For a fixed number of cases, power of a case-control study can be increased by enlarging the reference group. Our main analyses used a control:case ratio of 1.5:1 for each disease. The availability of the other 6 disease data sets gave us the opportunity to expand the reference group up to a ratio of ~7.5:1, with potential reciprocal benefits for the analysis of each disease. For BD and T2D the expanded reference group comprised the 58C and UKBS controls supplemented by the other 6 disease sets; for CAD and HT this expanded reference group was reduced to exclude HT and CAD respectively; for CD, RA and T1D, the reference group was augmented only by the cases from the non-autoimmune diseases.
