AU2020301025A1 - 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

Info

Publication number
AU2020301025A1
AU2020301025A1 AU2020301025A AU2020301025A AU2020301025A1 AU 2020301025 A1 AU2020301025 A1 AU 2020301025A1 AU 2020301025 A AU2020301025 A AU 2020301025A AU 2020301025 A AU2020301025 A AU 2020301025A AU 2020301025 A1 AU2020301025 A1 AU 2020301025A1
Authority
AU
Australia
Prior art keywords
target
sequences
site
specific
cut
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.)
Pending
Application number
AU2020301025A
Other languages
English (en)
Inventor
Gavin KURGAN
Heng Li
Matthew Mcneill
Yu Wang
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Integrated DNA Technologies Inc
Original Assignee
Integrated DNA Technologies 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 Integrated DNA Technologies Inc filed Critical Integrated DNA Technologies Inc
Publication of AU2020301025A1 publication Critical patent/AU2020301025A1/en
Pending legal-status Critical Current

Links

Classifications

    • 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
    • C12Q1/6844—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

Landscapes

  • 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)
AU2020301025A 2019-07-03 2020-07-02 Identification, characterization, and quantitation of CRISPR-introduced double-stranded DNA break repairs Pending AU2020301025A1 (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
AU2020301025A1 true AU2020301025A1 (en) 2022-01-20

Family

ID=74065411

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2020301025A Pending AU2020301025A1 (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
CA3144106A1 (en) 2021-01-07
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

Similar Documents

Publication Publication Date Title
US20250218536A1 (en) Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs
Höijer et al. CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations
US20240417795A1 (en) Screening for structural variants
Brinkman et al. Rapid quantitative evaluation of CRISPR genome editing by TIDE and TIDER
Haile et al. Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples
US20180355380A1 (en) Methods and kits for quality control
JP2026048971A (ja) 「ＣＴＬ－ｓｅｑ」（ＣＲＩＳＰＲ Ｔａｇ Ｌｉｎｅａｒ－ｓｅｑ）と称するヌクレアーゼオン／オフターゲット編集位置を指定するための方法
JP7724785B2 (ja) 複雑なゲノム領域を解析するための方法およびシステム
US20230366020A1 (en) Use of unique molecular identifiers for improved accuracy of long read sequencing and characterization of crispr editing
Su et al. Enhancing RNA-seq bias mitigation with the Gaussian self-benchmarking framework: towards unbiased sequencing data
CN117441026A (zh) 用于分析复杂基因组区域的方法和系统
Bemmelen et al. Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes
Nobles iGUIDE method for CRISPR off-target detection
WO2018026576A1 (en) Genomic analysis of cord blood
Varapula et al. Recent Applications of CRISPR-Cas9 in Genome Mapping and Sequencing
CA3010579C (en) Screening for structural variants
Burnham et al. An Enhancement of Extrachromosomal Circular DNA Enrichment and Amplification to Address the Extremely Low Overlap Between Replicates
US9637779B2 (en) Antisense transcriptomes of cells
Tang Retrotransposon Insertions in Cancer
HK40004815B (en) Method and device for acquiring fetal free dna concentration
HK40004815A (en) Method and device for acquiring fetal free dna concentration
WO2018066317A1 (ja) 必要なローカス数を決定する方法および必要なＳＮＰｓ座位数を決定する方法