In this study, we first generate the combined pedigrees with both the LinkageMS and CIDRSNP genotype data from COGA. Figure 2 demonstrates the structure of the combined pedigrees. Most individuals in the combined pedigrees were genotyped on microsatellite markers. A subset of individuals in the pedigrees was genotyped for dense SNPs. These individuals include one affected child in each of the families and other unrelated members chosen as a control group. All other individuals who have not been genotyped on SNPs are considered as the missing individuals. We use the program MERLIN [55] to read these combined pedigrees as input and infer the dosage probabilities of dense SNP genotypes for these missing individuals (described in detail below). All the trio combinations from the inferred pedigrees are extracted on the condition that the children were affected and at least one parent in the trio was genotyped on microsatellite markers. The dTDT is applied on these trio pedigrees using their inferred dosage probabilities. In addition, PLINK 77 is used to conduct a standard case-control study on the CIDRSNP data. With the idea
