in this interval from the combined Illumina and Affymetrix sets were analyzed for trait association using the quantitative pedigree disequilibrium test (QPDT) [2] as implemented in the program UNPHASED [3]. Our choice to use the Illumina SNP set (4,710 markers) for the first stage and the Affymetrix SNP set (11,120 markers) together with the Illumina set for the follow-up association analysis allowed us to carry out the initial genome screen and then proceed with fine-mapping in regions of linkage using the more densely spaced SNPs provided by Affymetrix.
