T_simple is d2/V, where d is the mean case pool PAF minus the mean control pool PAF and V is binomial sampling variance. vare_pool_2 and varSNPspecific are the two components of the pooling error – see appendix 2 of Macgregor et al. (2006) for full details. Since this method is based upon contrasting case and control pools, the effect of unequal amplification of alleles is minimal as such effects cancel out.
