Approaches to the analysis of genetic variation and genotype-phenotype relationships It is essential to keep the historical dimension in

mind, which has shaped approaches to the analysis of genetic variation in disease and, importantly, the concepts about, how to establish links between genotype and phenotype. This will allow putting past and present, approaches and the results they generated into perspective.39 For most, of the time, a comprehensive analysis of the entire variation given in candidate genes has been neither feasible nor practicable, nor efficient. Even though the sequences of numerous candidate genes of interest had become available in the late 1980s, the first, systematic candidate Inhibitors,research,lifescience,medical gene

analyses were not performed until the late 1990s. The methods at hand were indirect, ie, the variations were detected without directly analyzing DNA sequence. The variations Inhibitors,research,lifescience,medical were selected randomly, ie, without emphasis on specific functionally relevant, gene regions. They were selected out of context, ie, given variation in the other parts of the gene were not issues of primary Inhibitors,research,lifescience,medical relevance. What was feasible and what mattered was to be able to detect any polymorphism(s) at all in and around the gene to be able to test the candidate gene hypothesis. The limited availability of technologies to access genetic variation restricted Inhibitors,research,lifescience,medical the number of detectable polymorphisms and determined the type of variants identified. What counted were the ease and robustness of typing and the numbers and frequencies (inf ormativeness) of the alleles in order to be able to perform informative

association studies. For years, the variable sites utilized for such studies were largely represented by restriction fragment length polymorphisms (RFLPs), different, kinds Inhibitors,research,lifescience,medical of repeat, markers such as microsatcllites, short, tandem repeat (STR), or variable number of tandem repeats (VNTR) markers. The presence of variation within the restriction site of an enzyme or the presence of a repeat marker anywhere in the gene region were chance events that illustrate the randomness of these approaches. Later, the analysis of SNPs, the most, frequent, type of variation in the human genome, gained center stage. These were, in the early to mid 1990s, mostly identified by application of polymerase chain reaction (PCR)based mutation scanning methods, such as singlestranded conformation polymorphism Resveratrol (SSCP) detection or denaturing gradient gel electrophoresis (DGGE), which were supposed to detect, 80% to 95% of all variants. In the optimal case, they were found to cause a functionally significant amino acid exchange, which would allow the direct testing of potentially Adriamycin in vivo causative alleles.18 In the late 1990s, when the Human Genome Project was in progress, SNPs were generated randomly at. large scale in vitro and in silico.