set I, samples genotyped using Illumina HumanHap550v1 as described by Hom et al.11; set II, samples genotyped using Illumina HumanHap300 as described by Harley et al.10; and set III, samples genotyped using Affymetrix 5.0 as descri bed by Grahametal.8 The primary in ference ofthisstudyisbased on a female-only case–case (i.e., patients with SLE with nephritis versus patients with SLE without nephritis) analysis to minimize