# US 2021/0340576 A1 · Method for the monitoring of modified nucleases induced-gene editing events by molecular combing

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- Number: US 2021/0340576 A1
- Document ID: US20210340576A1
- Status: Published application
- Kind: A1
- Application number: 17/366,643
- Filed: 2021-07-02
- Published: 2021-11-04
- Earliest claimed: 2016-11-15
- Assignees: Genomic Vision
- Applicants: Genomic Vision SA
- Inventors: Sebastien BARRADEAU; Aaron BENSIMON; Laurent CAVAREC
- Web page: https://patentgrep.com/patent/US20210340576A1

## CPC

- C12N 15/907: {in mammalian cells}
- C12N 15/102: {Mutagenizing nucleic acids}
- C12N 15/11: DNA or RNA fragments; Modified forms thereof (DNA or RNA not used in recombinant technology, C07H21/00); {Non-coding nucleic acids having a biological activity}
- C12Q 1/6816: characterised by the detection means (C12Q1/6804 takes precedence)
- C12Q 1/6827: for detection of mutation or polymorphism
- C12Q 1/6841: In situ hybridisation
- C12N 2310/20: involving clustered regularly interspaced short palindromic repeats [CRISPR]
- C12N 2320/11: for the determination of target sites, i.e. of active nucleic acids
- C12N 2800/80: Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites
- C12Q 2537/143: Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

Methods for detecting and characterizing large genomic rearrangements induced by modified nucleases at high resolution and for quantifying the frequency of the large genomic or gene rearrangements induced by modified nucleases using Molecular Combing.

## Claims

### Claim 1

A method for detecting, characterizing, quantifying, or
determining the efficiency of, a gene or genome editing procedure or event comprising:
editing a target nucleic acid(s) in a gene or genome and detecting or quantifying at least one genetic modification, deletion, duplication, amplification, translocation, insertion or inversion in the edited target nucleic acid using molecular combing.

### Claim 2 (depends on 1)

The method of claim 1, wherein the editing comprises non-homologous end-joining (NHEJ) in a double strand break in the target nucleic acid(s).

### Claim 3 (depends on 1)

The method of claim 1, wherein the editing comprises homologous recombination in the target nucleic acid(s) comprising at least one of allelic homologous recombination, gene conversion, non-allelic homologous recombination (NAHR), break-induced replication (BIR), or single strand annealing (SSA).

### Claim 4 (depends on 1)

The method of claim 1, wherein the editing procedure comprises activating endogenous cellular repair machinery and contacting the target nucleic acid with a zinc finger nuclease.

### Claim 5 (depends on 1)

The method of claim 1, wherein the editing comprises activation of endogenous cellular repair machinery and contacting the target nucleic acid(s) with at least one TALEN (Transcription activator-like effector nuclease).

### Claim 6 (depends on 1)

The method of claim 1, wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with at least one meganuclease.

### Claim 7 (depends on 1)

The method of claim 1, wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with at least one meganuclease of the LAGLIDADG (SEQ. ID NO: 1) family.

### Claim 8 (depends on 1)

The method of claim 1, wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with at least one I-CreI or I-SceI meganuclease.

### Claim 9 (depends on 1)

The method of claim 1, wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a CRISPR/Cas9 system or CRISPR/Cas9 variant system.

### Claim 10 (depends on 1)

The method of claim 1,
wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a type I CRISPR/Cas9 system;
wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a type II CRISPR/Cas9 system;
wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a type III CRISPR/Cas9 system;
wherein the editing comprises activation of endogenous cellular repair machinery and contact of target nucleic acid(s) with a type IV CRISPR/Cas9 system;
wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a type V CRISPR/Cas9 system; or
wherein the editing comprises activating endogenous cellular repair machinery and contacting the target nucleic acid(s) with a type VI CRISPR/Cas9 system.

### Claim 11 (depends on 1)

The method of claim 1, wherein the editing produces a nucleic acid rearrangement that knocks out a gene.

### Claim 12 (depends on 1)

The method of claim 1,
wherein the editing produces a nucleic acid rearrangement that mutates the target nucleic acid(s);
wherein the editing produces a nucleic acid rearrangement comprising a gene correction;
wherein the editing produces a nucleic acid rearrangement comprising a deletion;
wherein the editing produces a nucleic acid rearrangement comprising an insertion;
wherein the editing produces a nucleic acid rearrangement comprising a duplication;
wherein the editing produces a nucleic acid rearrangement comprising an amplification;
wherein the editing produces a nucleic acid rearrangement comprising a translocation; or
wherein the editing produces a nucleic acid rearrangement comprising an inversion.

### Claim 13 (depends on 1)

The method of claim 1 that quantifies a number of nucleic acid rearrangements produced by the editing of the target nucleic acid(s).

### Claim 14 (depends on 1)

The method of claim 1 that quantifies a number of nucleic acid rearrangements produced by the editing of the target nucleic acid(s) faster or with a higher degree of accuracy than a conventional quantification method selected from the group consisting of restriction site selection, PAGE-based genotyping assay, enzymatic mismatch cleavage-based assay, subcloning a target region, high-resolution melting curve (HRM) analysis, Next-Gen gene sequencing, and droplet digital PCR.

### Claim 15 (depends on 1)

The method of claim 1, wherein the genome or gene editing procedure or event occurs in vivo or in a sample obtained from in vivo, optionally after treatment of a subject by gene therapy or with a polynucleotide, drug, radiation, immunological agent or other therapy.

### Claim 16 (depends on 1)

The method according to claim 1, wherein said editing comprises:
contacting the target nucleic acid that has been edited with an engineered nuclease or meganuclease(s), with an unedited control target sequence, and
comparing said edited target nucleic acid sequence with the sequence of the unedited control target sequence.

### Claim 17 (depends on 1)

The method according to claim 1, wherein a number of deletions or other unwanted or unexpected genetic events in the target nucleic acid(s) as well as a number of desired or expected edits to the target nucleic acid(s) are quantified by molecular combing.

### Claim 18 (depends on 17)

The method of claim 17, wherein the editing is performed using an engineered nuclease or meganuclease.

### Claim 19 (depends on 1)

The method according to claim 1, wherein said target nucleic acid(s) comprise BRCA1 genomic DNA.

### Claim 20

A method for determining the efficiency, accuracy or specificity of a polynucleotide editing procedure that uses at least one modified nuclease comprising:
(i) editing one or more polynucleotide(s) of interest using at least one modified nuclease,
(ii) contacting the edited polynucleotide(s) with labelled polynucleotide(s) that hybridize to them and performing molecular combing of the fluorescent labeled polynucleotides, and
(iii) comparing the edited polynucleotides hybridized to said labelled polynucleotides to one or more control polynucleotides, which have not been treated with the modified nuclease, hybridized to said labelled polynucleotide(s), thus determining the efficiency, accuracy or specificity of the polynucleotide editing procedure using the modified nuclease; and
(iv) optionally, selecting a modified nuclease based polynucleotide editing procedure that is most accurate or efficient for correction or modification of a particular polynucleotide of interest.

### Claim 21 (depends on 1)

The method according to claim 1, wherein the target nucleic acid(s) or a target polynucleotide of interest comprises BRCA1 genomic DNA.