I am using Plink to conduct a eQTL analysis for twins dataset. QFAM family based test can be used here. I came across a paper by Loukola et al. where they have explained :
"The QFAM family-based test of association was used for quantitative and categorical traits. QFAM performs a simple linear regression of phenotype on genotype. Adaptive permutation (up to 1x109 permutations) was used to correct for family structures. As the QFAM model allows no covariates, the original quantitative trait values were adjusted for gender (age-related traits) as well as testing age (all other traits), fitted to a linear model in R 2.12.0 2, and the resulting standardized residuals were used as analysis phenotypes". Also, "In all analyses, the DZ twin pairs were treated as regular siblings, whereas one individual from each MZ pair was included".
We have phenotype and genotype data for all individuals of DZ pair but for MZ, we have genotype data for 1 individual and phenotype data for both individuals. So, I am wondering how to include MZ twins in this analysis. Should I use phenotypes from both individuals of MZ pair or only one individual for which we have genotype data? Also how would QFAM consider the zygosity, should we include this information in the analysis?
Any help would be highly appreciated.