Association of expression levels with probabilities of imputed genotypes were tested in samples of related individuals using a two-step mixed model-based score test developed in the works of Aulchenko et al. and Chen and Abecasis 33,34 and implemented in the GenABEL/ProbABEL packages 35,36. Briefly, the approach is an approximation of a full linear mixed model where the first step includes a mixed model containing all terms but those involving SNPs fitted by maximum-likelihood i.e. fixed effects as well as kinship matrix based on genomic data. Fixed effects included age and experimental batch in the adipose and LCL analysis, while age, batch and sample processing were used in the skin analysis. This step is performed using the GenABEL software 35using the polygenic() function. The resulting object contains the inverse variance-covariance matrix of the estimates and expression trait residuals which are used in the second step together with posterior genotypic probabilities performing the score test in ProbABEL 36, using the “—mmscore” option. In total, 776 adipose, 777 LCL and 667 skin samples had both expression profiles and imputed genotypes and were included
