Computational Service
Cell Line Models
Scoped After Feasibility Review
Service Overview
A knockout line is only as good as the evidence that the gene is actually disrupted in every allele and that nothing else was. We design guides against the functionally critical exons rather than the first available PAM, assess off-target risk genome-wide, predict the indel spectrum each guide is likely to produce, and specify the sequencing and functional assays that will confirm the edit. Editing, clone isolation and screening are performed by your laboratory or a partner; the design and the analysis are ours.
Key Features & Advantages
Exon Choice Before Guide Choice
Targeting is directed at early constitutive exons shared by all protein-coding isoforms, avoiding the common failure in which an in-frame product or an alternative start site survives the edit.
Off-Target Assessment Genome-Wide
Candidate guides are scored against mismatch and bulge-tolerant genome-wide searches, with hits filtered by genomic context so that coding and regulatory off-targets are prioritised for checking.
Repair Outcome Predicted
Expected indel spectra are modelled per guide, which indicates how likely a frameshift is and how many clones will need screening to find biallelic disruption.
Validation Designed In
Amplicon sequencing primers, analysis strategy and the functional assay that demonstrates loss of protein are specified with the design, not improvised after clones appear.
Where This Service Is Used
1Target validation studies requiring complete loss of function rather than knockdown
2Generating isogenic control lines for phenotypic or drug-response comparison
3Removing a redundant paralogue to expose a phenotype masked by compensation
4Building reporter or sensitised backgrounds for screening campaigns
5Confirming on-target mechanism for a compound by comparing sensitivity in knockout and parental lines
How the Work Is Performed
1Locus analysis: isoform structure, constitutive exons, functional domains and regulatory elements
2Guide enumeration across compatible nucleases with PAM availability and chromatin accessibility considered
3On-target efficiency scoring with established models for the nuclease and delivery format in use
4Genome-wide off-target search with mismatch and bulge tolerance, filtered by genomic annotation
5Repair outcome and frameshift probability modelling per candidate guide
6Validation design: amplicon primers, editing analysis strategy, protein-level and functional confirmation
What We Need From You
1Target gene with species, reference genome build and the isoforms that matter
2Cell line and delivery method, since both affect guide performance and screening strategy
3Whether the gene is essential, which determines if a conditional strategy is required instead
4Any guides already tried and the outcome, including guides that failed to cut
What You Receive
1Ranked guide designs with on-target scores and the reasoning for the ranking
2Genome-wide off-target table per guide with the sites that warrant empirical checking
3Predicted repair outcomes and an estimate of clone screening effort
4Amplicon sequencing primer designs and the editing analysis workflow
5Written validation plan covering genotype, protein loss and functional confirmation
Questions We Are Asked Before Scoping
How many guides should we test?
▸Three to five. Predicted and measured cutting efficiency correlate only moderately, so testing a small ranked set reaches a working line faster than optimising one guide.
Can you guarantee no off-target editing?
▸No. We minimise and rank predicted risk and identify the sites worth checking. Empirical off-target profiling is required before any specificity claim.
What if the gene is essential?
▸A constitutive knockout will not survive. We would recommend an inducible or conditional strategy, or degron-based approaches, and design accordingly.
Interpretation and Limitations
This is a computational (in silico) service. Designs and predictions prioritise hypotheses and direct experimental effort; they do not by themselves establish that an edit, construct, molecule or assay will perform as intended. Laboratory execution — editing, cloning, expression, synthesis and testing — is planned with you and carried out by your own team or a qualified partner. Deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
Complete loss of function is needed rather than partial reduction
An isogenic control line is required for a clean phenotypic comparison
On-target mechanism for a compound must be confirmed against a null background
Consider another service when
The gene is essential and cells will not survive its loss
Gene Knockdown Cell Line Design A specific sequence must be inserted rather than disrupted
Stable Knock-in Cell Line Design What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
An in-frame product or downstream start codon surviving the edit
Targeting is directed at early constitutive exons shared by all coding isoforms, and the consequence is checked at protein level in the validation plan.
Off-target edits assumed absent because none were predicted
Genome-wide prediction identifies the sites worth checking; empirical profiling is named as the step that supports any specificity claim.
Clone screening effort underestimated
Predicted repair outcomes give an expected frameshift rate, so the number of clones to screen is estimated before the work starts.
A Worked Example
A knockout that kept expressing protein
The situation
Sequencing confirmed frameshift edits in both alleles, yet western blot still showed a band.
What the work involved
The locus was re-analysed for alternative start codons and isoform structure, and the original guide position was mapped against the transcript set.
What came back
The edit sat downstream of an internal start site that produced a truncated but stable product. New guides were designed in an earlier constitutive exon shared by every isoform.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the material and data you already hold.
2
Feasibility Review
We check that the target, system and available information can support the approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Design and Analysis
The design work runs on documented tools and parameters, with quality checks and alternatives compared where that is informative.
5
Delivery and Follow-Up
You receive the designs, the supporting analysis and a validation plan, plus support interpreting the results once the experiments run.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day