First, each study performed GWA analyses for BMI assuming an additive model implemented in either MACH2QTL (Y. Li, C.J.W., J. Ding, P.S. and G.R.A., unpublished data), Merlin48,49 or SNPTEST47. Covariates, trait transformation and strategies for excluding outliers or accounting for family relatedness varied according to each study's original design (Supplementary Tables 2 and 3), but the main results were essentially unchanged when we repeated meta-analysis after imposing a uniform set of analyses and procedures across the 15 study cohorts. For those samples based around case-control designs (such as those from FUSION and from the type 2 diabetes, coronary artery disease, and hypertension components of the Wellcome Trust Case Control Consortium), cases were analyzed separately from controls. To allow for relatedness in the SardiNIA and FUSION samples, regression coefficients were estimated in the context of a variance component model that modeled background polygenic effects49.
