R&D Tax Relief for Biotechnology
Case study: Reducing CRISPR Off-Target Editing
Explore how a UK biotechnology business could investigate guide and delivery configurations that preserve intended editing while reducing unwanted DNA cleavage. Based on published scientific and technological research, this example demonstrates how Lister AI helps businesses evaluate technical uncertainties, identify gaps in supporting evidence and improve their R&D tax relief explanations through ten guided questions.
This is an illustrative scenario, not an actual company project or HMRC claim.
Lister AI — guided questions
What the R&D aim of the project is
We want to investigate guide and delivery configurations that preserve intended editing while reducing unwanted DNA cleavage.
The objective is not yet tied to measurable technological criteria.
We aim to investigate guide and delivery configurations that preserve intended editing while reducing unwanted DNA cleavage. Our proposed technical result is an experimentally validated editing approach with improved on-target/off-target selectivity in a defined cell context. We have not yet established that this outcome was readily achievable using existing methods.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Define measurable acceptance criteria and a competent professional’s assessment of why the intended capability exceeds routine adaptation. Attach dated requirements and a baseline comparison. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We want to investigate guide and delivery configurations that preserve intended editing while reducing unwanted DNA cleavage. Specify the baseline performance and the proposed improvement using units, tolerances, operating conditions and an objective pass/fail criterion. Ask the technical lead to identify which parts of the work involve an unresolved capability rather than ordinary design, procurement or compliance. Retain the original specification and its approval date so later changes can be traced.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For the R&D aim, use this work to identify what the field had already achieved; specify a measurable capability not shown by the source, without assuming novelty. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
A review of the current state of knowledge
We have seen that guide-seq research demonstrated genome-wide off-target cleavage and variability between guide rnas, so computational predictions alone are not a sufficient baseline.
The baseline needs a traceable comparison to the specific proposed work.
GUIDE-seq research demonstrated genome-wide off-target cleavage and variability between guide RNAs, so computational predictions alone are not a sufficient baseline. This published work establishes existing knowledge; it does not demonstrate that our fictional company has performed experiments. We must compare the publication’s scope and limitations with our own requirements.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Prepare a dated literature table: author, year, institution, method, demonstrated capability, limitation, and the exact gap relevant to this project. Cite the source directly: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015). For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We have seen that guide-seq research demonstrated genome-wide off-target cleavage and variability between guide rnas, so computational predictions alone are not a sufficient baseline. For every cited paper, distinguish the authors' demonstrated results from their stated limitations; do not infer that a published limitation automatically applies to this project. Record the publication date relative to the project start, the relevant experimental conditions and the nearest comparable method. Ask a competent professional to explain the remaining gap and attach the actual source passages or stable identifiers.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For current knowledge, record the publication date, experimental context, tested conditions and documented limitations. Compare these directly with the fictional project rather than asserting a research gap without evidence. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
How the project sought an advance in a qualifying area of science or technology
We hope to achieve an experimentally validated editing approach with improved on-target/off-target selectivity in a defined cell context.
An advance for the company is not necessarily an advance in the field.
The proposed advance is an experimentally validated editing approach with improved on-target/off-target selectivity in a defined cell context. We seek to establish this through systematic technical investigation, not merely a new product or routine implementation.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Explain the advance in overall science or technology, identify the nearest published approaches, and document why a competent professional could not readily deduce the result. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We hope to achieve an experimentally validated editing approach with improved on-target/off-target selectivity in a defined cell context. Describe the intended improvement as a testable capability, not as novelty to the company, cost reduction or a commercial advantage. Compare the target with the strongest available published method and explain which technical inference could not readily be made. State the experimental evidence that would support or refute the proposed advance, and identify any limits on generalising the result.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For the proposed advance, explain how the targeted capability would go beyond the methods demonstrated in the cited work. Do not equate a different product design with an advance in the field. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Describe exactly which uncertainties you need to resolve
We are unsure whether changing guide design and nuclease exposure reduces off-target cleavage without losing useful on-target activity.
The uncertainty needs technical boundaries and a competent professional’s rationale.
Two central uncertainties are: (1) whether changing guide design and nuclease exposure reduces off-target cleavage without losing useful on-target activity; and (2) whether low-frequency off-target events remain detectable across cell lines and independent assays. Their technological character remains to be substantiated against the baseline.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
For each uncertainty record the prior method, what was unknown, why established approaches were inadequate, a falsifiable test, and the competent professional’s explanation. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We are unsure whether changing guide design and nuclease exposure reduces off-target cleavage without losing useful on-target activity. Express each uncertainty as a question that can be answered through investigation, with boundary conditions and observable outcomes. Separate uncertainty about scientific or technological feasibility from uncertainty about budget, schedule, customer acceptance or supplier availability. Record what a competent professional knew at the outset, the alternatives considered and the evidence needed to resolve each question.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For uncertainty, isolate the unresolved technical question and contrast it with the published method’s demonstrated operating range and limitations. Obtain a competent professional’s explanation. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Describe what made it a project to resolve a specified uncertainty
We began because published off-target findings make it uncertain whether an existing guide and delivery configuration meets the proposed specificity requirement.
Commercial necessity or customisation alone is not qualifying R&D.
