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Table 1 Different coding schemes for the SNP variable reflect different assumptions regarding XCI status

From: Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder

Assumed XCI statusCoding schemeCoding of the SNP variable (Eq. 1)Calculation of ORsa
Sex# copies of effect allele
SubjectClaytonM02NA\( {e}^{2{\beta}_1} \)\( {e}^{\beta_1} \)\( {e}^{2{\beta}_1} \)
EscapePLINKM01NA\( {e}^{\beta_1} \)\( {e}^{\beta_1} \)\( {e}^{2{\beta}_1} \)
  1. aExpressions for calculating the OR are shown for the effect of one allele copy in men (ORM) and one or two copies in women (ORW1 and ORW2). For men, but not women, the OR is calculated differently based on whether the SNP is believed to be subject to XCI (and hence the coding scheme, PLINK or Clayton, that is chosen)