The focus on protein-coding sequences has been reinforced by a practical problem, especially in mammals. Mutation mapping studies using whole-genome scanning techniques usually have not pinpointed the causative mutation or variation, and the affected region may encompass one megabase or more. Until recently, comparative sequencing of such regions was not feasible, and in any case it can be very difficult to sort the relevant polymorphism from the considerable background variation in huge intergenic and intronic regions, especially in outbred human populations. In most circumstances, understandably, investigators have resorted to analysing the most plausible candidate genes (recently including those expressing noncoding transcripts or ESTs [158],[161]) usually involving scanning of known exons (and sometimes the immediate 5′ flanking promoter sequences and UTRs) in the region by PCR amplification, in the hope that they can identify the causative mutation in these locations, which in turn are the ones that are then reported in the literature. However, there are many informal reports of mapping studies that have not identified such exonic mutations, and which consequently lie in abeyance, including (as noted already) the large
