Family-based linkage disequilibrium tests using general pedigrees

Linkage disequilibrium (LD) mapping has been established as a promising approach to identifying disease genes. The presence of a disease gene located near a marker locus may cause LD between the marker and the disease loci. In LD mapping, we assume that some of the affected individuals may have a common ancestor carrying the mutation and that mutation carriers are likely to share alleles at the markers loci close to the disease gene. This chapter reviews the concept of LD mapping and outlines the advantages and disadvantages of two LD mapping approaches capable of handling general pedigrees: the family-based association test (FBAT) and pseudomarker. In summary, the pseudomarker statistical approach and the FBAT approach are both expected to offer reasonable statistical power to detect genes underlying complex traits. However, when the pedigree structure is more complicated, or when the number of informative families is limited, the pseudomarker approach is anticipated to outperform FBAT.