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

Info

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
Authority
CA
Canada
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
CA3144106A
Other languages
English (en)
French (fr)
Inventor
Heng Li
Gavin KURGAN
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 CA3144106A1 publication Critical patent/CA3144106A1/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)
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
US62/870,471 2019-07-03
US62/870,426 2019-07-03
US201962952598P 2019-12-23 2019-12-23
US201962952603P 2019-12-23 2019-12-23
US62/952,603 2019-12-23
US62/952,598 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 (cg-RX-API-DMAC10.html)
EP (1) EP3994258A4 (cg-RX-API-DMAC10.html)
JP (2) JP7579817B2 (cg-RX-API-DMAC10.html)
AU (1) AU2020301025B2 (cg-RX-API-DMAC10.html)
CA (1) CA3144106A1 (cg-RX-API-DMAC10.html)
IL (1) IL289421A (cg-RX-API-DMAC10.html)
WO (1) WO2021003343A1 (cg-RX-API-DMAC10.html)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA3154370A1 (en) 2019-10-24 2021-04-29 Jessica WOODLEY Modified double-stranded donor templates
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
US20260049352A1 (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
CN105531375B (zh) 2012-12-10 2020-03-03 分析生物科学有限公司 靶向基因组分析的方法
AU2013381709A1 (en) 2013-03-15 2015-10-01 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
AU2015280069B2 (en) 2014-06-23 2021-08-12 The General Hospital Corporation Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq)
WO2016030899A1 (en) 2014-08-28 2016-03-03 Yeda Research And Development Co. Ltd. Methods of treating amyotrophic lateral scleroses
WO2016081798A1 (en) 2014-11-20 2016-05-26 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
EP3262189B1 (en) 2015-02-27 2021-12-08 Becton, Dickinson and Company Methods for barcoding nucleic acids for sequencing
US9790490B2 (en) 2015-06-18 2017-10-17 The Broad Institute Inc. CRISPR enzymes and systems
CA2989445A1 (en) 2015-06-22 2016-12-29 Mcmaster University Biosensor comprising tandem reactions of structure switching, nucleolytic digestion and amplification of a nucleic acid assembly
US10526590B2 (en) 2015-08-31 2020-01-07 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
JP7011590B2 (ja) 2015-10-12 2022-02-10 イー・アイ・デュポン・ドウ・ヌムール・アンド・カンパニー 細胞内での遺伝子組換えおよび相同組換えの増加のための保護ｄｎａ鋳型および使用方法
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
US20170145486A1 (en) 2015-11-25 2017-05-25 Integrated Dna Technologies, Inc. Methods for variant detection
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
CN118460529A (zh) 2016-12-20 2024-08-09 百时美施贵宝公司 提高细胞基因组中同源定向修复(hdr)效率的方法
CN111032867A (zh) 2017-06-16 2020-04-17 应用干细胞有限公司 具有提高的敲入效率的基因编辑方法
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
CN111315889A (zh) 2017-09-08 2020-06-19 生命技术公司 提高同源重组的方法和其组合物
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
EP3770256A4 (en) 2018-03-20 2021-12-22 Tokyo Institute of Technology ANTISENSE OLIGONUCLEOTIDE WITH REDUCED TOXICITY
WO2019246553A1 (en) * 2018-06-21 2019-12-26 Memorial Sloan Kettering Cancer Center Compositions & methods for monitoring dna repair
WO2020178772A1 (en) 2019-03-04 2020-09-10 King Abdullah University Of Science And Technology Compositions and methods of labeling nucleic acids and sequencing and analysis thereof
CA3154370A1 (en) 2019-10-24 2021-04-29 Jessica WOODLEY Modified double-stranded donor templates

Also Published As

Publication number Publication date
JP7579817B2 (ja) 2024-11-08
AU2020301025A1 (en) 2022-01-20
US12254959B2 (en) 2025-03-18
AU2020301025B2 (en) 2026-07-02
JP7898488B2 (ja) 2026-07-31
JP2025014002A (ja) 2025-01-28
JP2022540792A (ja) 2022-09-20
US20210002700A1 (en) 2021-01-07
EP3994258A1 (en) 2022-05-11
IL289421A (en) 2022-02-01
EP3994258A4 (en) 2022-10-26
WO2021003343A1 (en) 2021-01-07
US20250218536A1 (en) 2025-07-03

Similar Documents

Publication Publication Date Title
Höijer et al. CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations
US20250218536A1 (en) Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs
Brinkman et al. Rapid quantitative evaluation of CRISPR genome editing by TIDE and TIDER
US20240417795A1 (en) Screening for structural variants
Brinkman et al. Easy quantification of template-directed CRISPR/Cas9 editing
Haile et al. Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples
Shao et al. Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG)
Peng et al. Accurate detection and evaluation of the gene-editing frequency in plants using droplet digital PCR
Zhu et al. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
US20180355380A1 (en) Methods and kits for quality control
JP2022551551A (ja) ロングリードシークエンシングを用いたゲノム構造バリアントの同定
JP2024113001A (ja) デザイナヌクレアーゼを用いる修飾の特徴付け方法
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
Coffa et al. Analysis of MLPA data using novel software coffalyser .NET by MRC-Holland
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
US20240209442A1 (en) Methods and systems for analyzing complex genomic regions
Bemmelen et al. Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes
WO2018026576A1 (en) Genomic analysis of cord blood
Xian et al. GC content variation in angiosperm genomes reveals GC-biased gene conversion
US9637779B2 (en) Antisense transcriptomes of cells
HK40004815A (en) Method and device for acquiring fetal free dna concentration
HK40004815B (en) Method and device for acquiring fetal free dna concentration
Tang Retrotransposon Insertions in Cancer
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

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20240523

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 5TH ANNIV.) - STANDARD

Year of fee payment: 5

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20250610

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20250610

D15 Examination report completed

Free format text: ST27 STATUS EVENT CODE: A-2-2-D10-D15-D126 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: EXAMINER'S REPORT

Effective date: 20251023

P11 Amendment of application requested

Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P11-P100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: AMENDMENT RECEIVED - RESPONSE TO EXAMINER'S REQUISITION

Effective date: 20260112

P11 Amendment of application requested

Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P11-P102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: AMENDMENT DETERMINED COMPLIANT

Effective date: 20260129

P13 Application amended

Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P13-X000 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: APPLICATION AMENDED

Effective date: 20260129

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-2-2-W10-W00-W111 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: CORRESPONDENT DETERMINED COMPLIANT

Effective date: 20260129

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 6TH ANNIV.) - STANDARD

Year of fee payment: 6

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260609

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260609