Table 1.

Example of choice of weights for the weighted genetic risk score.

Case	wi	vi	zi	Comments
1	2δ(A = R)	1	2δ(B = R)	R denotes the risk allele and δ(X = Y) = 1 if X = Y is true and 0 otherwise
2	0	$V_i=\log \frac{\frac{p(T|X_i=1)}{1-p(T|X_i=1)}}{\frac{p(T|X_i=0)}{1-p(T|X_i=0)}}$	2vi	Xi = 0 when the ith SNP genotype is AA, and Xi = 1 when the genotype is AB. This is the standard coding for an additive model
3	0	$\log \frac{\frac{p(T|{\text{S}}_i=\text{AB})}{1-p(T|{\text{S}}_i=\text{AB})}}{\frac{p(T|{\text{S}}_i=\text{AA})}{1-p(T|{\text{S}}_i=\text{AA})}}$	$\log \frac{\frac{p(T|{\text{S}}_i=\text{BB})}{1-p(T|{\text{S}}_i=\text{BB})}}{\frac{p(T|{\text{S}}_i=\text{AA})}{1-p(T|{\text{S}}_i=\text{AA})}}$	The two weights represent the log-odds ratio relative to the referent genotype AA. This is the coding for genotypic model.

Case 1 is known as the “unweighted score” and case 2 is typically referred to as the “weighted genetic risk score.” Case 3 is the most general and flexible but it does not seem to be used.