Figure 2

Emulsion haplotype fusion PCR for determination of structural haplotypes. Two emulsion haplotype fusion systems are used to provide spatial information either side of the CNV as shown by the two large arrows (A). Amplicons are designed to fuse non copy-variable flanking regions to the gene in the first repeat, from either the telomeric or centromeric directions independently (B). DEFA1A3 repeat units are illustrated as arrows, with a black arrow representing the most telomeric or centromeric repeat, and a grey half arrow representing another repeat unit present to the right (for the telomeric system) or left (for the centromeric system). Amplicons to be fused and the final haplotypes are shown as filled rectangles. Primers used in the emulsion are shown. Integration of the telomeric and centromeric sequence data is used to determine the structural haplotype across the CNV (C). This is shown for NA06990.