Losses of heterozygosity (LOH) in LDGs from SLE patients. (A) LOH are prevalent in the ∆CNVhi SLE patients. The mean ± SEM of LOH >2 Mb for healthy controls (open blue bar, n = 9), SLE neutrophils (red open bar) and SLE LDGs (red filled bar). ∆CNVneg (n = 7) and ∆CNVhi (n = 6) SLE patients are indicated by unhatched and black-hatched bars, respectively. *Differs significantly from autologous normal-density SLE neutrophils, Wilcoxon signed-rank test, one-tailed, P <0.01. (B) A LOH at 5q23-q31 is observed in four SLE patient samples. The autologous pairs of neutrophils and LDGs are indicated by the dashed red line and solid red line, respectively. The affected 3.5 Mb interval is expanded to show the relative positions of genes indicated in the text, additional genes within the interval are not shown for the purposes of clarity. SLE patient 11 has a loss of heterozygosity that is restricted to the LDG sample. Refer to Additional file 5 information regarding SLE patients. Genomic positions based upon Human Genome Assembly Build 36.3. CNV, copy number variation; LDG, low-density granulocyte; SEM, standard error of the mean; SLE, systemic lupus erythematosus.