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So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region? I don't have environmental data, just the SNP information.

Since epigenetics refers to the variations in the gene expression without changing the DNA sequence, I don't really understand if there could be a connection.

Any help would be appreciated, thank you!

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  • $\begingroup$ Welcome to StackExchange! If I got this right your main interest are epigenetics and brain structure, I'm not sure how SNPs play into this since they are only loosely connected to either. I think you could improve your question by making clearer: 1) what kind of data you will/can work with (data types & internal/public resources), 2) What your approach to studying this is (project time frame, dry lab / wet lab, expected readout). $\endgroup$ – Nicolai Jun 25 '19 at 16:07
  • $\begingroup$ Thank you for your response! :) The SNPs are basically used to compute the probability of a gene being expressed in a brain region (thalamus for example) and then correlate that with the brain structure for patients with psychosis, in my case. The data is from public databases like BrainEAC that have information about the gene's SNPs. The title of my project suggests that I'm studying epigenetic variability of psychosis but I will be using SNPs associated to gene expression to determine the expression of a gene. My adviser is not available and I needed this to proceed with my lit. review. $\endgroup$ – Joana Jun 25 '19 at 16:22
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Starting from what appears to be your main question:

Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region?

I would strongly advise against using SNPs determine if genes are expressed (at all) in a given tissue.For one thing SNPs that affect expression (then often called eQTLs) will usually only have small +- effects on expression instead of switching it on/off and also have that effect in many/all cell types. Unless an (individual) SNP has clearly described /and validated effects on gene expression in a specific tissue/brain region, you should assume it has global effects.

Now, luckily for you gene expression in different cell types, tissues etc is a relatively well studied area and there are resources for gene expression in the brain available (brain atlas is probably closest to what you might look for).
You can uses these resources to determine which genes are expressed in your regions of interest and from there on check if SNPs associated with these genes correlate with certain structural brain features you are interest in.

One more thing you note:
The title of your questions (as well es comments) mention that you are interested in epigenetics. Neither gene expression nor SNPs/eQTLS are diretcly linked to epigenetics, so if this is your actual focus you should also look for availbale ChIP-seq data or similar and also include this into your analysis (correlation of SNPs with epigenetic marks is difficult but not impossible)

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  • $\begingroup$ I agree with Nicolai. Epigenetic variation is usually studied as DNA methylation (usually via bisulfite sequencing) and histone modification (via chip-seq). The study of gene expression is another topic. What is your research question? $\endgroup$ – Fabio Marroni Jul 15 '19 at 9:01

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