The investigation was proposed because published off-target findings make it uncertain whether an existing guide and delivery configuration meets the proposed specificity requirement. A customised solution alone would not be enough to show qualifying R&D.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Attach feasibility assessments and alternatives considered; distinguish routine configuration, commercial risk and scientific or technological uncertainty. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We began because published off-target findings make it uncertain whether an existing guide and delivery configuration meets the proposed specificity requirement. Reconstruct the decision to begin the investigation using dated feasibility notes, early calculations and the team's prior-knowledge review. Explain why straightforward application or adaptation of existing methods could not settle the issue. Identify the point where routine engineering ended and the experimental investigation began, and record the competent professional who made that judgement.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For the reason to undertake R&D, document why applying the published approach was not readily sufficient and which alternative approaches were considered before experimentation. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Describe the steps you plan to take to resolve them
We plan to establish sequencing baseline; vary guide and exposure; perform unbiased off-target profiling; replicate; compare editing efficiency.
A sequence of tasks is insufficient unless it tests identified uncertainty.
The proposed work is to establish sequencing baseline; vary guide and exposure; perform unbiased off-target profiling; replicate; compare editing efficiency. Each stage is intended to test a specific technical assumption rather than simply deliver the product.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Map each step to an uncertainty, a test or model, an acceptance threshold, a dated record, and a decision to continue, revise or stop. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We plan to establish sequencing baseline; vary guide and exposure; perform unbiased off-target profiling; replicate; compare editing efficiency. For each proposed activity, name the hypothesis, variables to change, controls to hold constant, measurement method and decision criterion. Preserve failed iterations as well as promising ones, with versioned models, protocols and test data. Distinguish planned steps from completed work; update the sequence when the project changes instead of rewriting the original plan retrospectively.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For the planned steps, use the publication’s method or evaluation measures as a technical comparator, while documenting the business’s own test plan, controls and acceptance criteria. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
What difficulties are foreseen for the project
We anticipate assay sensitivity, chromatin context, cell viability and trade-offs between specificity and efficacy.
Foreseeable risks must be distinguished from technological uncertainty.
The foreseeable difficulties include assay sensitivity, chromatin context, cell viability and trade-offs between specificity and efficacy. Some are routine risks; the company must identify which are linked to uncertainty beyond established capability.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Separate engineering execution risks from unresolved scientific or technological questions; document the effect each may have on experimental validity. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We anticipate assay sensitivity, chromatin context, cell viability and trade-offs between specificity and efficacy. Rank the foreseen technical obstacles by their effect on interpreting experimental results, and describe a mitigation or diagnostic test for each. Distinguish predictable implementation problems from limitations of existing scientific or technological knowledge. Record assumptions, expected failure modes, equipment constraints and the observations that would indicate the underlying uncertainty remains unresolved.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For foreseeable difficulties, distinguish limitations described by the authors from risks specific to the business. Explain how each could affect the proposed capability. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Information about any major changes to the aims, or new uncertainties encountered while running the project
We might need to change the design.
A hypothetical design change cannot be represented as actual evidence.
Illustrative change scenario, NOT an actual project result: a lower-exposure condition reduces apparent off-target events but also lowers on-target editing. This may require revisiting the original technical assumptions.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Replace this scenario with actual dated records. State the original assumption, new evidence, design change, and whether a new uncertainty genuinely arose. If none occurred, say so. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We might need to change the design. Use a dated change log to connect each unexpected observation to the original hypothesis and the resulting technical decision. Include the version of the design or protocol affected, the alternative explanation considered and the follow-up test proposed. Do not invent a new uncertainty merely to strengthen a claim; explicitly record 'none identified' if the actual project produced no new technological question.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For changes or newly discovered uncertainties, use the publication only as background; date and substantiate every actual design change or unexpected finding with company records. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
How the uncertainties and other challenges were overcome (or not)
We expect the design to improve.
An expected result is not a demonstrated resolution.
No project results have been supplied. The business would need to report measured on-target efficiency, detected off-target sites, detection limits and unresolved trade-offs. It must explicitly state which uncertainties were resolved, partially resolved or remained open.
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Do not claim success or failure without results. Supply raw measurements, controls, repeatability, acceptance criteria, deviations and a competent professional’s conclusion. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We expect the design to improve. For every uncertainty, state separately whether it was resolved, partly resolved or unresolved and identify the test evidence behind that status. Include negative findings, measurement error, sample size or repeatability where relevant, and any difference between simulated and observed behaviour. Do not convert a proposed target into a claimed achievement; have the competent professional sign off the interpretation of actual records.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For outcomes, do not infer success from the publication. Compare the company’s actual measured results with the literature baseline, identify unresolved questions and report negative results. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Details of any patent applications filed, or how any resultant, identified intellectual property is to be protected
We may protect any new intellectual property.
IP filing is not an R&D eligibility test.
No patent is assumed; distinguish published guide-design methods from any genuinely new protectable contribution
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/
- CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017), Massachusetts General Hospital / Harvard Medical School, USA: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/
Confirm the actual patent/application number and filing date if any. If none, say “No patent application filed”; explain any relevant confidentiality or other IP protection without suggesting that IP proves R&D eligibility. For the reducing crispr off-target editing investigation, relate this specifically to the business's stated issue: We may protect any new intellectual property. Separate an invention disclosure, an internal confidentiality decision and an actual patent filing; they are not interchangeable. If a filing exists, verify the application identifier, jurisdiction, date and the precise technical subject covered. If there is no filing or protectable result, state that plainly. Keep IP decisions distinct from the assessment of scientific or technological uncertainty and qualifying expenditure.
Published baseline: GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases (2015; Massachusetts General Hospital / Harvard Medical School, USA) — establishes an existing genome-wide method for measuring CRISPR off-target cleavage. Also compare CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets (2017) — establishes another off-target screening method and its experimental scope. For intellectual property, use the literature to check existing public disclosures and potential prior art; do not imply that a patent application was filed or that patentability has been established. Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4320685/; additional source: https://pmc.ncbi.nlm.nih.gov/articles/PMC5924695/