Question: What does it mean for a snp to be enriched?
1
gravatar for ehzed
3.7 years ago by
ehzed30
ehzed30 wrote:

Hello,

I have come across the term snp enrichment in many papers but I have yet to find a clear definition. From this post (SNP enrichment, how to test for it?), snp enrichment seems to be just a higher than average number of snps in a designated region. While in other papers, snp enrichment seems to be somehow linked to gwas studies. Or for instance in the introduction in this paper (http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1003449&representation=PDF), a snp is enriched if "it is more likely to be associated with a phenotype than others".

So my question is, what exactly does snp enrichment mean? And if I were to test for snp enrichment, what methods should I use (If the first definition is correct, I was thinking of constructing a sliding window plot of snp density in R, and then look at the regions that my genes of interest fall in and see if there are greater snps in those regions)? Thank you! 

snp next-gen R genome • 1.7k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 3.7 years ago by ehzed30
3

To quote Lewis Carroll:

“When I use a word,” Humpty Dumpty said, in rather a scornful tone, “it means just what I choose it to mean—neither more nor less.” “The question is,” said Alice, “whether you can make words mean so many different things.” “The question is,” said Humpty Dumpty, “which is to be master—that’s all.”

In other words, "SNP enrichment" could mean a lot of things. Figure out what you want to ask first and then come up with the term for it.

ADD REPLYlink written 3.7 years ago by Devon Ryan92k
2

What is your biological question?  In other words, why is it that you want to use "snp enrichment"?  You seem to be driving toward defining an algorithm, so it is good for us to understand what you want to do.

ADD REPLYlink written 3.7 years ago by Sean Davis25k

SNP enrichment was something my supervisor said I should look into, amidst several other suggestions. Originally, I wanted to make sure that I was testing for snp enrichment the correct way, but I didn't realize there was no formal definition, my apologies. I suppose for me, the question I want to answer is whether a list of given genes contain more snps than expected. Would my proposed method be a good way of testing then? Thank you! 

ADD REPLYlink written 3.7 years ago by ehzed30

It can be very difficult to test if a particular gene has consistently more SNPs than others. In part because each region of the genome has its own properties (GC content, recombination rate, etc) and these affect the number of SNPs. I would start looking at which genes show the highest diversity, but this is not a solution!

ADD REPLYlink written 3.7 years ago by abascalfederico1.1k

It would really help for you to explain the biological question and system in more detail.  

ADD REPLYlink written 3.7 years ago by Sean Davis25k

Currently, I have mapped three sets of whole genome chicken sequencing data to the ancestral jungle fowl genome. Each set of genome comes from a different domestic chicken strain. I need to compare the variants and see how the genomic changes between the broiler chickens and the wild chicken explain phenotypic differences in immunity (red jungle fowl tends to have a stronger immune system). I will compare the variants a number of different ways (snp density for a list of genes that was already provided to me, whether variants are found in transcription factors, etc), one of the things that was suggested to me was to look at snp enrichments. Hope that helps! 

ADD REPLYlink written 3.7 years ago by ehzed30
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