For the single-marker association analyses, we used a recently published method for combining family-based and population-based data. More precisely, family-based association testing of within-family information is combined with population-based analyses of between-family information and the association analyses of unrelated study subjects 27. This hybrid approach is inherently robust to population stratification and potentially increases statistical power compared to a classic meta-analysis design 27. As part of our analytical pipeline we therefore computed P-values for all autosomal markers and both the within and the between family information using PBAT 28. The two P-values were subsequently combined using a weighted Z-score statistic as implemented via METAL 29.
