A Basic Guide to Reducing Risk in Gene Editing Projects

Reducing Risk in Gene Editing Projects

Even equipped with the most advanced tools and techniques, gene editing projects still carry inherent risk. While no lab can guarantee a successful outcome at the onset of a project, sound planning and a full understanding of the challenges you can expect to face can help set more realistic expectations and prevent wasteful costs when projects don’t pan out.

Taking this one step further, we’ve developed a milestone-based approach to project development to better reflect the hard-to-predict nature of genomic manipulation.

Rather than swallow the bitter pill of a massive upfront cost without any insight into the chances of success, we recognize the risks at each phase of development and address them through honest communication and a sensible pricing model.

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If, at any point in the process, success begins to look less likely than it did before, we step back to discuss the details and reassess the project one-on-one, getting full approval before pushing forward.

Recognizing risks is important, but that doesn’t mean they can’t be mitigated. Here are a few ways to reduce the risks of gene editing and boost your chances of a successful outcome:

1. Optimize reagents

Newer gene editing tools like CRISPR, when used with advanced design software, generally do a good job of predicting the best reagent to build for a particular project. But even with the best tools available, prediction is only so accurate. Biological context still needs to be accounted for.

By building four or more different nucleases, we’re able to increase the odds that one of those will work well for the project, reducing the risk of putting all your eggs in one basket.

Simply put, some CRISPRs work better than others and those differences vary from gene to gene. Through a round of activity testing (an in vitro assay providing a prediction of a nucleases cutting efficiency), we can see which one is most likely to yield success before giving it a try in the project.

Rather than take on the risk of simply choosing a particular CRISPR without any indication it’s the best one for the task, optimization at this foundational level ensures we’re putting our best foot forward even before the project starts, whether knocking-in or knocking-out genes.

2. Review the project’s progress at regular milestones

As mentioned before, the milestone-based approach to gene editing doesn’t sugar coat the risks inherent to editing genes. Instead, it recognizes those risks and the possibility of impacting the viability and health of a cell while putting a system in place to deal with those potential hazards accordingly.

In the simplest terms, milestones, help reduce the risks that can threaten the project in its later stages without forcing you to pay a huge upfront costs.

Here at Transposagen, projects are carefully designed to maximize the chances of success and results from all stages are carefully reviewed with clients prior to proceeding. If negative or unexpected results occur, we can return to the original proposal and make the changes necessary before moving forward.

3. Optimize cell protocols

This is the first official milestone in Transposagen’s development process. We’ve broken it down into its three essential components:

  •  Transfection efficiency - Optimizing cell protocols during the first phase of a project can lead to significantly shorter timelines and fewer costs associated with screening clones. In one customer project, our optimization protocol for transfection efficiency led to a 10%increase in compared to what was originally provided to us in their protocol.
  •  Single cell cloning - This is important for cell engineering projects, in particular. If the ultimate goal is to have a genetically modified single cell clone, it’s important to know if that’s even possible or not at the beginning of the project, as some cells are able to do this better than others.

It would be a disaster to go through the entire project only to discover single cell cloning isn’t actually possible. Optimizing that process early on is essential for the later stages of the project. If efficiency is only 5%, for example, you should expect to screen many clones before you find what you’re looking for. Fixing those problems early on prevents these kinds of efficiency issues from being amplified later.

  •  Cell viability - While related to the other two, culturing conditions are important enough to consider on their own. The fewer cells lost to handling, the better your chances of success. After all, it would be extremely unfortunate to lose many of your clones that might have contained a gene edit.

These problems can be mitigated by collecting as much information as possible about the cell line, either from the lab’s own experience working with them or published materials. If a cell line is well-established, little extra work is needed. But for those who haven’t worked with a particular cell line before, everything must be optimized in the absence of information.

As with other early-stage preparation steps, every percentage gained early can save significant amounts of screening time later. The before-and-after graph below summarizes just how much impact optimizing cell protocols can have on projects at this crucial first milestone:


The table below breaks down an example comparison of effects in terms of estimated plates needed, underscoring the advantages of optimizing early.


4. Establish an open line of communication between labs

Tied closely with the first project milestone, the importance of gathering information early on can’t be stressed enough. Obviously those who have worked with cells before know quite a bit about them and getting those details during the planning phase is key.

Pacing is also something to consider. We can’t proceed to the next step until clients have had a chance to fully understand where the project is and provide their approval.

Unexpected discoveries can alter projects as well, as new research naturally lends itself to changes that aren’t always anticipated. If a new finding is made on either side, it’s important to inform the other side and consider how it might affect the project. By sharing data frequently, we can identify problems sooner and make the necessary adjustments needed.

5. Let helpful technologies assist in the process

Lastly, while it’s sometimes hard to find the time to learn how new systems are being used by scientists to improve their work, the right combination of tools and technology can dramatically affect the outcome of your project.

The Footprint-Free™ gene editing system is just one such technology that has opened new doors into what gene editing can accomplish.

This system combines CRISPR with the piggyBac™ transposon to provide the only commercially available system for seamless excision of resistance or reporter genes. Footprint-Free™ gene editing allows scientists to increase efficiencies by utilizing selection enrichment for gene edits, followed by “footprint-free” or “scarless” removal of the selection cassette, resulting in the cleanest genome edit.

In summary, the milestone-based approach to project development mitigates many of the risks common in editing gene projects. By optimizing reagents and cell protocols at the onset, we can avoid wading into expensive development project only to be let down at the later stages of the process.

Regular review and reconsideration at various milestones throughout the project, open communication between labs and the assistance of innovative new gene editing technologies all contribute to a more reliable outcome.

Looking for an experienced gene editing partner to help you put these tips to use? Get a free project evaluation and we'll clue you into possible strategies, target sites, donor vecot designs, project timelines, and more.

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Topics: piggyBac, CRISPR/Cas9, Gene Editing