Here we discuss some aspects of assessing significance in genomewide scans, and estimate a genomewide significance threshold for the UK Caucasian population using data from the recently completed Wellcome Trust Case-Control Consortium [2007] (WTCCC) study. We allow for a potentially saturated dense marker panel to distinguish the genomewide multiplicity of the experiment from the set of markers actually tested. This approach has a long history in linkage analysis [Morton, 1955; Lander and Kruglyak, 1995] but has generally not been taken up in association mapping. Our approach brings together previous ideas based on the hypothesized extent of multiplicity in the genome, with emerging marker data that allow this multiplicity to be estimated.
