Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?

Question

Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some CRISPR-like tools? I guess, that extensive databases of already performed experiments are available and human mind is required to select candidate genes for experiments. But maybe there are some methods, that allow computational select, planning of experiment, e.g. using: 1) already known biological pathways for different biological processes or incomplete pathways for the process under consideration; 2) protein-protein interaction models to predict some pathways and to select genes from them. Etc.

I am complete novice for this field, coming from computer science and only starting to read books about molecular cell biology, epigenetics and protein-protein interaction. Maybe there are special terms that allow me to Google for the subject of this question

Answer 1

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work with CRISPR-CAS9 is still limited to model organisms and tissue cultures.

Are you referring to Adiposis Dolorosa? Apparently the cause is not actually known yet. It's thought to be heritable, but it isn't known to be associated with a single gene or family of genes. The most common technique for analyzing what genes and gene mutations cause disease is Genome Wide Association Studies (GWAS), so you might use that as a staring point for your searches.

There are several computer programs that try to model what pathological effects a given mutation will have, but these are pure research at this point, and typically require extensive training for each gene or protein product. Try searching for "sequence based pathology prediction". However you may not find much related to Adiposis Dolorosa since the causative genes are apparently not known yet.