There were 315 microsatellites (11.53 cM average spacing), 4,596 Illumina SNPs (1.41 cM average spacing), and 10,801 Affymetrix SNPs (0.36 cM average spacing) provided across the autosomal chromosomes. In cases were there were multiple SNPs per locus, we carried out thinning by random sampling of one SNP per locus and then discarded others. This process thus resulted in 2,467 and 9,467 effective SNP loci for Illumina and Affymetrix, respectively, without affecting the original marker spacing. We then proceeded to use SOLAR [7] software to estimate marker allele frequencies from the data by maximum likelihood estimation method for both the microsatellite and the two sets of SNPs because of detected errors in the original frequency files provided with the data. Marker-specific identity by descent (IBD) for pairs of relatives and multipoint IBD were also estimated using the same software. Multipoint nonparametric linkage analyses across the 22 autosomal chromosomes at 1-cM intervals were performed using variance component procedure as implemented in SOLAR. Separate linkage analysis of age at onset was performed using each set of genetic markers.
