For family samples, Mendelian inheritance of all genotypes was evaluated using PedCheck (32). Genotype distribution deviation from Hardy-Weinberg equilibrium (HWE) and pair-wise marker linkage disequilibrium (LD) were examined using the program Haploview 4.0 (29), with genotype data from parents. Marker allele transmission from heterozygous parents to affected offspring (or marker allele sharing between affected sibling pairs) was examined using the Family-based Association Test (FBAT) program (33), assuming an additive model. Haplotype frequencies were estimated in the founders (or parents) and haplotype association analyses were performed using the Haplotype-based Association Test (HBAT) (34).
