The genotypes for all of the autosomal markers were analyzed using Pedigree Relationship Statistical Test (PREST) (McPeek and Sun, 2000) to detect sample and pedigree structure errors. DNA was reisolated from a stored frozen blood specimen and the genotyping repeated for any individual with a probable error. If re-genotyping failed to resolve the error, the problematic genotype was subsequently treated as missing. Fifteen families were identified with pedigree structure errors. Five were resolved following re-genotyping. The program Pedcheck was used to detect non-Mendelian inheritance (O’Connell and Weeks, 1998). Markers with a high frequency of Mendelian segregation errors were excluded from analysis, and for isolated Mendelian errors, the genotypes for the entire family were excluded for the specific marker that yielded the error. Pedcheck identified 3104 Mendelian errors resulting in 7714 lost genotypes and the exclusion of one marker. To further reduce errors, the probability that each genotype was correct was assessed using the error-checking algorithm implemented in MERLIN, and as suggested by the authors, genotypes that had a probability of less than 0.025 of being correct were removed from further
