JP7277058B2 - Dna配列のクラスター化のための方法 - Google Patents

Dna配列のクラスター化のための方法 Download PDF

Info

Publication number
JP7277058B2
JP7277058B2 JP2020520434A JP2020520434A JP7277058B2 JP 7277058 B2 JP7277058 B2 JP 7277058B2 JP 2020520434 A JP2020520434 A JP 2020520434A JP 2020520434 A JP2020520434 A JP 2020520434A JP 7277058 B2 JP7277058 B2 JP 7277058B2
Authority
JP
Japan
Prior art keywords
nucleic acid
target nucleic
nucleic acids
item
proximity
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
JP2020520434A
Other languages
English (en)
Japanese (ja)
Other versions
JP2020525046A (ja
JP2020525046A5 (https=
Inventor
イヴァン リアチコ,
ショーン トーマス サリバン,
カイル ラングフォード,
スティーブン エム. エーカー,
Original Assignee
フェーズ ジェノミクス インコーポレイテッド
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by フェーズ ジェノミクス インコーポレイテッド filed Critical フェーズ ジェノミクス インコーポレイテッド
Publication of JP2020525046A publication Critical patent/JP2020525046A/ja
Publication of JP2020525046A5 publication Critical patent/JP2020525046A5/ja
Priority to JP2023032861A priority Critical patent/JP2023065620A/ja
Application granted granted Critical
Publication of JP7277058B2 publication Critical patent/JP7277058B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1093General methods of preparing gene libraries, not provided for in other subgroups
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • C12Q1/6874Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
JP2020520434A 2017-06-26 2018-06-26 Dna配列のクラスター化のための方法 Active JP7277058B2 (ja)

Priority Applications (1)

Application Number Priority Date Filing Date Title
JP2023032861A JP2023065620A (ja) 2017-06-26 2023-03-03 Dna配列のクラスター化のための方法

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762524815P 2017-06-26 2017-06-26
US62/524,815 2017-06-26
PCT/US2018/039454 WO2019005763A1 (en) 2017-06-26 2018-06-26 METHOD FOR REGROUPING DNA SEQUENCES

Related Child Applications (1)

Application Number Title Priority Date Filing Date
JP2023032861A Division JP2023065620A (ja) 2017-06-26 2023-03-03 Dna配列のクラスター化のための方法

Publications (3)

Publication Number Publication Date
JP2020525046A JP2020525046A (ja) 2020-08-27
JP2020525046A5 JP2020525046A5 (https=) 2021-07-26
JP7277058B2 true JP7277058B2 (ja) 2023-05-18

Family

ID=64742178

Family Applications (2)

Application Number Title Priority Date Filing Date
JP2020520434A Active JP7277058B2 (ja) 2017-06-26 2018-06-26 Dna配列のクラスター化のための方法
JP2023032861A Pending JP2023065620A (ja) 2017-06-26 2023-03-03 Dna配列のクラスター化のための方法

Family Applications After (1)

Application Number Title Priority Date Filing Date
JP2023032861A Pending JP2023065620A (ja) 2017-06-26 2023-03-03 Dna配列のクラスター化のための方法

Country Status (5)

Country Link
US (2) US11753637B2 (https=)
EP (1) EP3645547A4 (https=)
JP (2) JP7277058B2 (https=)
CA (1) CA3066745A1 (https=)
WO (1) WO2019005763A1 (https=)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20220403371A1 (en) * 2019-11-15 2022-12-22 Phase Genomics, Inc. Chromosome conformation capture from tissue samples
CN116323973A (zh) * 2020-08-06 2023-06-23 上海绾塍生物科技有限公司 一种分析经固定的细胞的组分的方法

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2016537029A (ja) 2013-11-18 2016-12-01 エラスムス ユニベルジテート メディッシュ セントルム ロッテルダム 三次元dna構造におけるヌクレオチド配列の相互作用を分析する方法

