Single-marker case-control association analysis can be carried out with chi-square test, odds-ratio (OR), and confidence interval of OR. Typically, the control samples are randomly collected from a normal population with no need for correcting correlated samples, whereas case samples might be collected during the linkage analysis stage, thus are correlated. For allele-based analysis (Sasieni, 1997), denote the allele counts in case group as NA,case, NB,case and those in control group as NA,con, NB,con, the Pearson’s chi-square test statistic can be recalculated by replacing NA,case, NB,case with αNA,case and αNB,case: (10)Xe2=α(NA,caseNB,con−NB,caseNA,con)2(αNA,case+αNB,case+NA,con+NB,con)(NA,case+NB,case)(NA,con+NB,con)(αNA,case+NA,con)(αNB,case+NB,con).
