Genotyping and quality control (QC) for linkage analysis have been previously described in detail (28). Briefly, 1630 subjects were genotyped at the Center for Inherited Disease Research (CIDR) for the 6,008 SNPs Illumina Human Linkage IVb Marker Panel. An additional 266 subjects were genotyped at the Yale Keck Center with the 6,090 SNP Illumina Infinium-12 Human Linkage Marker Panel. We limited our analyses to 4,518 autosomal SNPs available in both panels. After QC (genotyping rate ≥ 95%, minor allele frequency (MAF) ≥0.1, and HWE P ≥0.01), 4,133 and 4,395 autosomal SNPs were retained for analysis in AAs and EAs, respectively. Mendelian inconsistencies and potential genotyping errors were identified and set as missing data using PedCheck (38) and Merlin (39) programs. We used the Pedigree RElationship Statistical Test (PREST) (40) to verify family relationships, which showed pedigree errors in two AA families and five EA families. Of these, the relationships in one AA family and five EA families were corrected based on the shared identical by decent (IBD) patterns and the re-assigned family relationships were verified by PREST. One AA family relationship could not be resolved and the family was excluded from further analysis.
