Verification of predicted hotspots of Alu/Alu-mediated rearrangements in the human genome

To identify the genome-wide impact of Alu/Alu-mediated rearrangement (AAMR) on variation and human health, we have developed a bioinformatic approach to characterize Alus involved in mediating CNVs and have predicted genome-wide AAMR hotspot loci. This prediction was validated by performing molecular biological experiments on 89 samples selected by correlating AAMR hotspot genes with a database of ~54,000 chromosomal microarrays. A custom-designed 8x60k Agilent microarray was developed using the Agilent SureDesign website. This array is targeting 15 predicted AAMR hotspot loci. We performed hybridization against sex-matched controls on 89 DNA samples derived from blood.