Question: Why GWASs cannot speculate what kind of mutation the SNP would cause?
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gravatar for francois
2.0 years ago by
francois10
francois10 wrote:

I am trying to understand results from GWAS studies, and I have this question:

Why can't GWAS studies speculate about what kind of consequence would the specific SNP have? As they information about the precise position on the genome + which base changes, I thought studies would speculate if the SNP in question causes a silent/missense/nonsense mutation, but they apparently do not (at least those I have read).

I guess some information is missing or uncertain to speculate about that... What is it? I was thinking maybe which frame is read?

Any guess?

snp gwas • 661 views
ADD COMMENTlink modified 2.0 years ago by Noushin N570 • written 2.0 years ago by francois10
2
gravatar for Noushin N
2.0 years ago by
Noushin N570
Baltimore, MD
Noushin N570 wrote:

Adding to the response by swbarnes2, many of the variants identified in GWAS are located in non-coding regions of the genome and will function not by altering the protein coding sequences, but by regulation of gene expression.

ADD COMMENTlink written 2.0 years ago by Noushin N570
3

My assumption is that generally the "lead" SNPs identified as most significant in GWAS are not necessarily the actual causal SNP because of linkage disequilibrium. Therefore trying to ascertain a function or effect of those SNPs would be misleading. I believe they generally try to do further studies on implicated loci (called "fine-mapping") to more precisely locate the likely causal variants (e.g., pmid: 26551672).

ADD REPLYlink written 2.0 years ago by Collin700

Great point! Thanks for the addition, Collin!

ADD REPLYlink written 2.0 years ago by Noushin N570
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gravatar for swbarnes2
2.0 years ago by
swbarnes27.4k
United States
swbarnes27.4k wrote:

It's easy to predict the amino acid change consequence of a mutation. What's hard is to predict the functional consequences of most changes.

ADD COMMENTlink written 2.0 years ago by swbarnes27.4k
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