How to understand likelihood ratio (LR) in GWAS?
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6.6 years ago
Carl.Q P ▴ 10

Hi guys,

I read some papers about GWAS. i'm interested in genetic risk assessment based on common variants. Authors computed likelihood ratios (LRs) for each SNP as the ratio of the probability of the genotype in an affected person to that of an unaffected person. LRs for each locus were computed from each case-control study be dividing the genotype frequency in cases by the frequency in controls, weighted by the sample size of the study. Thus, for an individual with genotype g in SNP x found in i = 2 ...s studies, each of size S(i). (Reference: https://genomemedicine.biomedcentral.com/articles/10.1186/gm462) The formula is as follows:

i'm confused with genotype frequencies. F(g in cases) means F(cases | Aa )+F(cases | aa ), and F(g in controls) means F(controls | Aa )+F(controls | aa )??? if not, how to compute the F(g | cases ) and F(g in controls)?

Thanks!!

SNP gwas plink • 2.2k views
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I don't know, but why not look at this as comparing given genotype at SNP position between cases and controls, and not mixing them. By that I mean 1) F(Aa) in cases vs F(Aa) in controls, 2) F(aa) cases vs F(aa) controls, 3) F(AA) cases vs F(AA) controls. To me these are genotype frequencies, not allele frequencies

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Entering edit mode

I've updated your post so the LR equation appears.