The Alzheimer Disease Genetics Consortium (ADGC) performed a genome-wide association study of late-onset Alzheimer disease using a three-stage design consisting of a discovery stage (stage 1) and two replication stages (stages 2 and 3). Both joint analysis and meta-analysis approaches were used. We obtained genome-wide significant results at MS4A4A (rs4938933; stages 1 and 2, meta-analysis P (P_M) = 1.7 × 10⁻⁹, joint analysis P (P_J) = 1.7 × 10⁻⁹; stages 1, 2 and 3, P_M = 8.2 × 10⁻¹²), CD2AP (rs9349407; stages 1, 2 and 3, P_M = 8.6 × 10⁻⁹), EPHA1 (rs11767557; stages 1, 2 and 3, P_M = 6.0 × 10⁻¹⁰) and CD33 (rs3865444; stages 1, 2 and 3, P_M = 1.6 × 10⁻⁹). We also replicated previous associations at CR1 (rs6701713; P_M = 4.6 × 10⁻¹⁰, P_J = 5.2 × 10⁻¹¹), CLU (rs1532278; P_M = 8.3 × 10⁻⁸, P_J = 1.9 × 10⁻⁸), BIN1 (rs7561528; P_M = 4.0 × 10⁻¹⁴, P_J = 5.2 × 10⁻¹⁴) and PICALM (rs561655; P_M = 7.0 × 10⁻¹¹, P_J = 1.0 × 10⁻¹⁰), but not at EXOC3L2, to late-onset Alzheimer's disease susceptibility^,,.