CRISPR gRNA Design

[TimothyStiles]

I'd like to be able to design CRISPR guide RNAs with Poly. Below is a draft spec for a new CRISPR package:

Spec

Our guide RNA design package should be lightweight and easily extendable and at its core will likely need

• [ ] A struct to hold information about the target and the CAS protein being used.
• [ ] A substruct to hold information about the CAS protein (PAM, references, functionality (cut, tag))
• [ ] Maybe a small embedded DB of common CAS variants and their properties.
• [ ] A basic heuristic for determining the viability of a potential gRNA candidate. This should include:
  • [ ] Checking for off-target hits in the target organism
  • [ ] Checking that the gRNA itself can be synthesized
  • [ ] Checking that gRNA GC content is within the 40-80% range.
  • [ ] sgRNA should be between 17-24 nucleotides

What this is not

• This likely won't ship as a single-function, end-to-end solution, but instead a core set of utilities, examples, and tutorials needed to design guide RNAs.

Help required

• [ ] A thorough review of common checks and constraints that will be needed in +95% of use cases
• [ ] A thorough description of biological context for documentation. What's crispr? What's a guide RNA? single-guide RNAs vs two part guide RNA?, etc.

I'd really love to talk to some people who regularly make guide inserts for gRNA plasmids so if you or someone you know can hang out and talk please reach out!

-Tim

[isaacguerreir]

About someone that regularly makes gRNA plasmids maybe could be interested to talk with someone from Eligo Bioscience. Xavier Duportet is the CEO and a former iGEM participant and they work using CRISPR as a tool for genetic engineering organisms. I don't have his personal contact but looks for me as someone approachable. Maybe someone from the company that is designing things for them could be also this bridge that we need to understand better the problem.

[isaacguerreir]

http://parts.igem.org/Collections/CRISPR

Could be a beginning to understand better the object we will need to create.

[isaacguerreir]

I remember seeing a presentation where someone from Ginkgo shows the heuristic they use for genome engineering using a cas system. I will contact the person and see what we can get from their experience.

[TimothyStiles]

@isaacguerreir any input from other people would be great. I'll likely start working on this after the holidays.

[ThomVett]

@TimothyStiles did you start on this feature?

[TimothyStiles]

@TimothyStiles did you start on this feature?

I haven't but anyone is welcome to start on it @ThomVett!

[ThomVett]

happy to start looking at it, but the problem is that I don't have enough domain knowledge to deeply understand the current scope of the feature. Is there a user that you had in mind that would start using this feature?

[TimothyStiles]

happy to start looking at it, but the problem is that I don't have enough domain knowledge to deeply understand the current scope of the feature. Is there a user that you had in mind that would start using this feature?

Scope is fairly generic and is just intended for anyone designing guide RNAs. How familiar are you with crispr-cas systems @ThomVett?

End user would be a developer in an organization where they're designing large numbers of crispr-cas gRNA inserts. Our package would allow them to stitch together their own function to achieve what they specifically need. I plan on using this in the future myself but was nudged to publish this spec after talking to someone the other month who wanted to knock out many genes across bacterial genomes for their experiments.

[ThomVett]

Familiar in terms of the biology, but not familiar in respect to what does designing a guide RNA mean. i.e not sure what the workflow would be from a scientists point of view.

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This issue has had no activity in the past 2 months. Marking as stale.