Combined cross analysis

A combined cross analysis was performed using data from the current cross and two previously published B6 × C3H and B6 × BALB intercrosses (Li et al. 2008; Rowlan et al. 2013a). Genotype data for the chromosomal regions where a suggestive or significant QTL was found in an individual cross were recoded as “High” for F2s homozygous for the allele contributing to a larger lesion size, “Low” for F2s homozygous for the allele contributing to a smaller lesion size, and “H” for F2s with heterozygous alleles at each marker. For all other regions where no QTL was found, alleles at each marker were recoded based on the progenitor strain phenotype as reported (Wergedal et al. 2007). Phenotype data on carotid lesion sizes were switched from the total lesion area to the average of the top five lesion sizes for each F2 mouse in all crosses.