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In this chapter we first study QTL mapping in human pedigrees and then consider for qualitative traits some more complicated issues that were not covered in Chap. 9.

Association studies are an alternative to linkage analysis as tools for the discovery of genetic factors that may contribute to the susceptibility to a disease. For reasons that will become apparent below, they can also be used in conjunction with linkage analysis to give a much more precise estimate of the location of a gene that has already been mapped to a chromosomal region. Whereas linkage analysis is based on sampling pedigrees and investigating the pattern of inheritance within families, in many approaches to association studies, unrelated genomes are sampled and compared. For example, in the case-control design (CC), samples of affected cases and unaffected controls, unrelated to each other, are collected. The genetic composition of one group is compared with the genetic composition of the other group at a set of genetic markers. Loci which show substantial between-groups divergence are taken to be associated with susceptibility to the disease.

In the previous chapter we discussed the association between phenotype and genotype for tests based on a single SNP marker. In this chapter we would like to consider tests of association that combine information from several markers.