Family Cites Families (51)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5856092A (en) 1989-02-13 1999-01-05 Geneco Pty Ltd Detection of a nucleic acid sequence or a change therein
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
US5744101A (en) 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US5800992A (en) 1989-06-07 1998-09-01 Fodor; Stephen P.A. Method of detecting nucleic acids
US5871928A (en) 1989-06-07 1999-02-16 Fodor; Stephen P. A. Methods for nucleic acid analysis
US5547839A (en) 1989-06-07 1996-08-20 Affymax Technologies N.V. Sequencing of surface immobilized polymers utilizing microflourescence detection
ES2204913T3 (es) 1993-04-12 2004-05-01 Northwestern University Metodo para formacion de oligonucleotidos.
US6045996A (en) 1993-10-26 2000-04-04 Affymetrix, Inc. Hybridization assays on oligonucleotide arrays
US6090555A (en) 1997-12-11 2000-07-18 Affymetrix, Inc. Scanned image alignment systems and methods
US5578832A (en) 1994-09-02 1996-11-26 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
US5631734A (en) 1994-02-10 1997-05-20 Affymetrix, Inc. Method and apparatus for detection of fluorescently labeled materials
US5571639A (en) 1994-05-24 1996-11-05 Affymax Technologies N.V. Computer-aided engineering system for design of sequence arrays and lithographic masks
US5795716A (en) 1994-10-21 1998-08-18 Chee; Mark S. Computer-aided visualization and analysis system for sequence evaluation
US5545531A (en) 1995-06-07 1996-08-13 Affymax Technologies N.V. Methods for making a device for concurrently processing multiple biological chip assays
US5780613A (en) 1995-08-01 1998-07-14 Northwestern University Covalent lock for self-assembled oligonucleotide constructs
US5733729A (en) 1995-09-14 1998-03-31 Affymetrix, Inc. Computer-aided probability base calling for arrays of nucleic acid probes on chips
US6114122A (en) 1996-03-26 2000-09-05 Affymetrix, Inc. Fluidics station with a mounting system and method of using
EP0902885A4 (en) 1996-05-16 2006-09-27 Affymetrix Inc SYSTEMS AND METHODS FOR DETECTION OF BRANDED PRODUCTS
US6420108B2 (en) 1998-02-09 2002-07-16 Affymetrix, Inc. Computer-aided display for comparative gene expression
US6188783B1 (en) 1997-07-25 2001-02-13 Affymetrix, Inc. Method and system for providing a probe array chip design database
US6223127B1 (en) 1997-08-15 2001-04-24 Affymetrix, Inc. Polymorphism detection utilizing clustering analysis
US6201639B1 (en) 1998-03-20 2001-03-13 James W. Overbeck Wide field of view and high speed scanning microscopy
US6185030B1 (en) 1998-03-20 2001-02-06 James W. Overbeck Wide field of view and high speed scanning microscopy
US5936324A (en) 1998-03-30 1999-08-10 Genetic Microsystems Inc. Moving magnet scanner
US6185561B1 (en) 1998-09-17 2001-02-06 Affymetrix, Inc. Method and apparatus for providing and expression data mining database
US6218803B1 (en) 1999-06-04 2001-04-17 Genetic Microsystems, Inc. Position sensing with variable capacitance transducers
US20030097222A1 (en) 2000-01-25 2003-05-22 Craford David M. Method, system, and computer software for providing a genomic web portal
US6386749B1 (en) 2000-06-26 2002-05-14 Affymetrix, Inc. Systems and methods for heating and mixing fluids
US6988040B2 (en) 2001-01-11 2006-01-17 Affymetrix, Inc. System, method, and computer software for genotyping analysis and identification of allelic imbalance
US20020183936A1 (en) 2001-01-24 2002-12-05 Affymetrix, Inc. Method, system, and computer software for providing a genomic web portal
US20030120432A1 (en) 2001-01-29 2003-06-26 Affymetrix, Inc. Method, system and computer software for online ordering of custom probe arrays
US6804679B2 (en) 2001-03-12 2004-10-12 Affymetrix, Inc. System, method, and user interfaces for managing genomic data
US20030100995A1 (en) 2001-07-16 2003-05-29 Affymetrix, Inc. Method, system and computer software for variant information via a web portal
US6872529B2 (en) 2001-07-25 2005-03-29 Affymetrix, Inc. Complexity management of genomic DNA
US20040002818A1 (en) 2001-12-21 2004-01-01 Affymetrix, Inc. Method, system and computer software for providing microarray probe data
US20030120431A1 (en) 2001-12-21 2003-06-26 Affymetrix, Inc. Method and computer software product for genomic alignment and assessment of the transcriptome
JP2004003989A (ja) 2002-03-15 2004-01-08 Affymetrix Inc 生物学的物質の走査のためのシステム、方法、および製品
US20040049354A1 (en) 2002-04-26 2004-03-11 Affymetrix, Inc. Method, system and computer software providing a genomic web portal for functional analysis of alternative splice variants
US20040126840A1 (en) 2002-12-23 2004-07-01 Affymetrix, Inc. Method, system and computer software for providing genomic ontological data
US20050042654A1 (en) 2003-06-27 2005-02-24 Affymetrix, Inc. Genotyping methods
US7317415B2 (en) 2003-08-08 2008-01-08 Affymetrix, Inc. System, method, and product for scanning of biological materials employing dual analog integrators
US20100227770A1 (en) 2005-09-13 2010-09-09 Randall True Brownian microbarcodes for bioassays
WO2008069906A2 (en) * 2006-11-14 2008-06-12 The Regents Of The University Of California Digital expression of gene analysis
WO2009002607A1 (en) * 2007-05-01 2008-12-31 Dana-Farber Cancer Institute, Inc. Compositions and methods for identifying transforming and tumor suppressor genes
EP2173509A4 (en) 2007-06-25 2013-11-06 Affymetrix Inc STRUCTURED MICROCODES
CA2939565C (en) * 2007-10-25 2018-05-01 Landmark Ip Holdings, Llc System and method for anaerobic digestion of biomasses
US9434985B2 (en) * 2008-09-25 2016-09-06 University Of Massachusetts Methods of identifying interactions between genomic loci
WO2015048595A1 (en) * 2013-09-27 2015-04-02 Jay Shendure Methods and systems for large scale scaffolding of genome assemblies
CN103981263B (zh) 2014-05-12 2016-06-29 浙江大学 土壤中抗生素抗性基因的定量检测方法
CA3002740A1 (en) * 2015-10-19 2017-04-27 Dovetail Genomics, Llc Methods for genome assembly, haplotype phasing, and target independent nucleic acid detection
GB201518843D0 (en) * 2015-10-23 2015-12-09 Isis Innovation Method of analysing DNA sequences

