Figure 8

Visualisation of regions of perfect LD. Marker pairs can have either two or three haplotypes present when D' = 1. Most programs do not distinguish between these graphically, despite the potential biological importance. (a) The BRCA1 region on chromosome 17. MIDAS shows only two haplotypes for many SNPs (perfect LD, r² = 1) using HapMap data [29,30]. (b) Allele frequencies from HapMap data [29,30] show that SNPs in regions with only two haplotypes share the same minor allele frequency (MAF) for many SNPs (eg BRCA1 region on chromosome 17) compared to (c) nearby regions which have a mixture of MAFs. Viewing MAF may therefore be a quick way to find regions of perfect LD, which can then be checked with MIDAS.