Some studies use a χ22 test that allows different OR estimates for the heterozygote and homozygote for the minor allele. Some refinement of our published methods for bias correction of per allele odds ratios [Zhong and Prentice, 2008] is needed to simultaneously bias-correct odds ratios for persons who are heterozygous and homozygous for the minor SNP allele. To do so, the same conditional likelihood approach can be applied, as was shown in a 2008 Department of Biostatistics doctoral dissertation by Hua Zhong. A brief description of these bias-corrected odds ratio estimates and confidence interval methods is given in the appendix. The likelihood ratio test to compare the bias-corrected estimate to the replication study estimate is given also in the appendix.
