Question: Do imputed variants tend to show weaker, stronger, or the same average association compared to genotyped variants
gravatar for Vincent Laufer
3.0 years ago by
Vincent Laufer1.1k
United States
Vincent Laufer1.1k wrote:

I was thinking about haplotype association analysis recently.

I was thinking that a lot of haplotype association methods use an EM algorithm independent of case control status under the null of no association.

I was then wondering if there are cases in which there are rare disease associated haplotypes that are absent or nearly absent from reference studies used for imputation purposes.

I reasoned, if this is true, one might see less extreme association summary statistics for imputed variants than for genotyped variants on such a haplotype, if say the imputation algorithm is selecting the best fit but the true fit is not represented.

So, last I wondered if anyone has ever tested the average test statistic for genotyped verses imputed variants across a large number of well-powered GWAS studies.

I conducted an initial search, but did not find a manuscript like this. Is any one aware of this?

To be clear - it need not address haplotypes. I am just interested in studies that looked at genotyped vs imputed variants in one or more GWAS.

gwas snp genotyped imputation • 754 views
ADD COMMENTlink written 3.0 years ago by Vincent Laufer1.1k
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