As stated above, the traditional TDT requires complete genotypic information from all members of the nuclear families. However, obtaining all genotypes cannot always be feasible for some diseases or families. Therefore the traditional TDT-type studies may not be useful to identify the presence of genetic determinants in data with relatively small amounts of complete trio information. One way to solve this type of issue is to reconstruct the missing parental genotypes under the assumption that they follow the probability distribution of the fully observed cases. However, most studies designed for this purpose do not incorporate the impact from LD and thus may introduce bias to the results. On the other hand, there are data available that have genotype information on both microsatellite and SNP markers for diseases; one example is alcoholism [54]. With both the linkage and association data, usually the microsatellite genotypic information from families for linkage analysis together with SNP data from the offspring who are genotyped for both linkage and GWAS, we can “infer” the transmission of SNPs for the rest of the family members who have
