what is the difference between Random ,differentiated and causal SNPs
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7.3 years ago
mms140130 ▴ 60

Hi,

I would like to know the difference between Random, differentiated and causal SNPs that are repeated in articles when they do simulation studies regard the population stratification in addtion what is the ancestral risk in admixed population??

Thank you,

snp • 1.5k views
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You may want to add an example of an article mentioning those terms.

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Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics. 2006 Aug;38(8):904. This is the article where I also am searching for the answer to the meaning of these three terms.

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Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

From the article you posted:

We simulated three categories of candidate SNPs to compare the effectiveness of different stratification correction methods. For the first category (random SNPs with no association to disease), we again used the Balding-Nichols model with FST ¼ 0.01 (see Methods). For the second category (differentiated SNPs with no association), we assumed population allele frequencies of 0.80 for population 1 and 0.20 for population 2. This category was motivated by previous studies of a SNP in the lactase (LCT) gene, which was shown to be spuriously associated to the height phenotype in European Americans because of stratification6; this SNP varies in frequency from 0.20 to 0.80 in European populations because of positive selection28. For the third category (causal SNPs), we used the Balding-Nichols model with FST ¼ 0.01 and a multiplicative disease risk model with a relative risk of 1.5 for the causal allele (see Methods).

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