Figure 1

Schematic map of the DEFA1A3 CNV region, based on the human genome assembly (March 2006, NCBI36/hg18), and showing the expected structure of a 2-copy allele. DEFA1A3 genes are found in the copy-variable 19 kb full repeat sequence and (with exactly one copy per haplotype) in the centromeric partial repeat. The positions of the three SNPs rs7825750, rs4300027 and rs4512398 in the centromeric flanking DNA are indicated as a, b and c respectively. The specific measurement points used in this study in the determination of copy number are shown as differently-shaped symbols below the relevant locations, with the nearby DEFA4 gene providing the reference locus for the DEFA4 PRT measurement (triangles). The MLT1A0 PRT (star) has a target site only in full, and not partial, repeat sequences, and for this reason measures one copy less per haplotype than the other assays; calibration of MLT1A0 PRT values is undertaken using the predicted total repeat unit count per sample, for ease of comparison with other measures.