How To Determine The Effect A Snp On The Expression Of The Gene
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Entering edit mode
8.5 years ago
win ▴ 890

Hi all, i have a list of SNPs for a gene. I want to know if there is a way to determine the effect of each of the SNPs on the expression of that gene.

snp • 5.5k views
2
Entering edit mode
8.5 years ago
munch ▴ 300

Here is a similar post: Anyone know a *general* variant (SNP/indel) effect predictor / annotator?

For this I used snpEff (http://snpeff.sourceforge.net/SnpEff.html) which provides variant annotation and effect prediction. As input you can use your SNP list in vcf format (http://www.1000genomes.org/node/101)

Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.

Usuage:

java -Xmx4g -jar snpEff.jar eff -v GRCh37.66 file.vcf > file.eff.vcf


see here for installation guide and examples: http://snpeff.sourceforge.net/examples.html

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Entering edit mode
8.5 years ago

It seems you are more interested in the effect on the expression. Hence you should focus on the regulatory regions. Have a look at regulomeDB then (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431494/).

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Entering edit mode
8.5 years ago

If only biology were that simple...

As a rule, no, there is not totally in silico way to predict that. You would have to see if someone has empirically tried to correlate SNPs in that approximate position with expression. This might be feasible in a species like mice, where the genetics are a bit simpler, since the mice come from inbred strains.

I suppose you could try and see if your SNPs sits on a known regulation site, and how much your SNPs changes that site from the canonical consensus sequence.

But if you are looking for a simple function where you put your SNP in, and biological consequences like expression changes come out, no, that doesn't exist.