Each individual genome scan was checked prior to inclusion using the following procedure. First, checks for Mendelian errors were performed using the 'pedtool' software for genetic data manipulation (written by author Scott Gordon). The algorithm used was a modified Lange-Goradia genotype elimination algorithm (see O'Connell and Weeks, 1999). Counts of errors, both per marker and per family, were used to identify problems either with the marker set, or particular families. Problematic markers (i.e. those producing exceptionally high numbers of Mendelian inconsistencies, or with significant differences in allele frequencies relative to other datasets) were excluded. Second, the heterozygosity of each individual for X-chromosome markers was examined and used to confirm recorded gender. Third, the autosomal markers were used to test the correctness of intra-family relationships and to test for inter-family relatedness. Version 2 of the program RELPAIR (Epstein et al., 2000), as well as other software such as GRR (Abecasis et al., 2001), were used. Fourth, MERLIN (version 0.10.1)(Abecasis et al., 2002) was used to identify unlikely recombination events, indicating problems with data such as miscoded pedigree structure. Fifth, the needed alterations to family structure, and deletion/relabelling of problem samples, were applied and tested by repeating the same procedure.
