 2003-02-06 2004-08-26 Bioresponse, Llc The combined use of cruciferous indoles and chelators for the treatment of papillomavirus-related conditions
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
PT1639122E (pt) 2003-07-02 2009-04-09 Dsm Ip Assets Bv Sistema de teste aperfeiçoado para determinar a presença de um antibiótico num fluido
GB0316075D0 (en) 2003-07-09 2003-08-13 Molecular Sensing Plc Protease detection assay
US8637650B2 (en) 2003-11-05 2014-01-28 Genovoxx Gmbh Macromolecular nucleotide compounds and methods for using the same
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
RU2006134341A (ru) 2004-02-28 2008-04-10 Чан-Нин ДжВАН Чан-Нин Дж. ВАН (US). (US) Комплексы нуклеиновых кислот
DE102004025694A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren und Oberfläche zu hochparallelen Analysen von Nukleinsäureketten
DE102004025696A1 (de) 2004-05-26 2006-02-23 Dmitry Cherkasov Verfahren, Oberfläche und Substrate 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
DE102004025744A1 (de) 2004-05-26 2005-12-29 Dmitry Cherkasov Oberfläche für die Analysen an einzelnen Nukleinsäuremolekülen
DE102004025746A1 (de) 2004-05-26 2005-12-15 Dmitry Cherkasov Verfahren, Oberfläche und Substrate zur hochparallelen Sequenzierung von Nukleinsäureketten
US7361468B2 (en) 2004-07-02 2008-04-22 Affymetrix, Inc. Methods for genotyping polymorphisms in humans
US20060024711A1 (en) 2004-07-02 2006-02-02 Helicos Biosciences Corporation Methods for nucleic acid amplification and sequence determination
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
US9035035B2 (en) 2004-11-05 2015-05-19 Genovoxx Gmbh Macromolecular nucleotide compounds and methods for using the same
WO2006073910A2 (en) * 2004-12-30 2006-07-13 Ventana Medical Systems, Inc. Low temperature deparaffinization
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
CN101466847B (zh) 2005-06-15 2014-02-19 考利达基因组股份有限公司 用于遗传和化学分析的单分子阵列
NZ564262A (en) 2005-07-04 2010-02-26 Univ Erasmus Medical Ct Chromosome conformation capture-on-chip (4C) assay
US20080233101A1 (en) 2005-09-15 2008-09-25 The Regents Of The University Of California RNA-mediated epigenetic regulation of gene transcription
DE102005060738A1 (de) * 2005-12-16 2007-06-21 Qiagen Gmbh Verfahren zur Extraktion von Biomolekülen aus fixierten Geweben
WO2007074747A1 (ja) 2005-12-26 2007-07-05 Kuraray Co., Ltd. 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
SG170028A1 (en) * 2006-02-24 2011-04-29 Callida Genomics Inc High throughput genome sequencing on dna arrays
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
US20080015494A1 (en) 2006-07-11 2008-01-17 Microchips, Inc. Multi-reservoir pump device for dialysis, biosensing, or delivery of substances
WO2008024473A2 (en) 2006-08-24 2008-02-28 University Of Massachusetts Medical School Mapping of genomic interactions
CA2665537A1 (en) 2006-10-04 2008-10-23 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
ES2634266T3 (es) 2007-01-11 2017-09-27 Erasmus University Medical Center Captura de conformación cromosómica circular (4C)
US20100093986A1 (en) 2007-02-02 2010-04-15 Zwick Michael E Methods of direct genomic selection using high density oligonucleotide microarrays
US9096906B2 (en) * 2007-03-27 2015-08-04 Rosetta Genomics Ltd. Gene expression signature for classification of tissue of origin of tumor samples
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
WO2009052214A2 (en) 2007-10-15 2009-04-23 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
JPWO2009078386A1 (ja) * 2007-12-14 2011-04-28 中外製薬株式会社 組織形態保持および核酸品質保持に優れた新規標本作製法
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
US20100099074A1 (en) 2008-07-25 2010-04-22 Garry Nolan Collection device and method for stimulating and stabilizing a biological sample
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
WO2010059731A2 (en) 2008-11-18 2010-05-27 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
WO2011032040A1 (en) 2009-09-10 2011-03-17 Centrillion Technology Holding 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
US9422542B2 (en) * 2010-02-26 2016-08-23 Qiagen Gmbh Process for parallel isolation and/or purification of RNA and DNA
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
RU2603082C2 (ru) 2010-07-09 2016-11-20 Сергентис Б.В. Способы секвенирования трехмерной структуры исследуемой области генома
DK2611916T3 (en) 2010-09-02 2017-04-10 Qiagen Gmbh PROCEDURE FOR INSULATING A TARGET NUCLEIC ACID, INCLUDING SMALL TARGET ACIDS, WITH HIGH Yield
WO2012047726A1 (en) 2010-09-29 2012-04-12 The Broad Institute, Inc. Methods for chromatin immuno-precipitations
EP2622103B2 (en) 2010-09-30 2022-11-16 Bio-Rad Laboratories, Inc. Sandwich assays in droplets
US20120197533A1 (en) 2010-10-11 2012-08-02 Complete Genomics, Inc. Identifying rearrangements in a sequenced genome
CA2815076C (en) 2010-10-22 2021-01-12 Cold Spring Harbor Laboratory Varietal counting of nucleic acids for obtaining genomic copy number information
