Thanks for the comment. This is actually quite helpful, as the effects of off-target edits or indels to promoter and enhancer regions is one of the primary uncertainties we have regarding feasibility of the proposal.
My prior for thinking that a few off-targets targets or indels wouldn’t necessarily be catastrophic was a paper I read that looked at the total accumulation of random mutations to neurons over the lifespan. I believe by age 40 the average person has about 1500.
Regulatory regions make up about 2% of the genome, so the average neuron has about 30 mutations in regulatory regions by the age of 40. So if we can keep our de novo mutations from increasing that number very much it will probably be ok.
Now it’s possible that the types of errors introduced by random mutations are of a different kind than those introduced by indels and off-targets from base and prime editors. A quick google search reveals that most de novos seem to be single base pair changes rather than insertion or deletion errors. So perhaps it WILL be an issue, at least for some editor variants.
I think the ideal approach to answer this question would be to use (or make) a computational model to predict the distribution of off-target edits and indels from editor variants, another to predict binding affinity as a function of sequence, and see how strongly such errors affect binding affinity. We could then compare those results to the affects of binding affinity from de novo mutations to see whether they were comparable in magnitude.
Perhaps others have already made such models. A quick search didn’t turn up anything, but I will continue looking.
The other option is to just test it empirically in cell cultures and then animal models.
If you have any other advice about how to approach this problem, I’d appreciate it.
Regulatory regions make up about 2% of the genome, so the average neuron has about 30 mutations in regulatory regions by the age of 40. So if we can keep our de novo mutations from increasing that number very much it will probably be ok.
I agree that in the grand scheme of things it would probably not make much of a difference. Also your 2% estimation is generous, if you consider that in any differentiated human cell most of the genes are inactivated. Mutations on those genes would thus be harmless
Thanks for the comment. This is actually quite helpful, as the effects of off-target edits or indels to promoter and enhancer regions is one of the primary uncertainties we have regarding feasibility of the proposal.
My prior for thinking that a few off-targets targets or indels wouldn’t necessarily be catastrophic was a paper I read that looked at the total accumulation of random mutations to neurons over the lifespan. I believe by age 40 the average person has about 1500.
Regulatory regions make up about 2% of the genome, so the average neuron has about 30 mutations in regulatory regions by the age of 40. So if we can keep our de novo mutations from increasing that number very much it will probably be ok.
Now it’s possible that the types of errors introduced by random mutations are of a different kind than those introduced by indels and off-targets from base and prime editors. A quick google search reveals that most de novos seem to be single base pair changes rather than insertion or deletion errors. So perhaps it WILL be an issue, at least for some editor variants.
I think the ideal approach to answer this question would be to use (or make) a computational model to predict the distribution of off-target edits and indels from editor variants, another to predict binding affinity as a function of sequence, and see how strongly such errors affect binding affinity. We could then compare those results to the affects of binding affinity from de novo mutations to see whether they were comparable in magnitude.
Perhaps others have already made such models. A quick search didn’t turn up anything, but I will continue looking.
The other option is to just test it empirically in cell cultures and then animal models.
If you have any other advice about how to approach this problem, I’d appreciate it.
I agree that in the grand scheme of things it would probably not make much of a difference. Also your 2% estimation is generous, if you consider that in any differentiated human cell most of the genes are inactivated. Mutations on those genes would thus be harmless