Genome scan for association and linkage

In this paper, a genome search is performed on the GAW Problem 1 data, in an attempt to determine which, if any, of the marker loci are associated and/or linked with the disease. Since there was no clear indication from the data of the likely mode of inheritance, methods were used which did not require such assumptions to be made. A two-stage procedure was used to test for association. Firstly a standard unmatched case-control test was applied to all the loci. The family-based method of Self et al. [1991] was then applied to those loci which gave a positive result in the first stage. This procedure correctly detected loci 1 and 2, and that disease risk was increased for homozygote carriers of the disease allele at each locus, although a false positive result was also found. The affected sib pair method of Holmans [1993] was also applied to the data, although the sample contained far too few sib-pairs for such an analysis to be effective. This analysis failed to find any of the disease loci.