WO2012083225A2 (en) 2010-12-16 2012-06-21 Gigagen, Inc. System and methods for massively parallel analysis of nycleic acids in single cells
WO2012103442A2 (en) * 2011-01-28 2012-08-02 The Broad Institute, Inc. Paired end bead amplification and high throughput sequencing
US10457936B2 (en) 2011-02-02 2019-10-29 University Of Washington Through Its Center For Commercialization Massively parallel contiguity mapping
WO2012116331A2 (en) 2011-02-25 2012-08-30 Illumina, Inc. Methods and systems for haplotype determination
WO2012150317A1 (en) 2011-05-05 2012-11-08 Institut National De La Sante Et De La Recherche Medicale (Inserm) Linear dna amplification
JP2014516514A (ja) 2011-04-14 2014-07-17 コンプリート・ジェノミックス・インコーポレイテッド 複合核酸配列データの処理および解析
WO2012159025A2 (en) 2011-05-18 2012-11-22 Life Technologies Corporation Chromosome conformation analysis
WO2012162267A2 (en) 2011-05-20 2012-11-29 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
EP4001427A1 (en) 2012-04-24 2022-05-25 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
EA201992285A1 (ru) 2012-07-13 2020-05-31 Икс-Чем, Инк. Днк-кодированные библиотеки, содержащие связи кодирующих олигонуклеотидов, не доступные для считывания полимеразами
WO2014047561A1 (en) 2012-09-21 2014-03-27 The Broad Institute Inc. Compositions and methods for labeling of agents
WO2014087137A1 (en) * 2012-12-07 2014-06-12 Sarissa Biomedical Limited Device including biosensor and holder
US9411930B2 (en) 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
CA3209385A1 (en) 2013-02-01 2014-08-07 The Regents Of The University Of California Methods for genome assembly and haplotype phasing
TWI462930B (zh) * 2013-06-06 2014-12-01 Rbc Bioscience Corp 福馬林固定石蠟包埋樣本核酸分離方法
GB201320351D0 (en) 2013-11-18 2014-01-01 Erasmus Universiteit Medisch Ct Method
EP3071706B1 (en) 2013-11-21 2018-04-25 Assistance Publique-Hôpitaux de Paris Method for detecting chromosomal rearrangements
AU2014362322B2 (en) 2013-12-11 2021-05-27 The Regents For Of The University Of California Methods for labeling DNA fragments to recontruct physical linkage and phase
WO2015123588A1 (en) 2014-02-13 2015-08-20 Bio-Rad Laboratories, Inc. Chromosome conformation capture in partitions
EP4219710A3 (en) 2014-08-01 2023-08-16 Dovetail Genomics, LLC Tagging nucleic acids for sequence assembly
JP6443450B2 (ja) * 2014-09-19 2018-12-26 コニカミノルタ株式会社 画像処理装置、画像処理方法、及びプログラム
BR122021026781B1 (pt) * 2014-10-17 2023-11-14 Illumina Cambridge Limited Transposon de preservação de contiguidade
EP3227462B1 (en) 2014-12-01 2020-04-22 The Broad Institute, Inc. Method for in situ determination of nucleic acid proximity
SG11201706730XA (en) 2015-02-17 2017-09-28 Dovetail Genomics Llc Nucleic acid sequence assembly
GB2554572B (en) 2015-03-26 2021-06-23 Dovetail Genomics Llc Physical linkage preservation in DNA storage
WO2016164313A1 (en) 2015-04-06 2016-10-13 The Regents Of The University Of California Methods and compositions for long-range haplotype phasing
WO2016168429A1 (en) * 2015-04-14 2016-10-20 Arizona Board Of Regents, A Body Corporate Of The State Of Arizona, Acting For And On Behalf Of Arizona State University Method and apparatus for extracting and collecting single cells from formalin-fixed paraffin embedded tissues
WO2016207653A1 (en) 2015-06-24 2016-12-29 Oxford Biodynamics Limited Detection of chromosome interactions
KR20180096586A (ko) 2015-10-19 2018-08-29 더브테일 제노믹스 엘엘씨 게놈 어셈블리, 하플로타입 페이징 및 표적 독립적 핵산 검출을 위한 방법
KR102723865B1 (ko) * 2015-12-04 2024-10-29 10엑스 제노믹스, 인크. 핵산 분석을 위한 방법 및 조성물
KR102744506B1 (ko) 2016-02-23 2024-12-18 더브테일 제노믹스 엘엘씨 게놈 어셈블리를 위한 페이징된 판독 세트의 생성 및 반수체형 페이징
US11173488B2 (en) * 2016-04-22 2021-11-16 Purdue Research Foundation High-throughput particle capture and analysis
SG11201810088SA (en) * 2016-05-13 2018-12-28 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
CA3060539A1 (en) 2017-04-18 2018-10-25 Dovetail Genomics, Llc Nucleic acid characteristics as guides for sequence assembly
CA3082050A1 (en) 2017-11-09 2019-05-16 Dovetail Genomics, Llc Structural variant analysis
CA3090102A1 (en) 2018-01-31 2019-08-08 Dovetail Genomics, Llc Sample prep for dna linkage recovery
US20220267826A1 (en) 2019-06-27 2022-08-25 Dovetail Genomics, Llc Methods and compositions for proximity ligation
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
WO2023091592A1 (en) 2021-11-19 2023-05-25 Dovetail Genomics, Llc Dendrimers for genomic analysis methods and compositions
CA3249871A1 (en) 2022-01-25 2023-08-03 Dovetail Genomics, Llc TYPING AND PHASING METHODS FOR HUMAN LEUKOCYTE ANTIGENS

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016044313A1 (en) * 2014-09-16 2016-03-24 The Board Of Trustees Of The Leland Stanford Junior University Methods and compositions for the removal of aldehyde adducts and crosslinks from biomolecules

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