WO2019232494A3 - Methods and systems for determining editing outcomes from repair of targeted endonuclease mediated cuts - Google Patents

Methods and systems for determining editing outcomes from repair of targeted endonuclease mediated cuts Download PDF

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Publication number
WO2019232494A3
WO2019232494A3 PCT/US2019/035079 US2019035079W WO2019232494A3 WO 2019232494 A3 WO2019232494 A3 WO 2019232494A3 US 2019035079 W US2019035079 W US 2019035079W WO 2019232494 A3 WO2019232494 A3 WO 2019232494A3
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Prior art keywords
methods
repair
systems
determining
editing outcomes
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PCT/US2019/035079
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French (fr)
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WO2019232494A2 (en
Inventor
David Conant
Timothy HSIAU
Richard STONER
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Synthego Corporation
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Publication date
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Publication of WO2019232494A2 publication Critical patent/WO2019232494A2/en
Publication of WO2019232494A3 publication Critical patent/WO2019232494A3/en

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    • 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
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • 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
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]
    • 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
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/11—Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids

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  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Organic Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Evolutionary Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Plant Pathology (AREA)
  • Microbiology (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Biochemistry (AREA)
  • Artificial Intelligence (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

The present disclosure provides a method for determining the probability distribution of editing outcomes, such as indel length or genotype, resulting from a targeted endonuclease mediated edit, as well as a method for determining a guide RNAs or donor polynucleotides able to produce a desired editing outcome. The editing outcomes can be cell-type specific. The methods can comprise the use of machine learning models to produce the probability distributions.
PCT/US2019/035079 2018-06-01 2019-05-31 Methods and systems for determining editing outcomes from repair of targeted endonuclease mediated cuts WO2019232494A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201862679678P 2018-06-01 2018-06-01
US62/679,678 2018-06-01

Publications (2)

Publication Number Publication Date
WO2019232494A2 WO2019232494A2 (en) 2019-12-05
WO2019232494A3 true WO2019232494A3 (en) 2020-01-09

Family

ID=68698485

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2019/035079 WO2019232494A2 (en) 2018-06-01 2019-05-31 Methods and systems for determining editing outcomes from repair of targeted endonuclease mediated cuts

Country Status (1)

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WO (1) WO2019232494A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3794130A4 (en) 2018-05-16 2022-07-27 Synthego Corporation Methods and systems for guide rna design and use
GB202003814D0 (en) * 2020-03-16 2020-04-29 Cancer Research Tech Ltd Optimised methods for cleavage of target sequences
CN111627492B (en) * 2020-05-25 2023-04-28 中国人民解放军军事科学院军事医学研究院 Cancer genome Hi-C data simulation method and device and electronic equipment

Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060074824A1 (en) * 2002-08-22 2006-04-06 Jinyan Li Prediction by collective likelihood from emerging patterns
US20140186843A1 (en) * 2012-12-12 2014-07-03 Massachusetts Institute Of Technology Methods, systems, and apparatus for identifying target sequences for cas enzymes or crispr-cas systems for target sequences and conveying results thereof
WO2016057961A1 (en) * 2014-10-10 2016-04-14 Editas Medicine, Inc. Compositions and methods for promoting homology directed repair
WO2016183402A2 (en) * 2015-05-13 2016-11-17 President And Fellows Of Harvard College Methods of making and using guide rna for use with cas9 systems
WO2017053879A1 (en) * 2015-09-24 2017-03-30 Editas Medicine, Inc. Use of exonucleases to improve crispr/cas-mediated genome editing
WO2017081097A1 (en) * 2015-11-09 2017-05-18 Ifom Fondazione Istituto Firc Di Oncologia Molecolare Crispr-cas sgrna library
US20180020646A1 (en) * 2014-12-26 2018-01-25 Riken Gene knockout method

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20060074824A1 (en) * 2002-08-22 2006-04-06 Jinyan Li Prediction by collective likelihood from emerging patterns
US20140186843A1 (en) * 2012-12-12 2014-07-03 Massachusetts Institute Of Technology Methods, systems, and apparatus for identifying target sequences for cas enzymes or crispr-cas systems for target sequences and conveying results thereof
WO2016057961A1 (en) * 2014-10-10 2016-04-14 Editas Medicine, Inc. Compositions and methods for promoting homology directed repair
US20180020646A1 (en) * 2014-12-26 2018-01-25 Riken Gene knockout method
WO2016183402A2 (en) * 2015-05-13 2016-11-17 President And Fellows Of Harvard College Methods of making and using guide rna for use with cas9 systems
WO2017053879A1 (en) * 2015-09-24 2017-03-30 Editas Medicine, Inc. Use of exonucleases to improve crispr/cas-mediated genome editing
WO2017081097A1 (en) * 2015-11-09 2017-05-18 Ifom Fondazione Istituto Firc Di Oncologia Molecolare Crispr-cas sgrna library

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
LIANG ET AL.: "Enhanced CRISPR/Cas9-Mediated Precise Genome Editing by Improved Design and Delivery of gRNA, Cas9 Nuclease, and Donor DNA", JOURNAL OF BIOTECHNOLOGY, vol. 241, 11 November 2016 (2016-11-11), pages 136 - 146, XP029860705, DOI: 10.1016/j.jbiotec.2016.11.011 *
SURUN ET AL.: "High Efficiency Gene Correction in Hematopoietic Cells by Donor-Template- Free CRISPR/Cas9 Genome Editing", MOLECULAR THERAPY: NUCLEIC ACIDS, vol. 10, 10 November 2017 (2017-11-10), pages 1 - 8, XP055606586, DOI: 10.1016/j.omtn.2017.11.001 *
WANG ET AL.: "CRISPR-DAV: CRISPR NGS Data Analysis and Visualization Pipeline", BIOINFORMATICS, vol. 33, no. 23, 14 August 2017 (2017-08-14), pages 3811 - 3812, XP055672196 *

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Publication number Publication date
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