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2016537029A (ja) 2013-11-18 2016-12-01 エラスムス ユニベルジテート メディッシュ セントルム ロッテルダム 三次元dna構造におけるヌクレオチド配列の相互作用を分析する方法

Also Published As

Publication number Publication date
CA3066745A1 (en) 2019-01-03
EP3645547A4 (en) 2021-04-21
JP2023065620A (ja) 2023-05-12
WO2019005763A1 (en) 2019-01-03
JP2020525046A (ja) 2020-08-27
EP3645547A1 (en) 2020-05-06
US11753637B2 (en) 2023-09-12
US20240060066A1 (en) 2024-02-22
US20200140943A1 (en) 2020-05-07

Similar Documents

Publication Publication Date Title
JP5986572B2 (ja) 固定化プライマーを使用した標的dnaの直接的な捕捉、増幅、および配列決定
EP3050976B1 (en) Multiplexed genomic gain and loss assays
JP6803327B2 (ja) 標的化されたシークエンシングからのデジタル測定値
JP2004524044A (ja) 制限部位タグ付きマイクロアレイを用いたハイスループットゲノム解析方法
WO2013192292A1 (en) Massively-parallel multiplex locus-specific nucleic acid sequence analysis
US20150024948A1 (en) Method for detecting balanced chromosomal aberrations in a genome
US20240060066A1 (en) Method for the clustering of dna sequences
EP3565906B1 (en) Quantifying dna sequences
US20230374574A1 (en) Compositions and methods for highly sensitive detection of target sequences in multiplex reactions
JP2024035110A (ja) 変異核酸の正確な並行定量するための高感度方法
CN101235418A (zh) 基因变异检体的检测方法、专用设备及用具组
KR20240037181A (ko) 핵산 농축 및 검출
KR20180053679A (ko) 단일 뉴클레오타이드 해상도를 가진 다가 프로브
HK40110042A (zh) 核酸的富集和检测
HK1148316B (en) Multiplexed genomic gain and loss assays

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20210602

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20210602

A977 Report on retrieval

Free format text: JAPANESE INTERMEDIATE CODE: A971007

Effective date: 20220418

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20220428

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20220725

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20220915

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20221027

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20221205

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20230303

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20230412

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20230504

R150 Certificate of patent or registration of utility model

Ref document number: 7277058

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150