Question

GWAS Summary statistic

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3.5 years ago

Kevin • 0

http://geneatlas.roslin.ed.ac.uk/downloads/?traits=2

What is a GWAS Summary statistic On this website, are the data below the graph already considered as a GWAS summary statistic? Furthermore, what is the difference between result and variant info? Thank you very much.

gwas • 1.7k views

ADD COMMENT • link 3.5 years ago by Kevin • 0

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May I also ask about what is the difference about genotyped and imputed data? Thank you very much.

ADD REPLY • link 3.5 years ago by Kevin • 0

score 3 · Accepted Answer · 2021-03-23

Hi, the summary statistic usually shows the significance of a particular variant and its effect size (how large it affects the probability of the trait). Genotyped data = SNPs that were directly read from the array or sequencing. Imputed = when we do not have an information about some particular variant (we have not sequeced it, it is absent in array design), we can use variants located close to the variant of interest and use the consideration that closely located variants are usually inherited together (thus, they are correlated). So despite the fact that we don't observe this variant, we can predict if it is presented or not.