CO2019004124A2 - Método y sistema para la preparación y secuenciación de biblioteca basada en crispr - Google Patents

Método y sistema para la preparación y secuenciación de biblioteca basada en crispr

Info

Publication number
CO2019004124A2
CO2019004124A2 CONC2019/0004124A CO2019004124A CO2019004124A2 CO 2019004124 A2 CO2019004124 A2 CO 2019004124A2 CO 2019004124 A CO2019004124 A CO 2019004124A CO 2019004124 A2 CO2019004124 A2 CO 2019004124A2
Authority
CO
Colombia
Prior art keywords
sequencing
share
crispr
preparation
end regions
Prior art date
Application number
CONC2019/0004124A
Other languages
English (en)
Inventor
Daniel Almonacid
Zachary Apte
Jessica Richman
Rodrigo Ortiz
Audrey Goddard
Sara Bird
Eduardo Morales
Original Assignee
Ubiome Inc
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 Ubiome Inc filed Critical Ubiome Inc
Publication of CO2019004124A2 publication Critical patent/CO2019004124A2/es

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1082—Preparation or screening gene libraries by chromosomal integration of polynucleotide sequences, HR-, site-specific-recombination, transposons, viral vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • 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
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
    • 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
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/113—PCR
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Analytical Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Virology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Chemical Kinetics & Catalysis (AREA)

Abstract

Representaciones de un método y sistema para mejorar la secuenciación de microbiomas puede incluir: generar complejos de RNA guia para un conjunto de objetivos correspondientes con un grupo de taxones asociados con la condición relacionada con microorganismos; procesar la muestra biológica con los complejos de gRNA para generar fragmentos de ácido nucleico de microorganismos que comprenden un conjunto de regiones extremas asociadas con el conjunto de objetivos; ligar el conjunto de regiones finales con un conjunto de adaptadores que comparten una secuencia de adaptador; y amplificar el conjunto de objetivos basado en el conjunto ligado de regiones finales y un conjunto de partidores que comparten una secuencia de partidor asociada con la secuencia adaptadora.
CONC2019/0004124A 2016-09-27 2019-04-25 Método y sistema para la preparación y secuenciación de biblioteca basada en crispr CO2019004124A2 (es)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662400401P 2016-09-27 2016-09-27
PCT/US2017/053822 WO2018064226A1 (en) 2016-09-27 2017-09-27 Method and system for crispr-based library preparation and sequencing

Publications (1)

Publication Number Publication Date
CO2019004124A2 true CO2019004124A2 (es) 2019-05-10

Family

ID=61687683

Family Applications (1)

Application Number Title Priority Date Filing Date
CONC2019/0004124A CO2019004124A2 (es) 2016-09-27 2019-04-25 Método y sistema para la preparación y secuenciación de biblioteca basada en crispr

Country Status (13)

Country Link
US (1) US11572555B2 (es)
EP (1) EP3519593A1 (es)
JP (1) JP7239988B2 (es)
KR (1) KR20190052132A (es)
CN (1) CN109790576A (es)
AU (1) AU2017335766A1 (es)
BR (1) BR112019005810A2 (es)
CA (1) CA3038661A1 (es)
CO (1) CO2019004124A2 (es)
EA (1) EA201990599A1 (es)
SG (1) SG11201901730QA (es)
WO (1) WO2018064226A1 (es)
ZA (1) ZA201901372B (es)

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CA3097742A1 (en) * 2018-04-18 2019-10-24 Ligandal, Inc. Methods and compositions for genome editing
WO2020041702A1 (en) * 2018-08-24 2020-02-27 Swift Biosciences, Inc. Asymmetric targeted amplification methods
CN110541026A (zh) * 2019-08-17 2019-12-06 昆明医科大学第一附属医院 一种检测溃疡性结肠炎的生物标志物及应用
CN112080571B (zh) * 2020-09-22 2022-11-11 扬州大学 基于CRISPR-Cas12b系统的空肠弯曲菌检测试剂盒和方法
CN112176048A (zh) * 2020-11-02 2021-01-05 光明乳业股份有限公司 一种发酵乳的杂菌检测方法
CN112029699B (zh) * 2020-11-04 2021-06-08 中国农业科学院北京畜牧兽医研究所 一种基于内源CRISPR-Cas系统的丁酸梭菌基因编辑系统及其应用
KR102304402B1 (ko) * 2021-03-26 2021-09-24 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 비만 여부를 판별하는 방법 및 진단 장치
KR20220158948A (ko) * 2021-05-25 2022-12-02 주식회사 에이치이엠파마 머신러닝 모델을 이용하여 복부팽만 유무를 판별하는 방법 및 진단 장치
CN113528633B (zh) * 2021-08-12 2024-06-11 湖北伯远合成生物科技有限公司 一种快速分析CRISPR/Cas9基因编辑载体构建情况的方法及应用

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JP2004536553A (ja) 2000-09-30 2004-12-09 ディヴァーサ コーポレイション 始原ゲノムの本質部分突然変異、突然変異の組合せおよび任意反復による全細胞工学
EP1590477B1 (en) 2003-01-29 2009-07-29 454 Corporation Methods of amplifying and sequencing nucleic acids
WO2007100384A2 (en) * 2005-10-24 2007-09-07 Invitrogen Corporation Three frame cdna expression libraries for functional screening of proteins
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Also Published As

Publication number Publication date
KR20190052132A (ko) 2019-05-15
US11572555B2 (en) 2023-02-07
AU2017335766A1 (en) 2019-03-28
BR112019005810A2 (pt) 2019-06-25
JP7239988B2 (ja) 2023-03-15
WO2018064226A1 (en) 2018-04-05
EA201990599A1 (ru) 2019-10-31
JP2019528752A (ja) 2019-10-17
ZA201901372B (en) 2019-11-27
CN109790576A (zh) 2019-05-21
CA3038661A1 (en) 2018-04-05
SG11201901730QA (en) 2019-03-28
US20180087051A1 (en) 2018-03-29
EP3519593A1 (en) 2019-08-07

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