CA3144106A1 - Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs - Google Patents

Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs Download PDF

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Publication number
CA3144106A1
CA3144106A1 CA3144106A CA3144106A CA3144106A1 CA 3144106 A1 CA3144106 A1 CA 3144106A1 CA 3144106 A CA3144106 A CA 3144106A CA 3144106 A CA3144106 A CA 3144106A CA 3144106 A1 CA3144106 A1 CA 3144106A1
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French (fr)
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Heng Li
Gavin KURGAN
Matthew Mcneill
Yu Wang
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Integrated DNA Technologies Inc
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Integrated DNA Technologies Inc
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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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • G16B20/30—Detection of binding sites or motifs
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B30/20—Sequence assembly
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

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  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3144106A 2019-07-03 2020-07-02 Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs Pending CA3144106A1 (en)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US201962870471P 2019-07-03 2019-07-03
US201962870426P 2019-07-03 2019-07-03
US62/870,426 2019-07-03
US62/870,471 2019-07-03
US201962952603P 2019-12-23 2019-12-23
US201962952598P 2019-12-23 2019-12-23
US62/952,598 2019-12-23
US62/952,603 2019-12-23
PCT/US2020/040621 WO2021003343A1 (en) 2019-07-03 2020-07-02 Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs

Publications (1)

Publication Number Publication Date
CA3144106A1 true CA3144106A1 (en) 2021-01-07

Family

ID=74065411

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3144106A Pending CA3144106A1 (en) 2019-07-03 2020-07-02 Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs

Country Status (7)

Country Link
US (2) US12254959B2 (https=)
EP (1) EP3994258A4 (https=)
JP (2) JP7579817B2 (https=)
AU (1) AU2020301025A1 (https=)
CA (1) CA3144106A1 (https=)
IL (1) IL289421A (https=)
WO (1) WO2021003343A1 (https=)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN119193713A (zh) 2019-10-24 2024-12-27 合成Dna技术公司 修饰的双链供体模板
CN119343462A (zh) 2022-05-13 2025-01-21 合成Dna技术公司 使用独特分子标识符改善长读测序的准确性和crispr编辑的表征
WO2026039499A1 (en) 2024-08-14 2026-02-19 Integrated Dna Technologies, Inc. Adaptered-tag blocking oligonucleotides

Family Cites Families (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9809904B2 (en) 2011-04-21 2017-11-07 University Of Washington Through Its Center For Commercialization Methods for retrieval of sequence-verified DNA constructs
CN111254500B (zh) 2012-12-10 2024-01-23 分析生物科学有限公司 靶向基因组分析的方法
CA2906365A1 (en) 2013-03-15 2014-09-18 Integrated Dna Technologies, Inc. Rnase h-based assays utilizing modified rna monomers
US11306328B2 (en) 2013-07-26 2022-04-19 President And Fellows Of Harvard College Genome engineering
WO2015113063A1 (en) * 2014-01-27 2015-07-30 Georgia Tech Research Corporation Methods and systems for identifying crispr/cas off-target sites
CN106604994B (zh) 2014-06-23 2021-12-14 通用医疗公司 通过测序评估的DSBs的全基因组无偏鉴定(GUIDE-Seq)
WO2016030899A1 (en) 2014-08-28 2016-03-03 Yeda Research And Development Co. Ltd. Methods of treating amyotrophic lateral scleroses
EP3221813A4 (en) 2014-11-20 2018-04-18 Children's Medical Center Corporation Methods relating to the detection of recurrent and non-specific double strand breaks in the genome
EP3234192B1 (en) * 2014-12-19 2021-07-14 The Broad Institute, Inc. Unbiased identification of double-strand breaks and genomic rearrangement by genome-wide insert capture sequencing
WO2016138500A1 (en) 2015-02-27 2016-09-01 Cellular Research, Inc. Methods and compositions for barcoding nucleic acids for sequencing
US9790490B2 (en) * 2015-06-18 2017-10-17 The Broad Institute Inc. CRISPR enzymes and systems
JP2018523991A (ja) 2015-06-22 2018-08-30 マクマスター・ユニバーシティＭｃｍａｓｔｅｒ Ｕｎｉｖｅｒｓｉｔｙ 構造スイッチングのタンデム反応、核酸分解消化および核酸アセンブリーの増幅を含むバイオセンサー
WO2017040511A1 (en) 2015-08-31 2017-03-09 Agilent Technologies, Inc. Compounds and methods for crispr/cas-based genome editing by homologous recombination
US20170081679A1 (en) 2015-09-22 2017-03-23 Jie Xu Methods of improving nuclease mediated homologous recombination
EP4144844B1 (en) 2015-10-12 2025-09-10 DuPont US Holding, LLC Protected dna templates for gene modification and increased homologous recombination in cells and methods of use
CN116814590A (zh) 2015-10-22 2023-09-29 布罗德研究所有限公司 Vi-b型crispr酶和系统
CN116064748A (zh) 2015-11-25 2023-05-05 综合基因技术公司 用于变体检测的方法
GB201602473D0 (en) 2016-02-11 2016-03-30 Horizon Discovery Ltd Replicative transposon system
US11810649B2 (en) * 2016-08-17 2023-11-07 The Broad Institute, Inc. Methods for identifying novel gene editing elements
ES2962711T3 (es) 2016-12-20 2024-03-20 Bristol Myers Squibb Co Métodos para aumentar la eficacia de la reparación dirigida por homología (HDR) en el genoma celular
US11981898B2 (en) 2017-06-16 2024-05-14 Applied Stemcell, Inc. Gene editing methods with increased knock-in efficiency
US20190062736A1 (en) * 2017-08-22 2019-02-28 Board Of Regents, The University Of Texas System In situ and in vivo analysis of chromatin interactions by biotinylated dcas9 protein
EP3679143A1 (en) 2017-09-08 2020-07-15 Life Technologies Corporation Methods for improved homologous recombination and compositions thereof
WO2019110067A1 (en) 2017-12-07 2019-06-13 Aarhus Universitet Hybrid nanoparticle
US12406749B2 (en) * 2017-12-15 2025-09-02 The Broad Institute, Inc. Systems and methods for predicting repair outcomes in genetic engineering
BR112020018902A2 (pt) 2018-03-20 2021-01-26 Tokyo Institute Of Technology oligonucleotídeo antissenso com toxicidade reduzida
WO2019246553A1 (en) * 2018-06-21 2019-12-26 Memorial Sloan Kettering Cancer Center Compositions & methods for monitoring dna repair
EP3935185A1 (en) 2019-03-04 2022-01-12 King Abdullah University Of Science And Technology Compositions and methods of labeling nucleic acids and sequencing and analysis thereof
CN119193713A (zh) 2019-10-24 2024-12-27 合成Dna技术公司 修饰的双链供体模板

Also Published As

Publication number Publication date
EP3994258A4 (en) 2022-10-26
WO2021003343A1 (en) 2021-01-07
JP7579817B2 (ja) 2024-11-08
AU2020301025A1 (en) 2022-01-20
US20250218536A1 (en) 2025-07-03
JP2022540792A (ja) 2022-09-20
US12254959B2 (en) 2025-03-18
JP2025014002A (ja) 2025-01-28
EP3994258A1 (en) 2022-05-11
US20210002700A1 (en) 2021-01-07
IL289421A (en) 2022-02-01

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