SNP genotypes could not be called automatically using the manufacture supplied program due to copy number differences which affected the allele signal intensities causing samples to fall between the heterozygous and homozygous genotypes. Genotype calls were made manually, assuming that the intermediate samples were either AAB or ABB depending on the location relative to the heterozygote cluster. The best estimate of copy number and genotype was made by integrating the real-time PCR measured copy number, Taqman derived genotype and pedigree structure. While the majority of subjects (85%) have 2 copies, 11% had 3 copies, and 4% had 1 copy. A small number (<2%) were considered to have greater than 3 copies based on real time PCR, but these measurements were not considered plausible based on Taqman derived genotype and pedigree information.
