Figure 4

The haplotypes defined by emulsion-fusion PCR at the DEFA1A3 locus on 8p23.1 are shown for NA12760 (panel A) and NA12878 (panel B). Haplotype copy number and the phase of SNPs within the genes across this CNV were established by combining sequence information from the telomeric and centromeric emulsion systems that link SNPs flanking the CNV to the copy-variable genes in the repeat array. Panel A illustrates some of the sequence data used to define the structural haplotype. Sequence of variant 1, which distinguishes DEFA1 (G) and DEFA3 (T), are shown for the four end repeats for NA12670, for example C at rs2738046 is on the same chromosome as a copy of DEFA1 and A at rs2738046 is on the same chromosome as a copy of DEFA3. Mixed positions (variants 2 and 6) and non-mixed positions (variant 4) are used provide spatial information regarding the five copies present in these individuals. The identity and position of the gene and sequence variants within each copy are shown. The phase of gene-specific sequence variants (numbers 2 to 8; see additional Table 1) are shown boxed, from variant number 2 on the left to number 8 on the right. Panel B shows the final structural haplotype for NA12878.