Linkage disequilibrium (LD) among markers can induce false-positive evidence of linkage in multipoint linkage analyses. Some of the 5861 SNPs were in LD. Kinship coefficient calculations by LOKI identified 42 completely unrelated genotyped individuals within the pedigrees. HAPLOVIEW was used to calculate marker LD in these 42 individuals. Markers in LD (on average 34% of markers per chromosome) were excluded according to HAPLOVIEW criteria including D′>0.5, with the exception of a single marker within a defined LD group (Figure S2). The resulting 3878 unlinked markers were used in the linkage analyses. The mean distance between unlinked markers was 1 cM, the minimum distance permitted by SOLAR (sequential oligogenic linkage analysis routine) [55]. Genetic map positions (cM) were derived from deCODE (Genethon, Marshfield). The logarithm of the odds (LOD) scores were computed from the 3878 markers not in LD using SOLAR.
