Our primary analysis consisted of two stages, applied to the cleaned SNP data. In the first stage we tested for genetic linkage using the SNP marker data provided by Illumina. Nonparametric two-point quantitative trait linkage analysis was performed using the "--qtl" option of the program MERLIN [1]. The method compares allele sharing among individuals with similar phenotypes; individuals at extreme ends of the distribution are given greater weight. We chose two-point rather than multipoint analysis because strong linkage disequilibrium (LD) among the densely spaced SNP markers could lead to inflated evidence for linkage if multipoint methods are used without accounting for marker-marker LD. Markers exhibiting linkage with a LOD score greater than 1.8 were used to define regions for further study. In the second stage a 20-cM interval centered at the marker was used to test for trait association. SNPs 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)
