Source 1primary paper2024Nature Communications
Toolkit/Integrated Classification Pipeline
Integrated Classification Pipeline
Also known as: ICP
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Integrated Classification Pipeline (ICP) is a computational method developed to decompose and categorize CRISPR/Cas9-generated mutations at genomic target sites in complex multicellular insects. It classifies mixed DNA double-strand break repair outcomes, including non-homologous end joining and homology-directed repair events within the same samples.
Usefulness & Problems
Why this is useful
ICP is useful for in-depth analysis of diverse gene editing outcomes in complex multicellular insect samples where multiple repair signatures coexist. The reported repair signatures also enable marker-free tracking of specific mutations in dynamic populations.
Source:
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
Problem solved
ICP addresses the problem of resolving heterogeneous CRISPR/Cas9-induced mutation signatures at single target sites in multicellular organisms. It helps distinguish and categorize mixed double-strand break repair outcomes such as NHEJ, HDR, MMEJ, and insertion-associated events observed across development.
Source:
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
computational classification of crispr/cas9-induced mutation signaturesdecomposition of mixed dna double-strand break repair outcomesTechniques
Computational DesignTarget processes
editingImplementation Constraints
ICP is a computational pipeline for analysis of CRISPR/Cas9-generated mutations at genomic target sites rather than a molecular reagent. The supplied evidence does not describe software requirements, input data formats, sequencing protocols, or parameter settings.
The supplied evidence supports ICP in complex multicellular insects, but does not establish performance in other taxa, editing systems, or sequencing contexts. Quantitative benchmarking, error rates, and direct independent replication are not provided in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
Approval Evidence
1 source5 linked approval claimsfirst-pass slug integrated-classification-pipeline
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
Source:
application capabilitysupports
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
Source:
biological observationsupports
The study reports highly reproducible lineage-specific mutation fingerprints in individual organisms.
We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms
Source:
developmental progressionsupports
The study reports a developmental progression of DSB repair in which MMEJ or insertion events predominate during early rapid mitotic cell cycles, then distinct subsets of NHEJ alleles predominate, and later HDR-based gene conversion predominates.
a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion
Source:
method developmentsupports
The study develops an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9-generated mutations on genomic target sites in complex multicellular insects.
Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects.
Source:
method outputsupports
ICP outputs graphic rank-ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints from different target sites and alternative inheritance patterns of CRISPR components.
The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components.
Source:
Comparisons
Source-backed strengths
The associated study reports highly reproducible lineage-specific mutation fingerprints in individual organisms, supporting consistent classification of editing outcomes. ICP was applied to reveal a developmental progression of repair in which MMEJ or insertion events predominate early, distinct subsets of NHEJ alleles predominate later, and HDR-based gene conversion predominates at later stages.
Ranked Citations
- 1.